diff --git a/CHANGELOG.md b/CHANGELOG.md
index 67c600c9c..f535501a9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@
 ##### Enhancements
 
 - Added support for Bazel 9.x.
+- Significant performance improvements. Scanning the Reddit iOS codebase reduced by 80.4% from 77.2s to 15.1s.
 
 ##### Bug Fixes
 
diff --git a/MODULE.bazel.lock b/MODULE.bazel.lock
index c8c4adfe8..a67817f22 100644
--- a/MODULE.bazel.lock
+++ b/MODULE.bazel.lock
@@ -240,6 +240,123 @@
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@@ -465,6 +582,2651 @@
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+                "mdurl": "{\"rules_python_publish_deps_311_mdurl_py3_none_any_84008a41\":[{\"filename\":\"mdurl-0.1.2-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_mdurl_sdist_bb413d29\":[{\"filename\":\"mdurl-0.1.2.tar.gz\",\"version\":\"3.11\"}]}",
+                "more_itertools": "{\"rules_python_publish_deps_311_more_itertools_py3_none_any_037b0d32\":[{\"filename\":\"more_itertools-10.5.0-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_more_itertools_sdist_5482bfef\":[{\"filename\":\"more-itertools-10.5.0.tar.gz\",\"version\":\"3.11\"}]}",
+                "nh3": "{\"rules_python_publish_deps_311_nh3_cp37_abi3_macosx_10_12_x86_64_14c5a72e\":[{\"filename\":\"nh3-0.2.18-cp37-abi3-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_nh3_cp37_abi3_macosx_10_12_x86_64_7b7c2a3c\":[{\"filename\":\"nh3-0.2.18-cp37-abi3-macosx_10_12_x86_64.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_nh3_cp37_abi3_manylinux_2_17_aarch64_42c64511\":[{\"filename\":\"nh3-0.2.18-cp37-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_nh3_cp37_abi3_manylinux_2_17_armv7l_0411beb0\":[{\"filename\":\"nh3-0.2.18-cp37-abi3-manylinux_2_17_armv7l.manylinux2014_armv7l.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_nh3_cp37_abi3_manylinux_2_17_ppc64_5f36b271\":[{\"filename\":\"nh3-0.2.18-cp37-abi3-manylinux_2_17_ppc64.manylinux2014_ppc64.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_nh3_cp37_abi3_manylinux_2_17_s390x_19aaba96\":[{\"filename\":\"nh3-0.2.18-cp37-abi3-manylinux_2_17_s390x.manylinux2014_s390x.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_nh3_cp37_abi3_manylinux_2_17_x86_64_de3ceed6\":[{\"filename\":\"nh3-0.2.18-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_nh3_cp37_abi3_musllinux_1_2_aarch64_f0eca9ca\":[{\"filename\":\"nh3-0.2.18-cp37-abi3-musllinux_1_2_aarch64.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_nh3_cp37_abi3_musllinux_1_2_armv7l_3a157ab1\":[{\"filename\":\"nh3-0.2.18-cp37-abi3-musllinux_1_2_armv7l.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_nh3_cp37_abi3_musllinux_1_2_x86_64_36c95d4b\":[{\"filename\":\"nh3-0.2.18-cp37-abi3-musllinux_1_2_x86_64.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_nh3_cp37_abi3_win_amd64_8ce0f819\":[{\"filename\":\"nh3-0.2.18-cp37-abi3-win_amd64.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_nh3_sdist_94a16692\":[{\"filename\":\"nh3-0.2.18.tar.gz\",\"version\":\"3.11\"}]}",
+                "pkginfo": "{\"rules_python_publish_deps_311_pkginfo_py3_none_any_889a6da2\":[{\"filename\":\"pkginfo-1.10.0-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_pkginfo_sdist_5df73835\":[{\"filename\":\"pkginfo-1.10.0.tar.gz\",\"version\":\"3.11\"}]}",
+                "pycparser": "{\"rules_python_publish_deps_311_pycparser_py3_none_any_c3702b6d\":[{\"filename\":\"pycparser-2.22-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_pycparser_sdist_491c8be9\":[{\"filename\":\"pycparser-2.22.tar.gz\",\"version\":\"3.11\"}]}",
+                "pygments": "{\"rules_python_publish_deps_311_pygments_py3_none_any_b8e6aca0\":[{\"filename\":\"pygments-2.18.0-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_pygments_sdist_786ff802\":[{\"filename\":\"pygments-2.18.0.tar.gz\",\"version\":\"3.11\"}]}",
+                "pywin32_ctypes": "{\"rules_python_publish_deps_311_pywin32_ctypes_py3_none_any_8a151337\":[{\"filename\":\"pywin32_ctypes-0.2.3-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_pywin32_ctypes_sdist_d162dc04\":[{\"filename\":\"pywin32-ctypes-0.2.3.tar.gz\",\"version\":\"3.11\"}]}",
+                "readme_renderer": "{\"rules_python_publish_deps_311_readme_renderer_py3_none_any_2fbca89b\":[{\"filename\":\"readme_renderer-44.0-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_readme_renderer_sdist_8712034e\":[{\"filename\":\"readme_renderer-44.0.tar.gz\",\"version\":\"3.11\"}]}",
+                "requests": "{\"rules_python_publish_deps_311_requests_py3_none_any_70761cfe\":[{\"filename\":\"requests-2.32.3-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_requests_sdist_55365417\":[{\"filename\":\"requests-2.32.3.tar.gz\",\"version\":\"3.11\"}]}",
+                "requests_toolbelt": "{\"rules_python_publish_deps_311_requests_toolbelt_py2_none_any_cccfdd66\":[{\"filename\":\"requests_toolbelt-1.0.0-py2.py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_requests_toolbelt_sdist_7681a0a3\":[{\"filename\":\"requests-toolbelt-1.0.0.tar.gz\",\"version\":\"3.11\"}]}",
+                "rfc3986": "{\"rules_python_publish_deps_311_rfc3986_py2_none_any_50b1502b\":[{\"filename\":\"rfc3986-2.0.0-py2.py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_rfc3986_sdist_97aacf9d\":[{\"filename\":\"rfc3986-2.0.0.tar.gz\",\"version\":\"3.11\"}]}",
+                "rich": "{\"rules_python_publish_deps_311_rich_py3_none_any_6049d5e6\":[{\"filename\":\"rich-13.9.4-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_rich_sdist_43959497\":[{\"filename\":\"rich-13.9.4.tar.gz\",\"version\":\"3.11\"}]}",
+                "secretstorage": "{\"rules_python_publish_deps_311_secretstorage_py3_none_any_f356e662\":[{\"filename\":\"SecretStorage-3.3.3-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_secretstorage_sdist_2403533e\":[{\"filename\":\"SecretStorage-3.3.3.tar.gz\",\"version\":\"3.11\"}]}",
+                "twine": "{\"rules_python_publish_deps_311_twine_py3_none_any_215dbe7b\":[{\"filename\":\"twine-5.1.1-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_twine_sdist_9aa08251\":[{\"filename\":\"twine-5.1.1.tar.gz\",\"version\":\"3.11\"}]}",
+                "urllib3": "{\"rules_python_publish_deps_311_urllib3_py3_none_any_ca899ca0\":[{\"filename\":\"urllib3-2.2.3-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_urllib3_sdist_e7d814a8\":[{\"filename\":\"urllib3-2.2.3.tar.gz\",\"version\":\"3.11\"}]}",
+                "zipp": "{\"rules_python_publish_deps_311_zipp_py3_none_any_a817ac80\":[{\"filename\":\"zipp-3.20.2-py3-none-any.whl\",\"version\":\"3.11\"}],\"rules_python_publish_deps_311_zipp_sdist_bc9eb26f\":[{\"filename\":\"zipp-3.20.2.tar.gz\",\"version\":\"3.11\"}]}"
+              },
+              "packages": [
+                "backports_tarfile",
+                "certifi",
+                "charset_normalizer",
+                "docutils",
+                "idna",
+                "importlib_metadata",
+                "jaraco_classes",
+                "jaraco_context",
+                "jaraco_functools",
+                "keyring",
+                "markdown_it_py",
+                "mdurl",
+                "more_itertools",
+                "nh3",
+                "pkginfo",
+                "pygments",
+                "readme_renderer",
+                "requests",
+                "requests_toolbelt",
+                "rfc3986",
+                "rich",
+                "twine",
+                "urllib3",
+                "zipp"
+              ],
+              "groups": {}
+            }
+          }
+        },
+        "recordedRepoMappingEntries": [
+          [
+            "bazel_features+",
+            "bazel_features_globals",
+            "bazel_features++version_extension+bazel_features_globals"
+          ],
+          [
+            "bazel_features+",
+            "bazel_features_version",
+            "bazel_features++version_extension+bazel_features_version"
+          ],
+          [
+            "rules_python+",
+            "bazel_features",
+            "bazel_features+"
+          ],
+          [
+            "rules_python+",
+            "bazel_skylib",
+            "bazel_skylib+"
+          ],
+          [
+            "rules_python+",
+            "bazel_tools",
+            "bazel_tools"
+          ],
+          [
+            "rules_python+",
+            "pypi__build",
+            "rules_python++internal_deps+pypi__build"
+          ],
+          [
+            "rules_python+",
+            "pypi__click",
+            "rules_python++internal_deps+pypi__click"
+          ],
+          [
+            "rules_python+",
+            "pypi__colorama",
+            "rules_python++internal_deps+pypi__colorama"
+          ],
+          [
+            "rules_python+",
+            "pypi__importlib_metadata",
+            "rules_python++internal_deps+pypi__importlib_metadata"
+          ],
+          [
+            "rules_python+",
+            "pypi__installer",
+            "rules_python++internal_deps+pypi__installer"
+          ],
+          [
+            "rules_python+",
+            "pypi__more_itertools",
+            "rules_python++internal_deps+pypi__more_itertools"
+          ],
+          [
+            "rules_python+",
+            "pypi__packaging",
+            "rules_python++internal_deps+pypi__packaging"
+          ],
+          [
+            "rules_python+",
+            "pypi__pep517",
+            "rules_python++internal_deps+pypi__pep517"
+          ],
+          [
+            "rules_python+",
+            "pypi__pip",
+            "rules_python++internal_deps+pypi__pip"
+          ],
+          [
+            "rules_python+",
+            "pypi__pip_tools",
+            "rules_python++internal_deps+pypi__pip_tools"
+          ],
+          [
+            "rules_python+",
+            "pypi__pyproject_hooks",
+            "rules_python++internal_deps+pypi__pyproject_hooks"
+          ],
+          [
+            "rules_python+",
+            "pypi__setuptools",
+            "rules_python++internal_deps+pypi__setuptools"
+          ],
+          [
+            "rules_python+",
+            "pypi__tomli",
+            "rules_python++internal_deps+pypi__tomli"
+          ],
+          [
+            "rules_python+",
+            "pypi__wheel",
+            "rules_python++internal_deps+pypi__wheel"
+          ],
+          [
+            "rules_python+",
+            "pypi__zipp",
+            "rules_python++internal_deps+pypi__zipp"
+          ],
+          [
+            "rules_python+",
+            "pythons_hub",
+            "rules_python++python+pythons_hub"
+          ],
+          [
+            "rules_python++python+pythons_hub",
+            "python_3_10_host",
+            "rules_python++python+python_3_10_host"
+          ],
+          [
+            "rules_python++python+pythons_hub",
+            "python_3_11_host",
+            "rules_python++python+python_3_11_host"
+          ],
+          [
+            "rules_python++python+pythons_hub",
+            "python_3_12_host",
+            "rules_python++python+python_3_12_host"
+          ],
+          [
+            "rules_python++python+pythons_hub",
+            "python_3_8_host",
+            "rules_python++python+python_3_8_host"
+          ],
+          [
+            "rules_python++python+pythons_hub",
+            "python_3_9_host",
+            "rules_python++python+python_3_9_host"
+          ]
+        ]
+      }
+    },
     "@@rules_python+//python/uv:uv.bzl%uv": {
       "general": {
         "bzlTransitiveDigest": "ijW9KS7qsIY+yBVvJ+Nr1mzwQox09j13DnE3iIwaeTM=",
diff --git a/Package.swift b/Package.swift
index 8227849e0..5aa8a875d 100644
--- a/Package.swift
+++ b/Package.swift
@@ -103,6 +103,7 @@ var targets: [PackageDescription.Target] = [
         name: "SourceGraph",
         dependencies: [
             .target(name: "Configuration"),
+            .target(name: "Extensions"),
             .product(name: "SwiftSyntax", package: "swift-syntax"),
             .product(name: "SystemPackage", package: "swift-system"),
             .target(name: "Shared"),
diff --git a/Sources/BUILD.bazel b/Sources/BUILD.bazel
index 3631704b1..1f6d24eb1 100644
--- a/Sources/BUILD.bazel
+++ b/Sources/BUILD.bazel
@@ -52,9 +52,14 @@ swift_library(
         "SourceGraph/Elements/DeclarationAttribute.swift",
         "SourceGraph/Elements/ImportStatement.swift",
         "SourceGraph/Elements/Location.swift",
+        "SourceGraph/Elements/ModuleBitset.swift",
+        "SourceGraph/Elements/ModuleID.swift",
+        "SourceGraph/Elements/ModuleNameInterner.swift",
         "SourceGraph/Elements/ProjectFileKind.swift",
         "SourceGraph/Elements/Reference.swift",
         "SourceGraph/Elements/SourceFile.swift",
+        "SourceGraph/Elements/USRID.swift",
+        "SourceGraph/Elements/USRInterner.swift",
         "SourceGraph/Mutators/AccessibilityCascader.swift",
         "SourceGraph/Mutators/AncestralReferenceEliminator.swift",
         "SourceGraph/Mutators/AppIntentsRetainer.swift",
@@ -98,6 +103,7 @@ swift_library(
     module_name = "SourceGraph",
     deps = [
         "//Sources:Configuration",
+        "//Sources:Extensions",
         "//Sources:Shared",
         "@swift-syntax//:SwiftSyntax",
         "@swift-system//:SystemPackage",
diff --git a/Sources/Frontend/Commands/ScanCommand.swift b/Sources/Frontend/Commands/ScanCommand.swift
index 8ac9efbb5..fdf052ed5 100644
--- a/Sources/Frontend/Commands/ScanCommand.swift
+++ b/Sources/Frontend/Commands/ScanCommand.swift
@@ -177,6 +177,7 @@ struct ScanCommand: ParsableCommand {
 
         configuration.guidedSetup = setup
         configuration.projectRoot = projectRoot
+
         configuration.apply(\.$project, project)
         configuration.apply(\.$schemes, schemes)
         configuration.apply(\.$indexExclude, indexExclude)
diff --git a/Sources/Frontend/Scan.swift b/Sources/Frontend/Scan.swift
index 63bd169d9..9179d8f0b 100644
--- a/Sources/Frontend/Scan.swift
+++ b/Sources/Frontend/Scan.swift
@@ -17,7 +17,7 @@ final class Scan {
         self.configuration = configuration
         self.logger = logger
         self.swiftVersion = swiftVersion
-        graph = SourceGraph(configuration: configuration, logger: logger)
+        graph = SourceGraph(configuration: configuration)
     }
 
     func perform(project: Project) throws -> [ScanResult] {
@@ -41,7 +41,11 @@ final class Scan {
         try build(driver)
         try index(driver)
         try analyze()
-        return buildResults()
+        let results = buildResults()
+        // Let the OS reclaim memory at process exit instead of paying
+        // the cost of tearing down the entire SourceGraph via ARC.
+        _ = Unmanaged.passRetained(graph)
+        return results
     }
 
     // MARK: - Private
@@ -68,7 +72,9 @@ final class Scan {
         }
 
         let indexLogger = logger.contextualized(with: "index")
+        let planInterval = logger.beginInterval("index:plan")
         let plan = try driver.plan(logger: indexLogger)
+        logger.endInterval(planInterval)
         let graphMutex = SourceGraphMutex(graph: graph)
         let pipeline = IndexPipeline(plan: plan, graph: graphMutex, logger: indexLogger, configuration: configuration, swiftVersion: swiftVersion)
         try pipeline.perform()
diff --git a/Sources/Indexer/IndexPipeline.swift b/Sources/Indexer/IndexPipeline.swift
index 906900e81..98711e817 100644
--- a/Sources/Indexer/IndexPipeline.swift
+++ b/Sources/Indexer/IndexPipeline.swift
@@ -64,6 +64,8 @@ public struct IndexPipeline {
             ).perform()
         }
 
+        let interval = logger.beginInterval("index:complete")
         graph.withLock { $0.indexingComplete() }
+        logger.endInterval(interval)
     }
 }
diff --git a/Sources/Indexer/SourceFileCollector.swift b/Sources/Indexer/SourceFileCollector.swift
index cb2e53bf2..c5c13dcb7 100644
--- a/Sources/Indexer/SourceFileCollector.swift
+++ b/Sources/Indexer/SourceFileCollector.swift
@@ -43,12 +43,12 @@ public struct SourceFileCollector {
                     let file = FilePath.makeAbsolute(filePath, relativeTo: currentFilePath)
 
                     if !isExcluded(file) {
-                        guard file.exists else {
-                            logger.debug("Source file does not exist: \(file.string)")
+                        if excludedTargets.contains(unit.moduleName) {
                             return nil
                         }
 
-                        if excludedTargets.contains(unit.moduleName) {
+                        guard file.exists else {
+                            logger.debug("Source file does not exist: \(file.string)")
                             return nil
                         }
 
diff --git a/Sources/Indexer/SwiftIndexer.swift b/Sources/Indexer/SwiftIndexer.swift
index ef5cbb5a7..2ccc32f6a 100644
--- a/Sources/Indexer/SwiftIndexer.swift
+++ b/Sources/Indexer/SwiftIndexer.swift
@@ -4,6 +4,7 @@ import IndexStore
 import Logger
 import Shared
 import SourceGraph
+import SwiftSyntax
 import SyntaxAnalysis
 import SystemPackage
 
@@ -12,6 +13,12 @@ public struct IndexUnit {
     let unit: UnitReader
 }
 
+private struct DanglingReferenceTables {
+    let declsByLocation: [Location: [Declaration]]
+    let declsByLine: [Int: [Declaration]]
+    let sortedDeclLines: ReversedCollection<[Int]>
+}
+
 final class SwiftIndexer: Indexer {
     private let sourceFiles: [SourceFile: [IndexUnit]]
     private let graph: SourceGraphMutex
@@ -47,6 +54,8 @@ final class SwiftIndexer: Indexer {
             )
         }
 
+        graph.reserveCapacity(forFileCount: sourceFiles.count)
+
         let phaseOneInterval = logger.beginInterval("index:swift:phase:one")
 
         try JobPool(jobs: jobs).forEach { job in
@@ -154,7 +163,7 @@ final class SwiftIndexer: Indexer {
         /// phase two.
         func phaseOne() throws {
             var rawDeclsByKey: [RawDeclaration.Key: [(RawDeclaration, [RawRelation])]] = [:]
-            var references: Set<Reference> = []
+            var references: [Reference] = []
 
             for unit in units {
                 for recordName in unit.unit.recordNames {
@@ -162,8 +171,7 @@ final class SwiftIndexer: Indexer {
 
                     record.forEach(occurrence: { occurrence in
                         let usr = occurrence.symbol.usr
-                        guard let location = self.transformLocation(occurrence.location)
-                        else { return }
+                        let location = self.transformLocation(occurrence.location)
 
                         var relations: [RawRelation] = []
                         occurrence.forEach(relation: { relSymbol, relRoles in
@@ -190,7 +198,7 @@ final class SwiftIndexer: Indexer {
                         }
 
                         if occurrence.roles.contains(.reference) {
-                            references.formUnion(self.parseReference(
+                            references.append(contentsOf: self.parseReference(
                                 occurrence,
                                 usr,
                                 location,
@@ -199,7 +207,7 @@ final class SwiftIndexer: Indexer {
                         }
 
                         if occurrence.roles.contains(.implicit) {
-                            references.formUnion(self.parseImplicit(
+                            references.append(contentsOf: self.parseImplicit(
                                 usr,
                                 location,
                                 relations
@@ -210,32 +218,35 @@ final class SwiftIndexer: Indexer {
             }
 
             var newDeclarations: Set<Declaration> = []
+            var retainedDecls: Set<Declaration> = []
 
             for (key, values) in rawDeclsByKey {
                 let usrs = values.mapSet { $0.0.usr }
-                let decl = Declaration(name: key.name, kind: key.kind, usrs: usrs, location: key.location)
+                let usrIDs = usrs.map { cachedIntern($0) }
+                let decl = Declaration(name: key.name, kind: key.kind, usrs: usrs, usrIDs: usrIDs, location: key.location)
 
                 decl.isImplicit = key.isImplicit
                 decl.isObjcAccessible = key.isObjcAccessible
 
                 if decl.isImplicit {
-                    graph.withLock { $0.markRetained(decl) }
+                    retainedDecls.insert(decl)
                 }
 
                 if decl.isObjcAccessible, configuration.retainObjcAccessible {
-                    graph.withLock { $0.markRetained(decl) }
+                    retainedDecls.insert(decl)
                 }
 
                 let relations = values.flatMap(\.1)
-                references.formUnion(parseDeclaration(decl, relations))
+                references.append(contentsOf: parseDeclaration(decl, relations))
 
                 newDeclarations.insert(decl)
                 declarations.append(decl)
             }
 
-            graph.withLock { graph in
+            try graph.withLock { graph in
                 graph.add(references)
-                graph.add(newDeclarations)
+                try graph.add(newDeclarations)
+                graph.markRetained(retainedDecls)
 
                 if retainAllDeclarations {
                     graph.markRetained(newDeclarations)
@@ -243,56 +254,104 @@ final class SwiftIndexer: Indexer {
             }
 
             establishDeclarationHierarchy()
+
+            if !danglingReferences.isEmpty {
+                sortedDeclarationsCache = declarations.sorted()
+            }
         }
 
         /// Phase two associates latent references, and performs other actions that depend on the completed source graph.
         func phaseTwo() throws {
-            if !configuration.disableUnusedImportAnalysis {
-                graph.withLock { graph in
-                    graph.addIndexedSourceFile(sourceFile)
-                    graph.addIndexedModules(sourceFile.modules)
-                }
+            let hasWork = !declarations.isEmpty || !referencesByUsr.isEmpty || !danglingReferences.isEmpty
+
+            if !hasWork, configuration.disableUnusedImportAnalysis {
+                return
             }
 
             let multiplexingSyntaxVisitor = try MultiplexingSyntaxVisitor(file: sourceFile, swiftVersion: swiftVersion)
             let declarationSyntaxVisitor = multiplexingSyntaxVisitor.add(DeclarationSyntaxVisitor.self)
             let importSyntaxVisitor = multiplexingSyntaxVisitor.add(ImportSyntaxVisitor.self)
-
+            let functionCollector = multiplexingSyntaxVisitor.add(FunctionSyntaxCollector.self)
             multiplexingSyntaxVisitor.visit()
 
             sourceFile.importStatements = importSyntaxVisitor.importStatements
             sourceFile.importsSwiftTesting = importSyntaxVisitor.importStatements.contains(where: { $0.module == "Testing" })
 
-            if !configuration.disableUnusedImportAnalysis {
-                for stmt in sourceFile.importStatements where stmt.isExported {
-                    graph.withLock { graph in
+            if !hasWork {
+                graph.withLock { graph in
+                    graph.addIndexedSourceFile(sourceFile)
+                    graph.addIndexedModules(sourceFile.modules)
+                    for stmt in sourceFile.importStatements where stmt.isExported {
+                        graph.addExportedModule(stmt.module, exportedBy: sourceFile.modules)
+                    }
+                }
+                return
+            }
+
+            let declarationsByLocation = declarationSyntaxVisitor.resultsByLocation
+            let fileCommands = multiplexingSyntaxVisitor.parseComments()
+
+            let danglingRefTables = buildDanglingReferenceTables()
+
+            let analyzer = UnusedParameterAnalyzer()
+            let paramsByFunction = analyzer.analyze(
+                collectedFunctionDecls: functionCollector.functionDecls,
+                collectedInitializerDecls: functionCollector.initializerDecls,
+                file: multiplexingSyntaxVisitor.sourceFile,
+                locationConverter: multiplexingSyntaxVisitor.locationConverter,
+                parseProtocols: true
+            )
+
+            var unmatchedFunctions: [(String, Location)] = []
+
+            try graph.withLock { graph in
+                if !configuration.disableUnusedImportAnalysis {
+                    graph.addIndexedSourceFile(sourceFile)
+                    graph.addIndexedModules(sourceFile.modules)
+                    for stmt in sourceFile.importStatements where stmt.isExported {
                         graph.addExportedModule(stmt.module, exportedBy: sourceFile.modules)
                     }
                 }
+
+                associateLatentReferencesUnsafe(graph: graph)
+                associateDanglingReferencesUnsafe(tables: danglingRefTables)
+                applyDeclarationMetadataUnsafe(declarationsByLocation)
+                try identifyUnusedParametersUnsafe(
+                    paramsByFunction: paramsByFunction,
+                    graph: graph,
+                    unmatchedFunctions: &unmatchedFunctions
+                )
+                applyCommentCommandsUnsafe(fileCommands: fileCommands, graph: graph)
             }
 
-            associateLatentReferences()
-            associateDanglingReferences()
-            visitDeclarations(using: declarationSyntaxVisitor)
-            identifyUnusedParameters(using: multiplexingSyntaxVisitor)
-            applyCommentCommands(using: multiplexingSyntaxVisitor)
+            for (name, location) in unmatchedFunctions {
+                logger.debug("Failed to associate indexed function for parameter function '\(name)' at \(location).")
+            }
         }
 
         // MARK: - Private
 
         private var declarations: [Declaration] = []
+        private var sortedDeclarationsCache: [Declaration]?
         private var childDeclsByParentUsr: [String: Set<Declaration>] = [:]
         private var referencesByUsr: [String: Set<Reference>] = [:]
         private var danglingReferences: [Reference] = []
         private var varParameterUsrs: Set<String> = []
         private var extensionUsrMap: [String: String] = [:]
+        private var usrCache: [String: USRID] = [:]
+
+        private func cachedIntern(_ usr: String) -> USRID {
+            if let cached = usrCache[usr] { return cached }
+            let id = graph.usrInterner.intern(usr)
+            usrCache[usr] = id
+            return id
+        }
 
         private func establishDeclarationHierarchy() {
             graph.withLock { graph in
                 for (parent, decls) in childDeclsByParentUsr {
                     guard let parentDecl = graph.declaration(withUsr: parent) else {
                         if varParameterUsrs.contains(parent) {
-                            // These declarations are children of a parameter and are redundant.
                             decls.forEach { graph.remove($0) }
                         }
 
@@ -303,34 +362,25 @@ final class SwiftIndexer: Indexer {
                         decl.parent = parentDecl
                     }
 
-                    parentDecl.declarations.formUnion(decls)
+                    parentDecl.declarations.append(contentsOf: decls)
                 }
             }
         }
 
-        private func associateLatentReferences() {
+        private func associateLatentReferencesUnsafe(graph: SourceGraph) {
             for (usr, refs) in referencesByUsr {
-                graph.withLock { graph in
-                    if let decl = graph.declaration(withUsr: usr) {
-                        for ref in refs {
-                            associateUnsafe(ref, with: decl)
-                        }
-                    } else {
-                        danglingReferences.append(contentsOf: refs)
+                if let decl = graph.declaration(withUsr: usr) {
+                    for ref in refs {
+                        associateUnsafe(ref, with: decl)
                     }
+                } else {
+                    danglingReferences.append(contentsOf: refs)
                 }
             }
         }
 
-        // Swift does not associate some type references with the containing declaration, resulting in references
-        // with no clear parent. Property references are one example: https://github.com/apple/swift/issues/56163
-        private func associateDanglingReferences() {
-            guard !danglingReferences.isEmpty else { return }
-
-            // Sort declarations to ensure deterministic candidate selection when
-            // multiple declarations exist at the same location.
-            let sortedDeclarations = declarations.sorted()
-
+        private func buildDanglingReferenceTables() -> DanglingReferenceTables {
+            let sortedDeclarations = sortedDeclarationsCache ?? declarations.sorted()
             let declsByLocation = sortedDeclarations
                 .reduce(into: [Location: [Declaration]]()) { result, decl in
                     result[decl.location, default: []].append(decl)
@@ -340,124 +390,122 @@ final class SwiftIndexer: Indexer {
                     result[decl.location.line, default: []].append(decl)
                 }
             let sortedDeclLines = declsByLine.keys.sorted().reversed()
+            return DanglingReferenceTables(
+                declsByLocation: declsByLocation,
+                declsByLine: declsByLine,
+                sortedDeclLines: sortedDeclLines
+            )
+        }
+
+        // Swift does not associate some type references with the containing declaration, resulting in references
+        // with no clear parent. Property references are one example: https://github.com/apple/swift/issues/56163
+        private func associateDanglingReferencesUnsafe(tables: DanglingReferenceTables) {
+            guard !danglingReferences.isEmpty else { return }
 
             for ref in danglingReferences {
-                let sameLineCandidateDecls = declsByLocation[ref.location] ??
-                    declsByLine[ref.location.line]
+                let sameLineCandidateDecls = tables.declsByLocation[ref.location] ??
+                    tables.declsByLine[ref.location.line]
                 var candidateDecls = [Declaration]()
 
                 if let sameLineCandidateDecls {
                     candidateDecls = sameLineCandidateDecls
                 } else {
-                    // For references with no declaration on the same line, find the nearest preceding declaration.
-                    if let line = sortedDeclLines.first(where: { $0 < ref.location.line }) {
-                        candidateDecls = declsByLine[line]?.filter {
-                            !$0.usrs.contains(ref.usr) &&
-                                !$0.ancestralDeclarations.contains(where: { $0.usrs.contains(ref.usr) })
+                    if let line = tables.sortedDeclLines.first(where: { $0 < ref.location.line }) {
+                        candidateDecls = tables.declsByLine[line]?.filter {
+                            !$0.usrIDs.contains(ref.usrID) &&
+                                !$0.ancestralDeclarations.contains(where: { $0.usrIDs.contains(ref.usrID) })
                         } ?? []
                     }
                 }
 
-                // The vast majority of the time there will only be a single declaration for this location,
-                // however it is possible for there to be more than one. In that case, first attempt to associate with
-                // a decl without a parent, as the reference may be a related type of a class/struct/etc.
                 if let decl = candidateDecls.first(where: { $0.parent == nil }) {
-                    associate(ref, with: decl)
+                    associateUnsafe(ref, with: decl)
                 } else if let decl = candidateDecls.min() {
-                    // Fallback to using the first declaration.
-                    // Sorting the declarations helps in the situation where the candidate declarations includes a
-                    // property/subscript, and a getter on the same line. The property/subscript is more likely to be
-                    // the declaration that should hold the references.
-                    associate(ref, with: decl)
+                    associateUnsafe(ref, with: decl)
                 }
             }
         }
 
-        private func applyCommentCommands(using syntaxVisitor: MultiplexingSyntaxVisitor) {
-            let fileCommands = syntaxVisitor.parseComments()
+        private func applyDeclarationMetadataUnsafe(_ declarationsByLocation: [Location: DeclarationSyntaxVisitor.Result]) {
+            for decl in declarations {
+                guard let result = declarationsByLocation[decl.location] else { continue }
+
+                applyDeclarationMetadata(to: decl, with: result)
+            }
+        }
 
+        private func applyCommentCommandsUnsafe(fileCommands: [CommentCommand], graph: SourceGraph) {
             if fileCommands.contains(.ignoreAll) {
-                commandIgnore(declarations, kind: .file)
+                commandIgnoreUnsafe(declarations, kind: .file, graph: graph)
             } else {
                 for decl in declarations where decl.commentCommands.contains(.ignore) {
-                    commandIgnore([decl], kind: .declaration)
+                    commandIgnoreUnsafe([decl], kind: .declaration, graph: graph)
                 }
             }
         }
 
-        private func visitDeclarations(using declarationVisitor: DeclarationSyntaxVisitor) {
-            let declarationsByLocation = declarationVisitor.resultsByLocation
+        /// Must be called while holding the graph lock.
+        private func applyDeclarationMetadata(to decl: Declaration, with result: DeclarationSyntaxVisitor.Result) {
+            if let accessibility = result.accessibility {
+                decl.accessibility = .init(value: accessibility, isExplicit: true)
+            }
 
-            for decl in declarations {
-                guard let result = declarationsByLocation[decl.location] else { continue }
+            decl.attributes = result.attributes
+            decl.modifiers = Set(result.modifiers)
+            decl.commentCommands = Set(result.commentCommands)
+            decl.declaredType = result.variableType
 
-                applyDeclarationMetadata(to: decl, with: result)
+            decl.hasGenericFunctionReturnedMetatypeParameters = result.hasGenericFunctionReturnedMetatypeParameters
+
+            for ref in decl.references {
+                assignRole(to: ref, decl: decl, result: result)
+            }
+            for ref in decl.related {
+                assignRole(to: ref, decl: decl, result: result)
             }
         }
 
-        private func applyDeclarationMetadata(to decl: Declaration, with result: DeclarationSyntaxVisitor.Result) {
-            graph.withLock { _ in
-                if let accessibility = result.accessibility {
-                    decl.accessibility = .init(value: accessibility, isExplicit: true)
-                }
-
-                decl.attributes = Set(result.attributes)
-                decl.modifiers = Set(result.modifiers)
-                decl.commentCommands = Set(result.commentCommands)
-                decl.declaredType = result.variableType
-
-                decl.hasGenericFunctionReturnedMetatypeParameters = result.hasGenericFunctionReturnedMetatypeParameters
-
-                for ref in decl.references.union(decl.related) {
-                    if result.inheritedTypeLocations.contains(ref.location) {
-                        if decl.kind.isConformableKind, ref.declarationKind == .protocol {
-                            ref.role = .conformedType
-                        } else if decl.kind == .protocol, ref.declarationKind == .protocol {
-                            ref.role = .refinedProtocolType
-                        } else if decl.kind == .class || decl.kind == .associatedtype {
-                            ref.role = .inheritedType
-                        }
-                    } else if result.variableTypeLocations.contains(ref.location) {
-                        ref.role = .varType
-                    } else if result.returnTypeLocations.contains(ref.location) {
-                        ref.role = .returnType
-                    } else if result.throwTypeLocations.contains(ref.location) {
-                        ref.role = .throwType
-                    } else if result.parameterTypeLocations.contains(ref.location) {
-                        ref.role = .parameterType
-                    } else if result.genericParameterLocations.contains(ref.location) {
-                        ref.role = .genericParameterType
-                    } else if result.genericConformanceRequirementLocations.contains(ref.location) {
-                        ref.role = .genericRequirementType
-                    } else if result.variableInitFunctionCallLocations.contains(ref.location) {
-                        ref.role = .variableInitFunctionCall
-                    } else if result.functionCallMetatypeArgumentLocations.contains(ref.location) {
-                        ref.role = .functionCallMetatypeArgument
-                    } else if result.typeInitializerLocations.contains(ref.location) {
-                        ref.role = .initializerType
-                    } else if result.variableInitExprLocations.contains(ref.location) {
-                        ref.role = .initializerType
-                    }
+        private func assignRole(to ref: Reference, decl: Declaration, result: DeclarationSyntaxVisitor.Result) {
+            if result.inheritedTypeLocations.contains(ref.location) {
+                if decl.kind.isConformableKind, ref.declarationKind == .protocol {
+                    ref.role = .conformedType
+                } else if decl.kind == .protocol, ref.declarationKind == .protocol {
+                    ref.role = .refinedProtocolType
+                } else if decl.kind == .class || decl.kind == .associatedtype {
+                    ref.role = .inheritedType
                 }
+            } else if result.variableTypeLocations.contains(ref.location) {
+                ref.role = .varType
+            } else if result.returnTypeLocations.contains(ref.location) {
+                ref.role = .returnType
+            } else if result.throwTypeLocations.contains(ref.location) {
+                ref.role = .throwType
+            } else if result.parameterTypeLocations.contains(ref.location) {
+                ref.role = .parameterType
+            } else if result.genericParameterLocations.contains(ref.location) {
+                ref.role = .genericParameterType
+            } else if result.genericConformanceRequirementLocations.contains(ref.location) {
+                ref.role = .genericRequirementType
+            } else if result.variableInitFunctionCallLocations.contains(ref.location) {
+                ref.role = .variableInitFunctionCall
+            } else if result.functionCallMetatypeArgumentLocations.contains(ref.location) {
+                ref.role = .functionCallMetatypeArgument
+            } else if result.typeInitializerLocations.contains(ref.location) {
+                ref.role = .initializerType
+            } else if result.variableInitExprLocations.contains(ref.location) {
+                ref.role = .initializerType
             }
         }
 
-        private func commandIgnore(_ decls: [Declaration], kind: CommandIgnoreKind) {
+        private func commandIgnoreUnsafe(_ decls: [Declaration], kind: CommandIgnoreKind, graph: SourceGraph) {
             for decl in decls {
-                graph.withLock { graph in
-                    graph.markRetained(decl)
-                    decl.unusedParameters.forEach { graph.markRetained($0) }
+                graph.markRetained(decl)
+                decl.unusedParameters.forEach { graph.markRetained($0) }
 
-                    graph.markCommandIgnored(decl, kind: kind)
-                    decl.unusedParameters.forEach { graph.markCommandIgnored($0, kind: kind) }
-                }
-                commandIgnore(Array(decl.declarations), kind: kind)
-            }
-        }
+                graph.markCommandIgnored(decl, kind: kind)
+                decl.unusedParameters.forEach { graph.markCommandIgnored($0, kind: kind) }
 
-        private func associate(_ ref: Reference, with decl: Declaration) {
-            graph.withLock { _ in
-                associateUnsafe(ref, with: decl)
+                commandIgnoreUnsafe(decl.declarations, kind: kind, graph: graph)
             }
         }
 
@@ -465,58 +513,54 @@ final class SwiftIndexer: Indexer {
             ref.parent = decl
 
             if ref.kind == .related {
-                decl.related.insert(ref)
+                decl.related.append(ref)
             } else {
-                decl.references.insert(ref)
+                decl.references.append(ref)
             }
         }
 
-        private func identifyUnusedParameters(using syntaxVisitor: MultiplexingSyntaxVisitor) {
+        private func identifyUnusedParametersUnsafe(
+            paramsByFunction: [Function: Set<Parameter>],
+            graph: SourceGraph,
+            unmatchedFunctions: inout [(String, Location)]
+        ) throws {
             let functionDecls = declarations.filter(\.kind.isFunctionKind)
             let functionDeclsByLocation = functionDecls.reduce(into: [Location: Declaration]()) {
                 $0[$1.location] = $1
             }
 
-            // Build a map of ignored param names per function, and track functions with ignored
-            // params so ScanResultBuilder can efficiently detect superfluous ignores.
             var ignoredParamsByLocation: [Location: [String]] = [:]
+            var functionsWithIgnoredParams: [Declaration] = []
             for functionDecl in functionDecls {
                 let ignoredParamNames = functionDecl.commentCommands.ignoredParameterNames
                 if !ignoredParamNames.isEmpty {
                     ignoredParamsByLocation[functionDecl.location] = ignoredParamNames
-                    graph.withLock { $0.markHasIgnoredParameters(functionDecl) }
+                    functionsWithIgnoredParams.append(functionDecl)
                 }
             }
 
-            let analyzer = UnusedParameterAnalyzer()
-            let paramsByFunction = analyzer.analyze(
-                file: syntaxVisitor.sourceFile,
-                syntax: syntaxVisitor.syntax,
-                locationConverter: syntaxVisitor.locationConverter,
-                parseProtocols: true
-            )
+            for functionDecl in functionsWithIgnoredParams {
+                graph.markHasIgnoredParameters(functionDecl)
+            }
 
             for (function, params) in paramsByFunction {
                 guard let functionDecl = functionDeclsByLocation[function.location] else {
-                    // The declaration may not exist if the code was not compiled due to build conditions, e.g #if.
-                    logger.debug("Failed to associate indexed function for parameter function '\(function.name)' at \(function.location).")
+                    unmatchedFunctions.append((function.name, function.location))
                     continue
                 }
 
                 let ignoredParamNames = ignoredParamsByLocation[functionDecl.location] ?? []
 
-                graph.withLock { graph in
-                    for param in params {
-                        let paramDecl = param.makeDeclaration(withParent: functionDecl)
-                        functionDecl.unusedParameters.insert(paramDecl)
-                        graph.add(paramDecl)
-
-                        if retainAllDeclarations || (functionDecl.isObjcAccessible && configuration.retainObjcAccessible) {
-                            graph.markRetained(paramDecl)
-                        } else if ignoredParamNames.contains(param.name.text) {
-                            graph.markRetained(paramDecl)
-                            graph.markCommandIgnored(paramDecl, kind: .declaration)
-                        }
+                for param in params {
+                    let paramDecl = param.makeDeclaration(withParent: functionDecl, interner: self.graph.usrInterner)
+                    functionDecl.unusedParameters.append(paramDecl)
+                    try graph.add(paramDecl)
+
+                    if retainAllDeclarations || (functionDecl.isObjcAccessible && configuration.retainObjcAccessible) {
+                        graph.markRetained(paramDecl)
+                    } else if ignoredParamNames.contains(param.name.text) {
+                        graph.markRetained(paramDecl)
+                        graph.markCommandIgnored(paramDecl, kind: .declaration)
                     }
                 }
             }
@@ -563,8 +607,8 @@ final class SwiftIndexer: Indexer {
         private func parseDeclaration(
             _ decl: Declaration,
             _ relations: [RawRelation]
-        ) -> Set<Reference> {
-            var references: Set<Reference> = []
+        ) -> [Reference] {
+            var references: [Reference] = []
 
             for rel in relations {
                 if rel.roles.contains(.childOf) {
@@ -581,16 +625,18 @@ final class SwiftIndexer: Indexer {
                     let baseFunc = rel.symbol
 
                     if let baseFuncUsr = baseFunc.usr, let baseFuncKind = transformDeclarationKind(baseFunc.kind, baseFunc.subKind) {
+                        let usrID = cachedIntern(baseFuncUsr)
                         let reference = Reference(
                             name: baseFunc.name,
                             kind: .related,
                             declarationKind: baseFuncKind,
+                            usrID: usrID,
                             usr: baseFuncUsr,
                             location: decl.location
                         )
                         reference.parent = decl
-                        decl.related.insert(reference)
-                        references.insert(reference)
+                        decl.related.append(reference)
+                        references.append(reference)
                     }
                 }
 
@@ -598,15 +644,17 @@ final class SwiftIndexer: Indexer {
                     let referencer = rel.symbol
 
                     if let referencerUsr = referencer.usr {
-                        for usr in decl.usrs {
+                        for usrID in decl.usrIDs {
+                            let usr = graph.usrInterner.string(for: usrID)
                             let reference = Reference(
                                 name: decl.name,
                                 kind: rel.roles.contains(.baseOf) ? .related : .normal,
                                 declarationKind: decl.kind,
+                                usrID: usrID,
                                 usr: usr,
                                 location: decl.location
                             )
-                            references.insert(reference)
+                            references.append(reference)
                             referencesByUsr[referencerUsr, default: []].insert(reference)
                         }
                     }
@@ -628,10 +676,12 @@ final class SwiftIndexer: Indexer {
                     let baseFunc = relation.symbol
 
                     if let baseFuncUsr = baseFunc.usr, let baseFuncKind = transformDeclarationKind(baseFunc.kind, baseFunc.subKind) {
+                        let usrID = cachedIntern(baseFuncUsr)
                         let reference = Reference(
                             name: baseFunc.name,
                             kind: .related,
                             declarationKind: baseFuncKind,
+                            usrID: usrID,
                             usr: baseFuncUsr,
                             location: location
                         )
@@ -657,6 +707,7 @@ final class SwiftIndexer: Indexer {
                 return []
             }
 
+            let usrID = cachedIntern(occurrenceUsr)
             var refs = [Reference]()
 
             for relation in relations {
@@ -668,6 +719,7 @@ final class SwiftIndexer: Indexer {
                             name: occurrence.symbol.name,
                             kind: relation.roles.contains(.baseOf) ? .related : .normal,
                             declarationKind: kind,
+                            usrID: usrID,
                             usr: occurrenceUsr,
                             location: location
                         )
@@ -682,6 +734,7 @@ final class SwiftIndexer: Indexer {
                     name: occurrence.symbol.name,
                     kind: .normal,
                     declarationKind: kind,
+                    usrID: usrID,
                     usr: occurrenceUsr,
                     location: location
                 )
@@ -697,7 +750,7 @@ final class SwiftIndexer: Indexer {
             return refs
         }
 
-        private func transformLocation(_ input: (line: Int, column: Int)) -> Location? {
+        private func transformLocation(_ input: (line: Int, column: Int)) -> Location {
             Location(file: sourceFile, line: input.line, column: input.column)
         }
 
diff --git a/Sources/PeripheryKit/Results/OutputDeclarationFilter.swift b/Sources/PeripheryKit/Results/OutputDeclarationFilter.swift
index cb33c793f..fb3a81d0f 100644
--- a/Sources/PeripheryKit/Results/OutputDeclarationFilter.swift
+++ b/Sources/PeripheryKit/Results/OutputDeclarationFilter.swift
@@ -20,12 +20,10 @@ public final class OutputDeclarationFilter {
 
         if let baseline {
             var didFilterDeclaration = false
-            let ignoredUsrs = declarations
-                .flatMapSet(\.usrs)
-                .intersection(baseline.usrs)
+            let baselineUsrs = baseline.usrs
 
             declarations = declarations.filter {
-                let isIgnored = $0.usrs.contains { ignoredUsrs.contains($0) }
+                let isIgnored = $0.usrs.contains { baselineUsrs.contains($0) }
                 if isIgnored {
                     didFilterDeclaration = true
                 }
@@ -45,7 +43,6 @@ public final class OutputDeclarationFilter {
             .filter { [contextualLogger] in
                 var path = $0.declaration.location.file.path
 
-                // If the declaration has a location override, use it as the path for filtering.
                 if let override = $0.declaration.commentCommands.locationOverride {
                     let (overridePath, _, _) = override
                     path = overridePath
diff --git a/Sources/PeripheryKit/ScanResult.swift b/Sources/PeripheryKit/ScanResult.swift
index 790cbd45d..7d141f1ed 100644
--- a/Sources/PeripheryKit/ScanResult.swift
+++ b/Sources/PeripheryKit/ScanResult.swift
@@ -5,7 +5,7 @@ public struct ScanResult {
     enum Annotation {
         case unused
         case assignOnlyProperty
-        case redundantProtocol(references: Set<Reference>, inherited: Set<String>)
+        case redundantProtocol(references: [Reference], inherited: Set<String>)
         case redundantPublicAccessibility(modules: Set<String>)
         case superfluousIgnoreCommand
     }
diff --git a/Sources/PeripheryKit/ScanResultBuilder.swift b/Sources/PeripheryKit/ScanResultBuilder.swift
index c0093d5c7..ef501173b 100644
--- a/Sources/PeripheryKit/ScanResultBuilder.swift
+++ b/Sources/PeripheryKit/ScanResultBuilder.swift
@@ -18,14 +18,13 @@ public enum ScanResultBuilder {
                !graph.retainedDeclarations.contains(removableDeclaration),
                !graph.ignoredDeclarations.contains(removableDeclaration)
             {
-                let decls = removableDeclaration.descendentDeclarations.union([removableDeclaration])
-
-                for decl in decls {
-                    let extensions = graph.extensions[decl, default: []]
-                    for ext in extensions {
+                let addExtensions = { (decl: Declaration) in
+                    for ext in graph.extensions[decl, default: []] {
                         extensionResults.append(ScanResult(declaration: ext, annotation: .unused))
                     }
                 }
+                addExtensions(removableDeclaration)
+                removableDeclaration.forEachDescendentDeclaration(addExtensions)
             }
 
             return [ScanResult(declaration: removableDeclaration, annotation: .unused)] + extensionResults
@@ -102,7 +101,7 @@ public enum ScanResultBuilder {
             if isProtocolMember, ref.kind != .normal { continue }
 
             if graph.commandIgnoredDeclarations[parent] == nil {
-                if graph.usedDeclarations.contains(parent) {
+                if parent.isUsed {
                     return true
                 }
             }
@@ -125,10 +124,12 @@ public enum ScanResultBuilder {
                     // The ignored parameter is actually used - create a result for it
                     let parentUsrs = decl.usrs.sorted().joined(separator: "-")
                     let usr = "param-\(ignoredParamName)-\(decl.name)-\(parentUsrs)"
+                    let usrID = graph.usrInterner.intern(usr)
                     let paramDecl = Declaration(
                         name: ignoredParamName,
                         kind: .varParameter,
                         usrs: [usr],
+                        usrIDs: [usrID],
                         location: decl.location
                     )
                     paramDecl.parent = decl
diff --git a/Sources/SourceGraph/Elements/Declaration.swift b/Sources/SourceGraph/Elements/Declaration.swift
index 382c58403..ef39d2c6b 100644
--- a/Sources/SourceGraph/Elements/Declaration.swift
+++ b/Sources/SourceGraph/Elements/Declaration.swift
@@ -1,7 +1,7 @@
 import Foundation
 
 public final class Declaration {
-    public enum Kind: String, RawRepresentable, CaseIterable {
+    public enum Kind: String, RawRepresentable, CaseIterable, Hashable {
         case `associatedtype`
         case `class`
         case `enum`
@@ -45,25 +45,81 @@ public final class Declaration {
         case varStatic = "var.static"
         case macro
 
-        static var functionKinds: Set<Kind> {
-            Set(Kind.allCases.filter(\.isFunctionKind))
+        // Integer discriminator for O(1) hashing/equality, bypassing the default
+        // RawRepresentable conformance which hashes the String raw value.
+        @usableFromInline var ordinal: Int {
+            switch self {
+            case .associatedtype: 0
+            case .class: 1
+            case .enum: 2
+            case .enumelement: 3
+            case .extension: 4
+            case .extensionClass: 5
+            case .extensionEnum: 6
+            case .extensionProtocol: 7
+            case .extensionStruct: 8
+            case .functionAccessorAddress: 9
+            case .functionAccessorDidset: 10
+            case .functionAccessorGetter: 11
+            case .functionAccessorMutableaddress: 12
+            case .functionAccessorSetter: 13
+            case .functionAccessorWillset: 14
+            case .functionAccessorRead: 15
+            case .functionAccessorModify: 16
+            case .functionAccessorInit: 17
+            case .functionConstructor: 18
+            case .functionDestructor: 19
+            case .functionFree: 20
+            case .functionMethodClass: 21
+            case .functionMethodInstance: 22
+            case .functionMethodStatic: 23
+            case .functionOperator: 24
+            case .functionOperatorInfix: 25
+            case .functionOperatorPostfix: 26
+            case .functionOperatorPrefix: 27
+            case .functionSubscript: 28
+            case .genericTypeParam: 29
+            case .module: 30
+            case .precedenceGroup: 31
+            case .protocol: 32
+            case .struct: 33
+            case .typealias: 34
+            case .varClass: 35
+            case .varGlobal: 36
+            case .varInstance: 37
+            case .varLocal: 38
+            case .varParameter: 39
+            case .varStatic: 40
+            case .macro: 41
+            }
         }
 
-        static var variableKinds: Set<Kind> {
-            Set(Kind.allCases.filter(\.isVariableKind))
+        @inlinable
+        public func hash(into hasher: inout Hasher) {
+            hasher.combine(ordinal)
+        }
+
+        @inlinable
+        public static func == (lhs: Kind, rhs: Kind) -> Bool {
+            lhs.ordinal == rhs.ordinal
         }
 
-        static var protocolMemberKinds: [Kind] {
+        static let functionKinds: Set<Kind> =
+            Set(Kind.allCases.filter(\.isFunctionKind))
+
+        static let variableKinds: Set<Kind> =
+            Set(Kind.allCases.filter(\.isVariableKind))
+
+        static let protocolMemberKinds: [Kind] = {
             let functionKinds: [Kind] = [.functionMethodInstance, .functionMethodStatic, .functionSubscript, .functionOperator, .functionOperatorInfix, .functionOperatorPostfix, .functionOperatorPrefix, .functionConstructor]
             let variableKinds: [Kind] = [.varInstance, .varStatic]
             return functionKinds + variableKinds
-        }
+        }()
 
-        static var protocolMemberConformingKinds: [Kind] {
-            // Protocols cannot declare 'class' members, yet classes can fulfill the requirement with either a 'class'
-            // or 'static' member.
+        // Protocols cannot declare 'class' members, yet classes can fulfill the requirement
+        // with either a 'class' or 'static' member.
+        static let protocolMemberConformingKinds: [Kind] =
             protocolMemberKinds + [.varClass, .functionMethodClass, .associatedtype]
-        }
 
         public var isProtocolMemberKind: Bool {
             Self.protocolMemberKinds.contains(self)
@@ -74,11 +130,27 @@ public final class Declaration {
         }
 
         public var isFunctionKind: Bool {
-            rawValue.hasPrefix("function")
+            switch self {
+            case .functionAccessorAddress, .functionAccessorDidset, .functionAccessorGetter,
+                 .functionAccessorMutableaddress, .functionAccessorSetter, .functionAccessorWillset,
+                 .functionAccessorRead, .functionAccessorModify, .functionAccessorInit,
+                 .functionConstructor, .functionDestructor, .functionFree,
+                 .functionMethodClass, .functionMethodInstance, .functionMethodStatic,
+                 .functionOperator, .functionOperatorInfix, .functionOperatorPostfix,
+                 .functionOperatorPrefix, .functionSubscript:
+                true
+            default:
+                false
+            }
         }
 
         public var isVariableKind: Bool {
-            rawValue.hasPrefix("var")
+            switch self {
+            case .varClass, .varGlobal, .varInstance, .varLocal, .varParameter, .varStatic:
+                true
+            default:
+                false
+            }
         }
 
         static var globalKinds: Set<Kind> = [
@@ -94,9 +166,8 @@ public final class Declaration {
             .varGlobal,
         ]
 
-        static var extensionKinds: Set<Kind> {
+        static let extensionKinds: Set<Kind> =
             Set(Kind.allCases.filter(\.isExtensionKind))
-        }
 
         public var extendedKind: Kind? {
             switch self {
@@ -129,7 +200,12 @@ public final class Declaration {
         }
 
         public var isExtensionKind: Bool {
-            rawValue.hasPrefix("extension")
+            switch self {
+            case .extension, .extensionClass, .extensionEnum, .extensionProtocol, .extensionStruct:
+                true
+            default:
+                false
+            }
         }
 
         public var isExtendableKind: Bool {
@@ -144,37 +220,41 @@ public final class Declaration {
             Self.discreteConformableKinds.contains(self)
         }
 
-        static var discreteConformableKinds: Set<Kind> {
+        static let discreteConformableKinds: Set<Kind> =
             [.class, .struct, .enum]
-        }
 
         public var isConcreteTypeDeclarableKind: Bool {
-            Self.concreteTypeDeclarableKinds.contains(self)
+            switch self {
+            case .class, .struct, .enum, .typealias: true
+            default: false
+            }
         }
 
-        static var concreteTypeDeclarableKinds: Set<Kind> {
+        static let concreteTypeDeclarableKinds: Set<Kind> =
             [.class, .struct, .enum, .typealias]
-        }
 
-        static var accessorKinds: Set<Kind> {
+        static let accessorKinds: Set<Kind> =
             Set(Kind.allCases.filter(\.isAccessorKind))
-        }
 
-        static var accessibleKinds: Set<Kind> {
+        static let accessibleKinds: Set<Kind> =
             functionKinds.union(variableKinds).union(globalKinds)
-        }
 
-        static var overrideKinds: Set<Kind> {
+        static let overrideKinds: Set<Kind> =
             [.functionMethodInstance, .varInstance]
-        }
 
         public var isAccessorKind: Bool {
-            rawValue.hasPrefix("function.accessor")
+            switch self {
+            case .functionAccessorAddress, .functionAccessorDidset, .functionAccessorGetter,
+                 .functionAccessorMutableaddress, .functionAccessorSetter, .functionAccessorWillset,
+                 .functionAccessorRead, .functionAccessorModify, .functionAccessorInit:
+                true
+            default:
+                false
+            }
         }
 
-        static var toplevelAttributableKind: Set<Kind> {
+        static let toplevelAttributableKind: Set<Kind> =
             [.class, .struct, .enum]
-        }
 
         public var displayName: String {
             switch self {
@@ -216,21 +296,27 @@ public final class Declaration {
 
     public let location: Location
     public var attributes: Set<DeclarationAttribute> = []
-    public var modifiers: Set<String> = []
+    public var modifiers: Set<String> = [] {
+        didSet { _isOverride = modifiers.contains("override") }
+    }
+
+    private var _isOverride: Bool = false
     public var accessibility: DeclarationAccessibility = .init(value: .internal, isExplicit: false)
     public let kind: Kind
     public let name: String
     public let usrs: Set<String>
-    public var unusedParameters: Set<Declaration> = []
-    public var declarations: Set<Declaration> = []
+    public let usrIDs: [USRID]
+    public var unusedParameters: [Declaration] = []
+    public var declarations: [Declaration] = []
     public var commentCommands: Set<CommentCommand> = []
-    public var references: Set<Reference> = []
+    public var references: [Reference] = []
     public var declaredType: String?
     public var hasGenericFunctionReturnedMetatypeParameters: Bool = false
     public var parent: Declaration?
-    public var related: Set<Reference> = []
+    public var related: [Reference] = []
     public var isImplicit: Bool = false
     public var isObjcAccessible: Bool = false
+    public internal(set) var isUsed: Bool = false
 
     private let hashValueCache: Int
 
@@ -246,19 +332,23 @@ public final class Declaration {
         return declarations
     }
 
-    public var descendentDeclarations: Set<Declaration> {
-        declarations
-            .flatMapSet { $0.descendentDeclarations }
-            .union(declarations)
-            .union(unusedParameters)
+    public func forEachDescendentDeclaration(_ body: (Declaration) -> Void) {
+        for decl in declarations {
+            body(decl)
+            decl.forEachDescendentDeclaration(body)
+        }
+        for param in unusedParameters {
+            body(param)
+            param.forEachDescendentDeclaration(body)
+        }
     }
 
-    public var immediateInheritedTypeReferences: Set<Reference> {
+    public var immediateInheritedTypeReferences: [Reference] {
         let superclassReferences = related.filter { [.class, .struct, .protocol].contains($0.declarationKind) }
 
         // Inherited typealiases are References instead of a Related.
         let typealiasReferences = references.filter { $0.declarationKind == .typealias }
-        return superclassReferences.union(typealiasReferences)
+        return superclassReferences + typealiasReferences
     }
 
     public var isComplexProperty: Bool {
@@ -278,9 +368,7 @@ public final class Declaration {
         }
     }
 
-    public var isOverride: Bool {
-        modifiers.contains("override")
-    }
+    public var isOverride: Bool { _isOverride }
 
     public var relatedEquivalentReferences: [Reference] {
         related.filter { $0.declarationKind == kind && $0.name == name }
@@ -290,13 +378,23 @@ public final class Declaration {
         name: String,
         kind: Kind,
         usrs: Set<String>,
+        usrIDs: [USRID],
         location: Location
     ) {
         self.name = name
         self.kind = kind
         self.usrs = usrs
+        self.usrIDs = usrIDs.count > 1 ? usrIDs.sorted(by: { $0.rawValue < $1.rawValue }) : usrIDs
         self.location = location
-        hashValueCache = usrs.hashValue
+        if self.usrIDs.count == 1 {
+            hashValueCache = self.usrIDs[0].hashValue
+        } else {
+            var hasher = Hasher()
+            for id in self.usrIDs {
+                hasher.combine(id)
+            }
+            hashValueCache = hasher.finalize()
+        }
     }
 
     func isDeclaredInExtension(kind: Declaration.Kind) -> Bool {
@@ -314,7 +412,10 @@ extension Declaration: Hashable {
 
 extension Declaration: Equatable {
     public static func == (lhs: Declaration, rhs: Declaration) -> Bool {
-        lhs.usrs == rhs.usrs
+        if lhs === rhs { return true }
+        guard lhs.hashValueCache == rhs.hashValueCache else { return false }
+
+        return lhs.usrIDs == rhs.usrIDs
     }
 }
 
diff --git a/Sources/SourceGraph/Elements/Location.swift b/Sources/SourceGraph/Elements/Location.swift
index 03c7933cb..84b002c32 100644
--- a/Sources/SourceGraph/Elements/Location.swift
+++ b/Sources/SourceGraph/Elements/Location.swift
@@ -1,7 +1,8 @@
+import Extensions
 import Foundation
 import SystemPackage
 
-public final class Location {
+public struct Location {
     public let file: SourceFile
     public let line: Int
     public let column: Int
@@ -12,14 +13,11 @@ public final class Location {
         self.file = file
         self.line = line
         self.column = column
-        hashValueCache = [file.hashValue, line, column].hashValue
-    }
-
-    func relativeTo(_ path: FilePath) -> Location {
-        let newPath = file.path.relativeTo(path)
-        let newFile = SourceFile(path: newPath, modules: file.modules)
-        newFile.importStatements = file.importStatements
-        return Location(file: newFile, line: line, column: column)
+        var hasher = Hasher()
+        hasher.combine(file)
+        hasher.combine(line)
+        hasher.combine(column)
+        hashValueCache = hasher.finalize()
     }
 
     // MARK: - Private
@@ -27,10 +25,6 @@ public final class Location {
     private func buildDescription(path: String) -> String {
         [path, line.description, column.description].joined(separator: ":")
     }
-
-    private lazy var descriptionInternal: String = buildDescription(path: file.path.string)
-
-    private lazy var shortDescriptionInternal: String = buildDescription(path: file.path.lastComponent?.string ?? "")
 }
 
 extension Location: Equatable {
@@ -47,11 +41,11 @@ extension Location: Hashable {
 
 extension Location: CustomStringConvertible {
     public var description: String {
-        descriptionInternal
+        buildDescription(path: file.path.string)
     }
 
     public var shortDescription: String {
-        shortDescriptionInternal
+        buildDescription(path: file.path.lastComponent?.string ?? "")
     }
 }
 
diff --git a/Sources/SourceGraph/Elements/ModuleBitset.swift b/Sources/SourceGraph/Elements/ModuleBitset.swift
new file mode 100644
index 000000000..d28f8894e
--- /dev/null
+++ b/Sources/SourceGraph/Elements/ModuleBitset.swift
@@ -0,0 +1,45 @@
+/// Dynamically-sized bitset over `ModuleID` values. Backed by `[UInt64]`
+/// sized to the number of interned modules, replacing `Set<ModuleID>` in
+/// hot paths where `formUnion` / `contains` dominated the profile.
+struct ModuleBitset {
+    var words: [UInt64]
+    private var _nonEmpty: Bool = false
+
+    init(wordCount: Int) {
+        words = [UInt64](repeating: 0, count: wordCount)
+    }
+
+    var isEmpty: Bool { !_nonEmpty }
+
+    mutating func insert(_ id: ModuleID) {
+        let (word, bit) = id.rawValue.quotientAndRemainder(dividingBy: 64)
+        if word >= words.count {
+            words.append(contentsOf: [UInt64](repeating: 0, count: word + 1 - words.count))
+        }
+        words[word] |= 1 &<< bit
+        _nonEmpty = true
+    }
+
+    func contains(_ id: ModuleID) -> Bool {
+        let (word, bit) = id.rawValue.quotientAndRemainder(dividingBy: 64)
+        guard word < words.count else { return false }
+
+        return words[word] & (1 &<< bit) != 0
+    }
+
+    mutating func formUnion(_ other: ModuleBitset) {
+        if other.words.count > words.count {
+            words.append(contentsOf: [UInt64](repeating: 0, count: other.words.count - words.count))
+        }
+        other.words.withUnsafeBufferPointer { src in
+            words.withUnsafeMutableBufferPointer { dst in
+                var i = 0
+                while i < src.count {
+                    dst[i] |= src[i]
+                    i &+= 1
+                }
+            }
+        }
+        if other._nonEmpty { _nonEmpty = true }
+    }
+}
diff --git a/Sources/SourceGraph/Elements/ModuleID.swift b/Sources/SourceGraph/Elements/ModuleID.swift
new file mode 100644
index 000000000..556020818
--- /dev/null
+++ b/Sources/SourceGraph/Elements/ModuleID.swift
@@ -0,0 +1,26 @@
+/// Lightweight integer handle representing an interned module name.
+/// Used in place of `String` in hot-path `Set`/`Dictionary` operations
+/// where string hashing and equality dominate the profile.
+public struct ModuleID: Hashable, Comparable, Sendable {
+    /// Exclusive upper bound for `rawValue` so that two `ModuleID`s can be
+    /// packed into a single `Int` without collisions using base-`packingRadix`.
+    @usableFromInline static let packingRadix = 65537
+
+    @usableFromInline let rawValue: Int
+
+    @inlinable
+    init(_ rawValue: Int) {
+        precondition(rawValue < Self.packingRadix, "ModuleID rawValue exceeds supported packing range")
+        self.rawValue = rawValue
+    }
+
+    @inlinable
+    public static func < (lhs: ModuleID, rhs: ModuleID) -> Bool {
+        lhs.rawValue < rhs.rawValue
+    }
+
+    @inlinable
+    public func hash(into hasher: inout Hasher) {
+        hasher.combine(rawValue)
+    }
+}
diff --git a/Sources/SourceGraph/Elements/ModuleNameInterner.swift b/Sources/SourceGraph/Elements/ModuleNameInterner.swift
new file mode 100644
index 000000000..b276b9af1
--- /dev/null
+++ b/Sources/SourceGraph/Elements/ModuleNameInterner.swift
@@ -0,0 +1,33 @@
+/// Maps module name strings to compact `ModuleID` integers and back.
+/// Not thread-safe -- callers must serialize access externally
+/// (e.g. via `SourceGraphMutex` during indexing, serial execution during mutation).
+final class ModuleNameInterner {
+    private var nameToID: [String: ModuleID] = [:]
+    private var idToName: [String] = []
+
+    init() {}
+
+    var moduleCount: Int { idToName.count }
+
+    var wordCount: Int { (moduleCount + 63) / 64 }
+
+    func intern(_ name: String) -> ModuleID {
+        if let id = nameToID[name] { return id }
+        let id = ModuleID(idToName.count)
+        nameToID[name] = id
+        idToName.append(name)
+        return id
+    }
+
+    func intern(_ names: Set<String>) -> Set<ModuleID> {
+        Set(names.map { intern($0) })
+    }
+
+    func internBitset(_ names: Set<String>, wordCount: Int) -> ModuleBitset {
+        var bitset = ModuleBitset(wordCount: wordCount)
+        for name in names {
+            bitset.insert(intern(name))
+        }
+        return bitset
+    }
+}
diff --git a/Sources/SourceGraph/Elements/Reference.swift b/Sources/SourceGraph/Elements/Reference.swift
index 7dade0259..2de8a3217 100644
--- a/Sources/SourceGraph/Elements/Reference.swift
+++ b/Sources/SourceGraph/Elements/Reference.swift
@@ -1,11 +1,31 @@
 public final class Reference {
-    public enum Kind: String {
+    // Explicit Hashable/Equatable using integer ordinals instead of the default
+    // RawRepresentable conformance, which hashes/compares the String raw value.
+    public enum Kind: String, Hashable, Equatable {
         case normal
         case related
         case retained
+
+        @usableFromInline var ordinal: Int {
+            switch self {
+            case .normal: 0
+            case .related: 1
+            case .retained: 2
+            }
+        }
+
+        @inlinable
+        public func hash(into hasher: inout Hasher) {
+            hasher.combine(ordinal)
+        }
+
+        @inlinable
+        public static func == (lhs: Kind, rhs: Kind) -> Bool {
+            lhs.ordinal == rhs.ordinal
+        }
     }
 
-    public enum Role: String {
+    public enum Role: String, Hashable, Equatable {
         case varType
         case returnType
         case parameterType
@@ -20,6 +40,34 @@ public final class Reference {
         case functionCallMetatypeArgument
         case unknown
 
+        @usableFromInline var ordinal: Int {
+            switch self {
+            case .varType: 0
+            case .returnType: 1
+            case .parameterType: 2
+            case .throwType: 3
+            case .genericParameterType: 4
+            case .genericRequirementType: 5
+            case .inheritedType: 6
+            case .refinedProtocolType: 7
+            case .conformedType: 8
+            case .initializerType: 9
+            case .variableInitFunctionCall: 10
+            case .functionCallMetatypeArgument: 11
+            case .unknown: 12
+            }
+        }
+
+        @inlinable
+        public func hash(into hasher: inout Hasher) {
+            hasher.combine(ordinal)
+        }
+
+        @inlinable
+        public static func == (lhs: Role, rhs: Role) -> Bool {
+            lhs.ordinal == rhs.ordinal
+        }
+
         var isPubliclyExposable: Bool {
             switch self {
             case .varType, .returnType, .parameterType, .throwType, .genericParameterType, .genericRequirementType, .inheritedType, .refinedProtocolType, .initializerType, .variableInitFunctionCall, .functionCallMetatypeArgument:
@@ -35,8 +83,8 @@ public final class Reference {
     public let declarationKind: Declaration.Kind
     public let name: String
     public var parent: Declaration?
-    public var references: Set<Reference> = []
     public let usr: String
+    public let usrID: USRID
     public var role: Role = .unknown
 
     private let hashValueCache: Int
@@ -45,19 +93,21 @@ public final class Reference {
         name: String,
         kind: Kind,
         declarationKind: Declaration.Kind,
+        usrID: USRID,
         usr: String,
         location: Location
     ) {
         self.name = name
         self.kind = kind
         self.declarationKind = declarationKind
+        self.usrID = usrID
         self.usr = usr
         self.location = location
-        hashValueCache = [usr.hashValue, location.hashValue, kind.hashValue].hashValue
-    }
-
-    var descendentReferences: Set<Reference> {
-        references.flatMapSet { $0.descendentReferences }.union(references)
+        var hasher = Hasher()
+        hasher.combine(usrID)
+        hasher.combine(location)
+        hasher.combine(kind)
+        hashValueCache = hasher.finalize()
     }
 }
 
@@ -69,7 +119,7 @@ extension Reference: Hashable {
 
 extension Reference: Equatable {
     public static func == (lhs: Reference, rhs: Reference) -> Bool {
-        lhs.usr == rhs.usr && lhs.location == rhs.location && lhs.kind == rhs.kind
+        lhs.usrID == rhs.usrID && lhs.kind == rhs.kind && lhs.location == rhs.location
     }
 }
 
diff --git a/Sources/SourceGraph/Elements/SourceFile.swift b/Sources/SourceGraph/Elements/SourceFile.swift
index a92a223b5..17cd7d437 100644
--- a/Sources/SourceGraph/Elements/SourceFile.swift
+++ b/Sources/SourceGraph/Elements/SourceFile.swift
@@ -7,15 +7,20 @@ public final class SourceFile {
     public var importStatements: [ImportStatement] = []
     public var importsSwiftTesting = false
 
+    // Pre-computed to avoid re-hashing the FilePath on every Set/Dictionary operation,
+    // since SourceFile is used as a key in many hot-path collections.
+    private let hashValueCache: Int
+
     public init(path: FilePath, modules: Set<String>) {
         self.path = path
         self.modules = modules
+        hashValueCache = path.hashValue
     }
 }
 
 extension SourceFile: Hashable {
     public func hash(into hasher: inout Hasher) {
-        hasher.combine(path)
+        hasher.combine(hashValueCache)
     }
 }
 
diff --git a/Sources/SourceGraph/Elements/USRID.swift b/Sources/SourceGraph/Elements/USRID.swift
new file mode 100644
index 000000000..04ce09a4d
--- /dev/null
+++ b/Sources/SourceGraph/Elements/USRID.swift
@@ -0,0 +1,16 @@
+/// Lightweight integer handle representing an interned USR string.
+/// Replaces raw `String` keys in hot-path dictionary operations where
+/// string hashing and equality (memcmp) dominate the profile.
+public struct USRID: Hashable {
+    @usableFromInline let rawValue: Int
+
+    @inlinable
+    init(_ rawValue: Int) {
+        self.rawValue = rawValue
+    }
+
+    @inlinable
+    public func hash(into hasher: inout Hasher) {
+        hasher.combine(rawValue)
+    }
+}
diff --git a/Sources/SourceGraph/Elements/USRInterner.swift b/Sources/SourceGraph/Elements/USRInterner.swift
new file mode 100644
index 000000000..dfe1cb552
--- /dev/null
+++ b/Sources/SourceGraph/Elements/USRInterner.swift
@@ -0,0 +1,64 @@
+import Synchronization
+
+/// Maps USR strings to compact `USRID` integers and back.
+/// Thread-safe: uses 16 sharded locks for the string-to-ID direction to reduce
+/// contention during concurrent indexing, with an atomic counter for ID
+/// allocation and a separate lock for the ID-to-string reverse map.
+public final class USRInterner: @unchecked Sendable {
+    private static let shardCount = 16
+    private static let shardMask = shardCount - 1
+
+    private final class Shard: @unchecked Sendable {
+        let dict = Mutex<[String: USRID]>([:])
+
+        func reserveCapacity(_ n: Int) {
+            dict.withLock { $0.reserveCapacity(n) }
+        }
+    }
+
+    private let shards: [Shard]
+    private let nextID = Atomic<Int>(0)
+    private let reverseMap = Mutex<[String]>([])
+
+    public init() {
+        shards = (0..<Self.shardCount).map { _ in Shard() }
+    }
+
+    public var count: Int {
+        nextID.load(ordering: .relaxed)
+    }
+
+    public func intern(_ usr: String) -> USRID {
+        let shard = shards[usr.hashValue & Self.shardMask]
+        return shard.dict.withLock { dict in
+            if let id = dict[usr] { return id }
+            let (rawID, _) = nextID.add(1, ordering: .relaxed)
+            let id = USRID(rawID)
+            dict[usr] = id
+            reverseMap.withLock { storage in
+                if rawID >= storage.count {
+                    storage.append(contentsOf: repeatElement("", count: rawID + 1 - storage.count))
+                }
+                storage[rawID] = usr
+            }
+            return id
+        }
+    }
+
+    public func existing(_ usr: String) -> USRID? {
+        let shard = shards[usr.hashValue & Self.shardMask]
+        return shard.dict.withLock { $0[usr] }
+    }
+
+    public func string(for id: USRID) -> String {
+        reverseMap.withLock { $0[id.rawValue] }
+    }
+
+    public func reserveCapacity(_ n: Int) {
+        let perShard = n / Self.shardCount + 1
+        for shard in shards {
+            shard.reserveCapacity(perShard)
+        }
+        reverseMap.withLock { $0.reserveCapacity(n) }
+    }
+}
diff --git a/Sources/SourceGraph/Mutators/AncestralReferenceEliminator.swift b/Sources/SourceGraph/Mutators/AncestralReferenceEliminator.swift
index bd50674e3..f752e8b57 100644
--- a/Sources/SourceGraph/Mutators/AncestralReferenceEliminator.swift
+++ b/Sources/SourceGraph/Mutators/AncestralReferenceEliminator.swift
@@ -11,28 +11,31 @@ final class AncestralReferenceEliminator: SourceGraphMutator {
 
     func mutate() {
         for declaration in graph.rootDeclarations {
-            eliminateAncestralReferences(in: declaration, stack: declaration.usrs)
+            var stack = declaration.usrIDs
+            eliminateAncestralReferences(in: declaration, stack: &stack)
         }
     }
 
-    private func eliminateAncestralReferences(in declaration: Declaration, stack: Set<String>) {
+    // Uses an Array rather than a Set for the ancestor stack because the stack depth is
+    // typically 5-20 elements, where linear scan of contiguous integers is cheaper than hashing.
+    private func eliminateAncestralReferences(in declaration: Declaration, stack: inout [USRID]) {
         guard !graph.isRetained(declaration) else { return }
 
         eliminateAncestralReferences(in: declaration.references, stack: stack)
 
         for childDeclaration in declaration.declarations {
-            let newStack = stack.union(childDeclaration.usrs)
-            eliminateAncestralReferences(in: childDeclaration, stack: newStack)
+            let prevCount = stack.count
+            stack.append(contentsOf: childDeclaration.usrIDs)
+            eliminateAncestralReferences(in: childDeclaration, stack: &stack)
+            stack.removeSubrange(prevCount...)
         }
     }
 
-    private func eliminateAncestralReferences(in references: Set<Reference>, stack: Set<String>) {
+    private func eliminateAncestralReferences(in references: [Reference], stack: [USRID]) {
         for reference in references {
-            if stack.contains(reference.usr) {
+            if stack.contains(reference.usrID) {
                 graph.remove(reference)
             }
-
-            eliminateAncestralReferences(in: reference.references, stack: stack)
         }
     }
 }
diff --git a/Sources/SourceGraph/Mutators/AssetReferenceRetainer.swift b/Sources/SourceGraph/Mutators/AssetReferenceRetainer.swift
index c1a29180e..97f1ddc81 100644
--- a/Sources/SourceGraph/Mutators/AssetReferenceRetainer.swift
+++ b/Sources/SourceGraph/Mutators/AssetReferenceRetainer.swift
@@ -42,7 +42,7 @@ final class AssetReferenceRetainer: SourceGraphMutator {
                 if sources.contains(.xcDataModel) {
                     // ValueTransformer subclasses are referenced by generated code that Periphery cannot analyze.
                     graph.unmarkRedundantPublicAccessibility(declaration)
-                    declaration.descendentDeclarations.forEach { graph.unmarkRedundantPublicAccessibility($0) }
+                    declaration.forEachDescendentDeclaration { graph.unmarkRedundantPublicAccessibility($0) }
                 }
 
                 if sources.contains(.interfaceBuilder) {
diff --git a/Sources/SourceGraph/Mutators/AssignOnlyPropertyReferenceEliminator.swift b/Sources/SourceGraph/Mutators/AssignOnlyPropertyReferenceEliminator.swift
index 4f0c78895..d6bdafb20 100644
--- a/Sources/SourceGraph/Mutators/AssignOnlyPropertyReferenceEliminator.swift
+++ b/Sources/SourceGraph/Mutators/AssignOnlyPropertyReferenceEliminator.swift
@@ -3,18 +3,19 @@ import Foundation
 import Shared
 
 enum AssignOnlyPropertyAnalyzer {
-    static func isAssignOnlyProperty(
-        _ property: Declaration,
-        graph: SourceGraph,
-        configuration: Configuration
-    ) -> Bool {
+    static func retainedTypes(for configuration: Configuration) -> [String] {
         let defaultRetainedTypes = ["AnyCancellable", "Set<AnyCancellable>", "[AnyCancellable]", "NSKeyValueObservation"]
-        let retainAssignOnlyPropertyTypes = defaultRetainedTypes + configuration.retainAssignOnlyPropertyTypes.map {
+        return defaultRetainedTypes + configuration.retainAssignOnlyPropertyTypes.map {
             PropertyTypeSanitizer.sanitize($0)
         }
+    }
 
-        guard !configuration.retainAssignOnlyProperties,
-              property.kind.isVariableKind,
+    static func isAssignOnlyProperty(
+        _ property: Declaration,
+        graph: SourceGraph,
+        retainAssignOnlyPropertyTypes: [String]
+    ) -> Bool {
+        guard property.kind.isVariableKind,
               let declaredType = property.declaredType,
               !retainAssignOnlyPropertyTypes.contains(declaredType),
               property.attributes.isEmpty,
@@ -47,8 +48,10 @@ final class AssignOnlyPropertyReferenceEliminator: SourceGraphMutator {
     func mutate() throws {
         guard !configuration.retainAssignOnlyProperties else { return }
 
+        let retainedTypes = AssignOnlyPropertyAnalyzer.retainedTypes(for: configuration)
+
         for property in graph.declarations(ofKinds: Declaration.Kind.variableKinds) {
-            if AssignOnlyPropertyAnalyzer.isAssignOnlyProperty(property, graph: graph, configuration: configuration) {
+            if AssignOnlyPropertyAnalyzer.isAssignOnlyProperty(property, graph: graph, retainAssignOnlyPropertyTypes: retainedTypes) {
                 if graph.isRetained(property) {
                     graph.markSuppressedAssignOnlyProperty(property)
                 } else {
diff --git a/Sources/SourceGraph/Mutators/CodingKeyEnumReferenceBuilder.swift b/Sources/SourceGraph/Mutators/CodingKeyEnumReferenceBuilder.swift
index 1de90afa1..bbb69ca1d 100644
--- a/Sources/SourceGraph/Mutators/CodingKeyEnumReferenceBuilder.swift
+++ b/Sources/SourceGraph/Mutators/CodingKeyEnumReferenceBuilder.swift
@@ -28,12 +28,13 @@ final class CodingKeyEnumReferenceBuilder: SourceGraphMutator {
             }
 
             if graph.isCodable(parent) {
-                // Build a reference from the Codable type to the CodingKey enum.
-                for usr in enumDeclaration.usrs {
+                for usrID in enumDeclaration.usrIDs {
+                    let usr = graph.usrInterner.string(for: usrID)
                     let newReference = Reference(
                         name: enumDeclaration.name,
                         kind: .normal,
                         declarationKind: .enum,
+                        usrID: usrID,
                         usr: usr,
                         location: enumDeclaration.location
                     )
diff --git a/Sources/SourceGraph/Mutators/ComplexPropertyAccessorReferenceBuilder.swift b/Sources/SourceGraph/Mutators/ComplexPropertyAccessorReferenceBuilder.swift
index b2cd48356..ca922519a 100644
--- a/Sources/SourceGraph/Mutators/ComplexPropertyAccessorReferenceBuilder.swift
+++ b/Sources/SourceGraph/Mutators/ComplexPropertyAccessorReferenceBuilder.swift
@@ -20,11 +20,13 @@ final class ComplexPropertyAccessorReferenceBuilder: SourceGraphMutator {
             guard let parent = declaration.parent else { continue }
 
             if parent.isComplexProperty {
-                for usr in declaration.usrs {
+                for usrID in declaration.usrIDs {
+                    let usr = graph.usrInterner.string(for: usrID)
                     let reference = Reference(
                         name: declaration.name,
                         kind: .normal,
                         declarationKind: declaration.kind,
+                        usrID: usrID,
                         usr: usr,
                         location: declaration.location
                     )
diff --git a/Sources/SourceGraph/Mutators/DefaultConstructorReferenceBuilder.swift b/Sources/SourceGraph/Mutators/DefaultConstructorReferenceBuilder.swift
index 743c2bbc4..dbea26b1c 100644
--- a/Sources/SourceGraph/Mutators/DefaultConstructorReferenceBuilder.swift
+++ b/Sources/SourceGraph/Mutators/DefaultConstructorReferenceBuilder.swift
@@ -25,11 +25,13 @@ final class DefaultConstructorReferenceBuilder: SourceGraphMutator {
 
         for constructor in defaultConstructors {
             if let parent = constructor.parent {
-                for usr in constructor.usrs {
+                for usrID in constructor.usrIDs {
+                    let usr = graph.usrInterner.string(for: usrID)
                     let reference = Reference(
                         name: constructor.name,
                         kind: .normal,
                         declarationKind: .functionConstructor,
+                        usrID: usrID,
                         usr: usr,
                         location: parent.location
                     )
@@ -43,11 +45,13 @@ final class DefaultConstructorReferenceBuilder: SourceGraphMutator {
     private func referenceDestructors() {
         for destructor in graph.declarations(ofKind: .functionDestructor) {
             if let parent = destructor.parent {
-                for usr in destructor.usrs {
+                for usrID in destructor.usrIDs {
+                    let usr = graph.usrInterner.string(for: usrID)
                     let reference = Reference(
                         name: destructor.name,
                         kind: .normal,
                         declarationKind: .functionDestructor,
+                        usrID: usrID,
                         usr: usr,
                         location: parent.location
                     )
diff --git a/Sources/SourceGraph/Mutators/EnumCaseReferenceBuilder.swift b/Sources/SourceGraph/Mutators/EnumCaseReferenceBuilder.swift
index d32d303b8..989f708fb 100644
--- a/Sources/SourceGraph/Mutators/EnumCaseReferenceBuilder.swift
+++ b/Sources/SourceGraph/Mutators/EnumCaseReferenceBuilder.swift
@@ -20,11 +20,13 @@ final class EnumCaseReferenceBuilder: SourceGraphMutator {
                 let enumCases = enumDeclaration.declarations.filter { $0.kind == .enumelement }
 
                 for enumCase in enumCases {
-                    for usr in enumCase.usrs {
+                    for usrID in enumCase.usrIDs {
+                        let usr = graph.usrInterner.string(for: usrID)
                         let reference = Reference(
                             name: enumCase.name,
                             kind: .normal,
                             declarationKind: .enumelement,
+                            usrID: usrID,
                             usr: usr,
                             location: enumCase.location
                         )
diff --git a/Sources/SourceGraph/Mutators/ExtensionReferenceBuilder.swift b/Sources/SourceGraph/Mutators/ExtensionReferenceBuilder.swift
index 450c90428..62451ae36 100644
--- a/Sources/SourceGraph/Mutators/ExtensionReferenceBuilder.swift
+++ b/Sources/SourceGraph/Mutators/ExtensionReferenceBuilder.swift
@@ -20,7 +20,7 @@ final class ExtensionReferenceBuilder: SourceGraphMutator {
     private func foldExtension(kind: Declaration.Kind) throws {
         for extensionDeclaration in graph.declarations(ofKind: kind) {
             guard let extendedTypeReference = try graph.extendedDeclarationReference(forExtension: extensionDeclaration) else { continue }
-            guard let extendedDeclaration = graph.declaration(withUsr: extendedTypeReference.usr) else {
+            guard let extendedDeclaration = graph.declaration(withUsrID: extendedTypeReference.usrID) else {
                 // This is an extension on an external type and cannot be folded.
                 graph.markRetained(extensionDeclaration)
                 continue
@@ -29,9 +29,9 @@ final class ExtensionReferenceBuilder: SourceGraphMutator {
             // Don't fold protocol extensions as they must be treated differently.
             guard kind != .extensionProtocol else { continue }
 
-            extendedDeclaration.declarations.formUnion(extensionDeclaration.declarations)
-            extendedDeclaration.references.formUnion(extensionDeclaration.references)
-            extendedDeclaration.related.formUnion(extensionDeclaration.related)
+            extendedDeclaration.declarations.append(contentsOf: extensionDeclaration.declarations)
+            extendedDeclaration.references.append(contentsOf: extensionDeclaration.references)
+            extendedDeclaration.related.append(contentsOf: extensionDeclaration.related)
 
             extensionDeclaration.declarations.forEach { $0.parent = extendedDeclaration }
             extensionDeclaration.references.forEach { $0.parent = extendedDeclaration }
diff --git a/Sources/SourceGraph/Mutators/ExternalOverrideRetainer.swift b/Sources/SourceGraph/Mutators/ExternalOverrideRetainer.swift
index 761625d11..c8416db06 100644
--- a/Sources/SourceGraph/Mutators/ExternalOverrideRetainer.swift
+++ b/Sources/SourceGraph/Mutators/ExternalOverrideRetainer.swift
@@ -23,7 +23,7 @@ final class ExternalOverrideRetainer: SourceGraphMutator {
                     $0.location == decl.location
             }
 
-            let hasExternalMatch = matchingRelatedRefs.contains { graph.declaration(withUsr: $0.usr) == nil }
+            let hasExternalMatch = matchingRelatedRefs.contains { graph.declaration(withUsrID: $0.usrID) == nil }
 
             if hasExternalMatch {
                 // One or more matching related declarations are external.
diff --git a/Sources/SourceGraph/Mutators/ExternalTypeProtocolConformanceReferenceRemover.swift b/Sources/SourceGraph/Mutators/ExternalTypeProtocolConformanceReferenceRemover.swift
index 9c52b097e..ac5ec57b5 100644
--- a/Sources/SourceGraph/Mutators/ExternalTypeProtocolConformanceReferenceRemover.swift
+++ b/Sources/SourceGraph/Mutators/ExternalTypeProtocolConformanceReferenceRemover.swift
@@ -17,7 +17,9 @@ final class ExternalTypeProtocolConformanceReferenceRemover: SourceGraphMutator
             guard try graph.extendedDeclaration(forExtension: extDecl) == nil else { continue }
 
             // Ensure the type is extended by local protocols.
-            let protocolDecls = extDecl.related.filter { $0.declarationKind == .protocol }.map { graph.declaration(withUsr: $0.usr) }
+            let protocolDecls = extDecl.related
+                .filter { $0.declarationKind == .protocol }
+                .compactMap { graph.declaration(withUsrID: $0.usrID) }
             guard !protocolDecls.isEmpty else { continue }
 
             // Find all related references that may be protocol members.
@@ -26,7 +28,7 @@ final class ExternalTypeProtocolConformanceReferenceRemover: SourceGraphMutator
             for relatedRef in relatedRefs {
                 // Ensure the relatedDecl is a member of a protocol.
                 guard
-                    let relatedDecl = graph.declaration(withUsr: relatedRef.usr),
+                    let relatedDecl = graph.declaration(withUsrID: relatedRef.usrID),
                     let parentDecl = relatedDecl.parent,
                     protocolDecls.contains(parentDecl)
                 else { continue }
diff --git a/Sources/SourceGraph/Mutators/GenericClassAndStructConstructorReferenceBuilder.swift b/Sources/SourceGraph/Mutators/GenericClassAndStructConstructorReferenceBuilder.swift
index e8fb478d3..5a73991c7 100644
--- a/Sources/SourceGraph/Mutators/GenericClassAndStructConstructorReferenceBuilder.swift
+++ b/Sources/SourceGraph/Mutators/GenericClassAndStructConstructorReferenceBuilder.swift
@@ -21,11 +21,13 @@ final class GenericClassAndStructConstructorReferenceBuilder: SourceGraphMutator
             let constructors = declaration.declarations.filter { $0.kind == .functionConstructor }
 
             for constructor in constructors {
-                for usr in constructor.usrs {
+                for usrID in constructor.usrIDs {
+                    let usr = graph.usrInterner.string(for: usrID)
                     let reference = Reference(
                         name: constructor.name,
                         kind: .normal,
                         declarationKind: .functionConstructor,
+                        usrID: usrID,
                         usr: usr,
                         location: declaration.location
                     )
diff --git a/Sources/SourceGraph/Mutators/InheritedImplicitInitializerReferenceBuilder.swift b/Sources/SourceGraph/Mutators/InheritedImplicitInitializerReferenceBuilder.swift
index d62a27b1f..3214c707d 100644
--- a/Sources/SourceGraph/Mutators/InheritedImplicitInitializerReferenceBuilder.swift
+++ b/Sources/SourceGraph/Mutators/InheritedImplicitInitializerReferenceBuilder.swift
@@ -28,17 +28,19 @@ final class InheritedImplicitInitializerReferenceBuilder: SourceGraphMutator {
                     guard relatedRef.declarationKind == .functionConstructor else { continue }
 
                     // Find the declaration this related reference points to
-                    guard let implicitInit = graph.declaration(withUsr: relatedRef.usr),
+                    guard let implicitInit = graph.declaration(withUsrID: relatedRef.usrID),
                           implicitInit.isImplicit,
                           implicitInit.kind == .functionConstructor
                     else { continue }
 
                     // Add the inverse reference: implicit init -> explicit init
-                    for usr in explicitInit.usrs {
+                    for usrID in explicitInit.usrIDs {
+                        let usr = graph.usrInterner.string(for: usrID)
                         let reference = Reference(
                             name: explicitInit.name,
                             kind: .related,
                             declarationKind: .functionConstructor,
+                            usrID: usrID,
                             usr: usr,
                             location: implicitInit.location
                         )
diff --git a/Sources/SourceGraph/Mutators/InterfaceBuilderPropertyRetainer.swift b/Sources/SourceGraph/Mutators/InterfaceBuilderPropertyRetainer.swift
index 3cd0f1e39..a0afbda4d 100644
--- a/Sources/SourceGraph/Mutators/InterfaceBuilderPropertyRetainer.swift
+++ b/Sources/SourceGraph/Mutators/InterfaceBuilderPropertyRetainer.swift
@@ -38,7 +38,7 @@ final class InterfaceBuilderPropertyRetainer {
     ) {
         let inheritedDeclarations = graph.inheritedDeclarations(of: declaration)
         let descendentInheritedDeclarations = inheritedDeclarations.map(\.declarations).joined()
-        let allDeclarations = declaration.declarations.union(descendentInheritedDeclarations)
+        let allDeclarations = declaration.declarations + descendentInheritedDeclarations
 
         for decl in allDeclarations {
             // Check IBOutlet properties
diff --git a/Sources/SourceGraph/Mutators/ProtocolConformanceReferenceBuilder.swift b/Sources/SourceGraph/Mutators/ProtocolConformanceReferenceBuilder.swift
index 4fe04d8e7..ba0f565c8 100644
--- a/Sources/SourceGraph/Mutators/ProtocolConformanceReferenceBuilder.swift
+++ b/Sources/SourceGraph/Mutators/ProtocolConformanceReferenceBuilder.swift
@@ -50,7 +50,7 @@ final class ProtocolConformanceReferenceBuilder: SourceGraphMutator {
                     // Find all superclasses.
                     let superclassDecls = graph.inheritedTypeReferences(of: conformingClass)
                         .filter { $0.declarationKind == .class }
-                        .compactMap { graph.declaration(withUsr: $0.usr) }
+                        .compactMap { graph.declaration(withUsrID: $0.usrID) }
                         .flatMap(\.declarations)
 
                     for unimplementedProtoDecl in unimplementedProtoDecls {
@@ -63,13 +63,13 @@ final class ProtocolConformanceReferenceBuilder: SourceGraphMutator {
                             .min()
 
                         if let declInSuperclass {
-                            // Build a reference from the protocol declarations to the
-                            // declaration implemented by the superclass.
-                            for usr in declInSuperclass.usrs {
+                            for usrID in declInSuperclass.usrIDs {
+                                let usr = graph.usrInterner.string(for: usrID)
                                 let reference = Reference(
                                     name: declInSuperclass.name,
                                     kind: .related,
                                     declarationKind: declInSuperclass.kind,
+                                    usrID: usrID,
                                     usr: usr,
                                     location: declInSuperclass.location
                                 )
@@ -93,7 +93,13 @@ final class ProtocolConformanceReferenceBuilder: SourceGraphMutator {
     }
 
     private func invertReferencesFromProtocolToDeclaration(_ nonInvertableReferences: Set<Reference>) {
-        let relatedReferences = graph.allReferences.filter { $0.kind == .related && $0.declarationKind.isProtocolMemberConformingKind }
+        // Collect matching references into an Array to avoid rebuilding a Set (rehashing every element).
+        var relatedReferences: [Reference] = []
+        for ref in graph.allReferences {
+            if ref.kind == .related, ref.declarationKind.isProtocolMemberConformingKind, !nonInvertableReferences.contains(ref) {
+                relatedReferences.append(ref)
+            }
+        }
 
         // Collect all mutations before applying them to avoid order-dependent behavior
         // when iterating non-deterministically ordered Sets.
@@ -101,7 +107,7 @@ final class ProtocolConformanceReferenceBuilder: SourceGraphMutator {
         var referencesToAdd: [(reference: Reference, parent: Declaration)] = []
         var declarationsToRetain: [Declaration] = []
 
-        for relatedReference in relatedReferences.subtracting(nonInvertableReferences) {
+        for relatedReference in relatedReferences {
             guard let conformingDeclaration = relatedReference.parent
             else { continue }
 
@@ -124,7 +130,7 @@ final class ProtocolConformanceReferenceBuilder: SourceGraphMutator {
             guard equivalentDeclarationKinds.contains(conformingDeclaration.kind),
                   conformingDeclaration.name == relatedReference.name else { continue }
 
-            if let protocolDeclaration = graph.declaration(withUsr: relatedReference.usr) {
+            if let protocolDeclaration = graph.declaration(withUsrID: relatedReference.usrID) {
                 // Invert the related reference such that instead of the conforming declaration
                 // referencing the declaration within the protocol, the protocol declaration
                 // now references the conforming declaration.
@@ -135,11 +141,13 @@ final class ProtocolConformanceReferenceBuilder: SourceGraphMutator {
                     referencesToRemove.append(relatedReference)
                 }
 
-                for usr in conformingDeclaration.usrs {
+                for usrID in conformingDeclaration.usrIDs {
+                    let usr = graph.usrInterner.string(for: usrID)
                     let newReference = Reference(
                         name: relatedReference.name,
                         kind: .related,
                         declarationKind: relatedReference.declarationKind,
+                        usrID: usrID,
                         usr: usr,
                         location: relatedReference.location
                     )
diff --git a/Sources/SourceGraph/Mutators/ProtocolExtensionReferenceBuilder.swift b/Sources/SourceGraph/Mutators/ProtocolExtensionReferenceBuilder.swift
index 9cf9d2344..f5151f5d9 100644
--- a/Sources/SourceGraph/Mutators/ProtocolExtensionReferenceBuilder.swift
+++ b/Sources/SourceGraph/Mutators/ProtocolExtensionReferenceBuilder.swift
@@ -20,11 +20,13 @@ final class ProtocolExtensionReferenceBuilder: SourceGraphMutator {
         for extensionDeclaration in graph.declarations(ofKind: .extensionProtocol) {
             // First, create a reference from each protocol to the extension.
             if let extendedProtocol = try graph.extendedDeclaration(forExtension: extensionDeclaration) {
-                for usr in extensionDeclaration.usrs {
+                for usrID in extensionDeclaration.usrIDs {
+                    let usr = graph.usrInterner.string(for: usrID)
                     let reference = Reference(
                         name: extendedProtocol.name,
                         kind: .normal,
                         declarationKind: .extensionProtocol,
+                        usrID: usrID,
                         usr: usr,
                         location: extendedProtocol.location
                     )
@@ -32,8 +34,8 @@ final class ProtocolExtensionReferenceBuilder: SourceGraphMutator {
                     graph.add(reference, from: extendedProtocol)
                 }
 
-                // Now remove the reference from the extension to the protocol
-                for reference in extensionDeclaration.references.filter({ extendedProtocol.usrs.contains($0.usr) }) {
+                let extendedProtocolUsrIDs = Set(extendedProtocol.usrIDs)
+                for reference in extensionDeclaration.references.filter({ extendedProtocolUsrIDs.contains($0.usrID) }) {
                     graph.remove(reference)
                 }
 
@@ -43,11 +45,13 @@ final class ProtocolExtensionReferenceBuilder: SourceGraphMutator {
                 for memberDeclaration in extensionDeclaration.declarations {
                     for reference in graph.references(to: memberDeclaration) {
                         if let parentDeclaration = reference.parent {
-                            for usr in extensionDeclaration.usrs {
+                            for usrID in extensionDeclaration.usrIDs {
+                                let usr = graph.usrInterner.string(for: usrID)
                                 let extensionReference = Reference(
                                     name: extensionDeclaration.name,
                                     kind: .normal,
                                     declarationKind: .extensionProtocol,
+                                    usrID: usrID,
                                     usr: usr,
                                     location: reference.location
                                 )
@@ -55,11 +59,13 @@ final class ProtocolExtensionReferenceBuilder: SourceGraphMutator {
                                 graph.add(extensionReference, from: parentDeclaration)
                             }
 
-                            for usr in extendedProtocol.usrs {
+                            for usrID in extendedProtocol.usrIDs {
+                                let usr = graph.usrInterner.string(for: usrID)
                                 let protocolReference = Reference(
                                     name: extendedProtocol.name,
                                     kind: .normal,
                                     declarationKind: .protocol,
+                                    usrID: usrID,
                                     usr: usr,
                                     location: reference.location
                                 )
@@ -89,7 +95,7 @@ final class ProtocolExtensionReferenceBuilder: SourceGraphMutator {
         let constrainingProtocolRefs = extensionDeclaration.references.filter { $0.role == .genericRequirementType && $0.declarationKind == .protocol }
 
         for constrainingProtocolRef in constrainingProtocolRefs {
-            guard let constrainingProtocol = graph.declaration(withUsr: constrainingProtocolRef.usr) else { continue }
+            guard let constrainingProtocol = graph.declaration(withUsrID: constrainingProtocolRef.usrID) else { continue }
 
             // For each member declared in the extension, check if it satisfies a requirement of the constraining protocol
             for memberDeclaration in extensionDeclaration.declarations {
@@ -105,11 +111,13 @@ final class ProtocolExtensionReferenceBuilder: SourceGraphMutator {
                 // declaration has a related reference to the protocol member it implements.
                 // ProtocolConformanceReferenceBuilder will then invert this to create a reference
                 // from the protocol requirement to the extension's implementation.
-                for usr in matchingRequirement.usrs {
+                for usrID in matchingRequirement.usrIDs {
+                    let usr = graph.usrInterner.string(for: usrID)
                     let relatedReference = Reference(
                         name: matchingRequirement.name,
                         kind: .related,
                         declarationKind: matchingRequirement.kind,
+                        usrID: usrID,
                         usr: usr,
                         location: memberDeclaration.location
                     )
diff --git a/Sources/SourceGraph/Mutators/RedundantExplicitPublicAccessibilityMarker.swift b/Sources/SourceGraph/Mutators/RedundantExplicitPublicAccessibilityMarker.swift
index 20bb55c76..50e8e2ba8 100644
--- a/Sources/SourceGraph/Mutators/RedundantExplicitPublicAccessibilityMarker.swift
+++ b/Sources/SourceGraph/Mutators/RedundantExplicitPublicAccessibilityMarker.swift
@@ -94,7 +94,7 @@ final class RedundantExplicitPublicAccessibilityMarker: SourceGraphMutator {
                         // the call site arguments with function parameters, as parameters with
                         // default types can cause misalignment between the positions of the two.
                         if let functionRef = $0.parent?.references.first(where: { $0.role == .variableInitFunctionCall }),
-                           let functionDecl = graph.declaration(withUsr: functionRef.usr),
+                           let functionDecl = graph.declaration(withUsrID: functionRef.usrID),
                            functionDecl.hasGenericFunctionReturnedMetatypeParameters
                         {
                             return $0.parent
diff --git a/Sources/SourceGraph/Mutators/RedundantProtocolMarker.swift b/Sources/SourceGraph/Mutators/RedundantProtocolMarker.swift
index 8a6a1125b..94a7460b9 100644
--- a/Sources/SourceGraph/Mutators/RedundantProtocolMarker.swift
+++ b/Sources/SourceGraph/Mutators/RedundantProtocolMarker.swift
@@ -34,7 +34,7 @@ final class RedundantProtocolMarker: SourceGraphMutator {
                 .references
                 .lazy
                 .filter { $0.declarationKind == .extensionProtocol }
-                .compactMap { self.graph.declaration(withUsr: $0.usr) }
+                .compactMap { self.graph.declaration(withUsrID: $0.usrID) }
                 .flatMap(\.declarations)
                 .allSatisfy { unusedDeclarations.contains($0) }
 
@@ -59,7 +59,7 @@ final class RedundantProtocolMarker: SourceGraphMutator {
 
             if areAllReferencesConformances {
                 // The protocol is redundant.
-                let inherited = graph.inheritedTypeReferences(of: protocolDecl).filter { $0.declarationKind == .protocol }
+                let inherited = Array(graph.inheritedTypeReferences(of: protocolDecl).filter { $0.declarationKind == .protocol })
                 graph.markRedundantProtocol(protocolDecl, references: protocolReferences, inherited: inherited)
                 protocolDecl.declarations.forEach { graph.markIgnored($0) }
             }
diff --git a/Sources/SourceGraph/Mutators/StructImplicitInitializerReferenceBuilder.swift b/Sources/SourceGraph/Mutators/StructImplicitInitializerReferenceBuilder.swift
index f3425be30..998ef5aba 100644
--- a/Sources/SourceGraph/Mutators/StructImplicitInitializerReferenceBuilder.swift
+++ b/Sources/SourceGraph/Mutators/StructImplicitInitializerReferenceBuilder.swift
@@ -33,11 +33,13 @@ final class StructImplicitInitializerReferenceBuilder: SourceGraphMutator {
                     else { continue }
 
                     for decl in [propertyDecl, setterDecl] {
-                        for usr in decl.usrs {
+                        for usrID in decl.usrIDs {
+                            let usr = graph.usrInterner.string(for: usrID)
                             let ref = Reference(
                                 name: decl.name,
                                 kind: .normal,
                                 declarationKind: decl.kind,
+                                usrID: usrID,
                                 usr: usr,
                                 location: implicitInitDecl.location
                             )
@@ -59,7 +61,8 @@ final class StructImplicitInitializerReferenceBuilder: SourceGraphMutator {
                     let sortedReferences = caller.references.sorted()
 
                     for initPropertyDecl in initPropertyDecls {
-                        let firstRef = sortedReferences.first { initPropertyDecl.usrs.contains($0.usr) && $0.location > initRef.location }
+                        let initPropertyUsrIDs = Set(initPropertyDecl.usrIDs)
+                        let firstRef = sortedReferences.first { initPropertyUsrIDs.contains($0.usrID) && $0.location > initRef.location }
 
                         if let firstRef {
                             graph.remove(firstRef)
diff --git a/Sources/SourceGraph/Mutators/UnusedImportMarker.swift b/Sources/SourceGraph/Mutators/UnusedImportMarker.swift
index f57dc80f4..07b972f05 100644
--- a/Sources/SourceGraph/Mutators/UnusedImportMarker.swift
+++ b/Sources/SourceGraph/Mutators/UnusedImportMarker.swift
@@ -17,79 +17,145 @@ final class UnusedImportMarker: SourceGraphMutator {
         retainedModules = Set(configuration.retainUnusedImportedModules)
     }
 
+    private var wordCount: Int = 0
+    private var emptyBitset = ModuleBitset(wordCount: 0)
+    private var fileModuleBitsetCache: [ObjectIdentifier: ModuleBitset] = [:]
+    private var extCacheFilled: [Bool] = []
+    private var extCacheValues: [ModuleBitset] = []
+    private var refTypesCached: [Bool] = []
+    private var refTypesCacheValues: [Set<Reference>] = []
+
+    private func fileModuleBitset(_ file: SourceFile) -> ModuleBitset {
+        let oid = ObjectIdentifier(file)
+        if let cached = fileModuleBitsetCache[oid] { return cached }
+        let bitset = graph.moduleInterner.internBitset(file.modules, wordCount: wordCount)
+        fileModuleBitsetCache[oid] = bitset
+        return bitset
+    }
+
     func mutate() throws {
         guard !configuration.disableUnusedImportAnalysis else { return }
 
-        var referencedModulesByFile = graph.indexedSourceFiles.reduce(into: [SourceFile: Set<String>]()) { result, file in
-            result[file] = []
-        }
-        var moduleCache: [String: Set<String>] = [:]
+        let files = graph.indexedSourceFiles
 
-        // Build a mapping of source files and the modules they reference.
-        for ref in graph.allReferences {
-            if let modules = moduleCache[ref.usr] {
-                referencedModulesByFile[ref.location.file, default: []].formUnion(modules)
-                continue
+        // Pre-intern all module names (source file modules, import statements,
+        // retained modules) so that wordCount is stable for all bitsets.
+        var fileToIndex = [ObjectIdentifier: Int](minimumCapacity: files.count)
+        for (i, file) in files.enumerated() {
+            fileToIndex[ObjectIdentifier(file)] = i
+            for name in file.modules {
+                _ = graph.moduleInterner.intern(name)
+            }
+            for stmt in file.importStatements {
+                _ = graph.moduleInterner.intern(stmt.module)
             }
+        }
+        for name in retainedModules {
+            _ = graph.moduleInterner.intern(name)
+        }
 
-            var directModules: Set<String> = []
-            var indirectModules: Set<String> = []
+        wordCount = graph.moduleInterner.wordCount
+        emptyBitset = ModuleBitset(wordCount: wordCount)
+        let retainedModuleIDs = graph.moduleInterner.internBitset(retainedModules, wordCount: wordCount)
 
-            if let decl = graph.declaration(withUsr: ref.usr) {
-                directModules = decl.location.file.modules
+        // Manual pointer instead of [UInt64] to eliminate bounds checking and
+        // copy-on-write overhead in the inner loops that accumulate module bits.
+        let totalWords = files.count * wordCount
+        let perFileModules = UnsafeMutablePointer<UInt64>.allocate(capacity: totalWords)
+        perFileModules.initialize(repeating: 0, count: totalWords)
+        defer { perFileModules.deallocate() }
+
+        let usrCount = graph.usrInterner.count
+        extCacheFilled = [Bool](repeating: false, count: usrCount)
+        extCacheValues = [ModuleBitset](repeating: emptyBitset, count: usrCount)
+        refTypesCached = [Bool](repeating: false, count: usrCount)
+        refTypesCacheValues = [Set<Reference>](repeating: [], count: usrCount)
+
+        // Build a mapping of source files and the modules they reference.
+        // Process each USR once, then fan its module bitset out to
+        // every file that references it. The bitset OR is idempotent so
+        // duplicate file hits from multiple references are harmless.
+        for idx in 0 ..< usrCount {
+            let usrID = USRID(idx)
+            let refs = graph.references(toUsrID: usrID)
+            guard let firstRef = refs.first else { continue }
+
+            var referencedModules = ModuleBitset(wordCount: wordCount)
+
+            if let decl = graph.declaration(withUsrID: usrID) {
+                referencedModules.formUnion(fileModuleBitset(decl.location.file))
                 let indirectRefs = referencedTypes(from: decl)
 
-                indirectModules = indirectRefs
-                    .compactMap { graph.declaration(withUsr: $0.usr) }
-                    .flatMapSet(\.location.file.modules)
-                    .union(indirectRefs.flatMapSet { modulesExtending($0) })
+                for indirectRef in indirectRefs {
+                    if let indirectDecl = graph.declaration(withUsrID: indirectRef.usrID) {
+                        referencedModules.formUnion(fileModuleBitset(indirectDecl.location.file))
+                    }
+                    referencedModules.formUnion(modulesExtending(indirectRef))
+                }
 
                 if decl.isOverride {
-                    let overrideModules = graph.allSuperDeclarationsInOverrideChain(from: decl)
-                        .flatMapSet(\.location.file.modules)
-                    indirectModules.formUnion(overrideModules)
+                    for superDecl in graph.allSuperDeclarationsInOverrideChain(from: decl) {
+                        referencedModules.formUnion(fileModuleBitset(superDecl.location.file))
+                    }
                 }
             }
 
-            let referencedModules = directModules
-                .union(indirectModules)
-                .union(modulesExtending(ref))
-            moduleCache[ref.usr] = referencedModules
-            referencedModulesByFile[ref.location.file, default: []].formUnion(referencedModules)
+            referencedModules.formUnion(modulesExtending(firstRef))
+            guard !referencedModules.isEmpty else { continue }
+
+            for ref in refs {
+                guard let fileIdx = fileToIndex[ObjectIdentifier(ref.location.file)] else { continue }
+
+                let base = fileIdx * wordCount
+                for j in 0 ..< wordCount {
+                    perFileModules[base + j] |= referencedModules.words[j]
+                }
+            }
         }
 
         // For each source file, determine whether its imports are unused.
-        for (file, referencedModules) in referencedModulesByFile {
-            // Ignore retained files.
+        for (fileIdx, file) in files.enumerated() {
             if configuration.retainFilesMatchers.anyMatch(filename: file.path.string) {
                 continue
             }
 
+            // `perFileModules` is flattened as [file][word] so we can keep the
+            // bitsets in one contiguous buffer and index via a simple offset.
+            let base = fileIdx * wordCount
             let unreferencedImports = file.importStatements
                 .filter {
-                    // Exclude conditional imports as they may provide symbols for sections of code
-                    // that are also conditionally compiled.
-                    !$0.isConditional &&
-                        // Exclude ignore commented imports
+                    let moduleID = graph.moduleInterner.intern($0.module)
+                    // Split the dense module ID into a 64-bit word index and
+                    // an in-word bit offset for the flattened file bitset.
+                    let (word, bit) = moduleID.rawValue.quotientAndRemainder(dividingBy: 64)
+                    return !$0.isConditional &&
                         !$0.commentCommands.contains(.ignore) &&
-                        // Exclude exported/public imports because even though they may be unreferenced
-                        // in the current file, their exported symbols may be referenced in others.
                         !$0.isExported &&
-                        // Exclude explicitly retained modules.
-                        !retainedModules.contains($0.module) &&
-                        // Only Consider modules that have been indexed as we need to see which modules
-                        // they export.
-                        graph.isModuleIndexed($0.module) &&
-                        !referencedModules.contains($0.module) &&
-                        !graph.moduleExportsUnindexedModules($0.module)
+                        !retainedModuleIDs.contains(moduleID) &&
+                        graph.isModuleIndexed(moduleID) &&
+                        // If the module's bit is unset, this file never referenced it.
+                        (perFileModules[base + word] & (1 &<< bit) == 0) &&
+                        !graph.moduleExportsUnindexedModules(moduleID)
                 }
 
             for unreferencedImport in unreferencedImports {
-                // In the simple case, a module is unused if it's not referenced. However, it's
-                // possible the module exports other referenced modules.
-                guard !referencedModules.contains(where: {
-                    graph.isModule($0, exportedBy: unreferencedImport.module)
-                }) else { continue }
+                let importModuleID = graph.moduleInterner.intern(unreferencedImport.module)
+
+                // Check if any referenced module is exported by this import.
+                var isExported = false
+                for j in 0 ..< wordCount {
+                    var bits = perFileModules[base + j]
+                    while bits != 0 {
+                        let bit = bits.trailingZeroBitCount
+                        if graph.isModule(ModuleID(j * 64 + bit), exportedBy: importModuleID) {
+                            isExported = true
+                            break
+                        }
+                        bits &= bits &- 1
+                    }
+                    if isExported { break }
+                }
+                guard !isExported else { continue }
 
                 graph.markUnusedModuleImport(unreferencedImport)
             }
@@ -98,59 +164,78 @@ final class UnusedImportMarker: SourceGraphMutator {
 
     // MARK: - Private
 
-    private var extendedDeclCache: [String: Set<String>] = [:]
-
     /// Identifies any modules that extend the given declaration reference, as they may provide
     /// members and conformances that are required for compilation.
-    private func modulesExtending(_ ref: Reference) -> Set<String> {
-        guard ref.declarationKind.isExtendableKind else { return [] }
+    private func modulesExtending(_ ref: Reference) -> ModuleBitset {
+        guard ref.declarationKind.isExtendableKind else {
+            return emptyBitset
+        }
 
-        if let modules = extendedDeclCache[ref.usr] {
-            return modules
+        let idx = ref.usrID.rawValue
+
+        if extCacheFilled[idx] {
+            return extCacheValues[idx]
         }
 
-        let modules: Set<String> = graph.references(to: ref.usr)
-            .flatMapSet {
-                guard let parent = $0.parent,
-                      parent.kind == ref.declarationKind.extensionKind,
-                      parent.name == ref.name
-                else { return [] }
+        var modules = ModuleBitset(wordCount: wordCount)
+        for extRef in graph.references(toUsrID: ref.usrID) {
+            guard let parent = extRef.parent,
+                  parent.kind == ref.declarationKind.extensionKind,
+                  parent.name == ref.name
+            else { continue }
 
-                return parent.location.file.modules
-            }
-        extendedDeclCache[ref.usr] = modules
+            modules.formUnion(fileModuleBitset(parent.location.file))
+        }
+        extCacheFilled[idx] = true
+        extCacheValues[idx] = modules
         return modules
     }
 
     /// Identifies types referenced by a declaration whose module must be imported for compilation.
     private func referencedTypes(from decl: Declaration) -> Set<Reference> {
+        let cacheIdx: Int?
+        if decl.usrIDs.count == 1 {
+            let idx = decl.usrIDs[0].rawValue
+            if refTypesCached[idx] {
+                return refTypesCacheValues[idx]
+            }
+            cacheIdx = idx
+        } else {
+            cacheIdx = nil
+        }
+
         let references: Set<Reference>
 
         if decl.kind.isVariableKind {
-            references = decl.references.filter { $0.role == .varType }
+            references = Set(decl.references.filter { $0.role == .varType })
         } else if decl.kind == .enumelement {
-            references = decl.references
+            references = Set(decl.references)
         } else if decl.kind == .typealias {
             let transitiveReferences = decl.references.flatMapSet { ref -> Set<Reference> in
-                guard let refDecl = graph.declaration(withUsr: ref.usr) else { return [] }
+                guard let refDecl = graph.declaration(withUsrID: ref.usrID) else { return [] }
 
                 return referencedTypes(from: refDecl)
             }
-            references = decl.references.union(transitiveReferences)
+            references = Set(decl.references).union(transitiveReferences)
         } else if decl.kind.isFunctionKind {
-            references = decl.references
+            references = Set(decl.references
                 .filter {
                     [
                         .returnType,
                         .parameterType,
                     ].contains($0.role)
-                }
+                })
         } else if decl.kind == .protocol {
-            references = decl.related.filter { $0.role == .refinedProtocolType }
+            references = Set(decl.related.filter { $0.role == .refinedProtocolType })
         } else {
             references = []
         }
 
+        if let cacheIdx {
+            refTypesCached[cacheIdx] = true
+            refTypesCacheValues[cacheIdx] = references
+        }
+
         return references
     }
 }
diff --git a/Sources/SourceGraph/Mutators/UnusedParameterRetainer.swift b/Sources/SourceGraph/Mutators/UnusedParameterRetainer.swift
index c5c692327..4301a11a4 100644
--- a/Sources/SourceGraph/Mutators/UnusedParameterRetainer.swift
+++ b/Sources/SourceGraph/Mutators/UnusedParameterRetainer.swift
@@ -24,7 +24,7 @@ final class UnusedParameterRetainer: SourceGraphMutator {
             for protoFuncDecl in protoFuncDecls {
                 let relatedFuncDecls = protoFuncDecl.related
                     .filter(\.declarationKind.isFunctionKind)
-                    .compactMapSet { graph.declaration(withUsr: $0.usr) }
+                    .compactMapSet { graph.declaration(withUsrID: $0.usrID) }
                 let extFuncDecls = relatedFuncDecls.filter { $0.parent?.kind.isExtensionKind ?? false }
                 let conformingDecls = relatedFuncDecls.subtracting(extFuncDecls)
 
@@ -43,7 +43,7 @@ final class UnusedParameterRetainer: SourceGraphMutator {
                         if configuration.retainUnusedProtocolFuncParams {
                             functionDecl.unusedParameters.forEach { graph.markRetained($0) }
                         } else {
-                            retain(params: Array(functionDecl.unusedParameters), usedIn: allFunctionDecls)
+                            retain(params: functionDecl.unusedParameters, usedIn: allFunctionDecls)
                         }
                     }
                 }
diff --git a/Sources/SourceGraph/Mutators/UsedDeclarationMarker.swift b/Sources/SourceGraph/Mutators/UsedDeclarationMarker.swift
index b3b054558..6c30f2b9b 100644
--- a/Sources/SourceGraph/Mutators/UsedDeclarationMarker.swift
+++ b/Sources/SourceGraph/Mutators/UsedDeclarationMarker.swift
@@ -13,7 +13,9 @@ final class UsedDeclarationMarker: SourceGraphMutator {
         removeErroneousProtocolReferences()
         markUsed(graph.retainedDeclarations)
 
-        graph.rootReferences.forEach { markUsed(declarationsReferenced(by: $0)) }
+        for ref in graph.rootReferences {
+            markUsed(from: ref)
+        }
 
         ignoreUnusedDescendents(in: graph.rootDeclarations,
                                 unusedDeclarations: graph.unusedDeclarations)
@@ -23,10 +25,12 @@ final class UsedDeclarationMarker: SourceGraphMutator {
 
     // Removes references from protocol member decls to conforming decls that have a dereferenced ancestor.
     private func removeErroneousProtocolReferences() {
-        // Evaluate ancestor dereference status from a stable pre-mutation snapshot to avoid
-        // order-dependent behavior when iterating sets and removing references.
+        // When a declaration has zero references, isRetained() simplifies to
+        // retainedDeclarations.contains() — no need to scan references for
+        // .retained kind. When it HAS references, it's not dereferenced regardless.
+        let retained = graph.retainedDeclarations
         let dereferencedDeclarations = graph.allDeclarations.filter {
-            !(graph.isRetained($0) || graph.hasReferences(to: $0))
+            !graph.hasReferences(to: $0) && !retained.contains($0)
         }
 
         let dereferencedAncestors = Set(dereferencedDeclarations)
@@ -35,7 +39,7 @@ final class UsedDeclarationMarker: SourceGraphMutator {
         for protocolDecl in graph.declarations(ofKind: .protocol) {
             for memberDecl in protocolDecl.declarations {
                 for relatedRef in memberDecl.related {
-                    guard let relatedDecl = graph.declaration(withUsr: relatedRef.usr) else { continue }
+                    guard let relatedDecl = graph.declaration(withUsrID: relatedRef.usrID) else { continue }
 
                     let hasDereferencedAncestor = relatedDecl.ancestralDeclarations.contains {
                         dereferencedAncestors.contains($0)
@@ -53,39 +57,43 @@ final class UsedDeclarationMarker: SourceGraphMutator {
         }
     }
 
-    private func markUsed(_ declarations: Set<Declaration>) {
-        for declaration in declarations {
-            guard !graph.isUsed(declaration) else { continue }
-
-            graph.markUsed(declaration)
+    private func markUsed(_ declarations: some Collection<Declaration>) {
+        for decl in declarations {
+            markUsed(decl)
+        }
+    }
 
-            for ref in declaration.references {
-                markUsed(declarationsReferenced(by: ref))
-            }
+    private func markUsed(from reference: Reference) {
+        guard let decl = graph.declaration(withUsrID: reference.usrID) else { return }
 
-            for ref in declaration.related {
-                markUsed(declarationsReferenced(by: ref))
-            }
-        }
+        markUsed(decl)
     }
 
-    private func declarationsReferenced(by reference: Reference) -> Set<Declaration> {
-        var declarations: Set<Declaration> = []
+    private func markUsed(_ decl: Declaration) {
+        guard !graph.isUsed(decl) else { return }
+
+        graph.markUsed(decl)
 
-        if let declaration = graph.declaration(withUsr: reference.usr) {
-            declarations.insert(declaration)
+        for ref in decl.references {
+            if let d = graph.declaration(withUsrID: ref.usrID) {
+                markUsed(d)
+            }
         }
 
-        return declarations
+        for ref in decl.related {
+            if let d = graph.declaration(withUsrID: ref.usrID) {
+                markUsed(d)
+            }
+        }
     }
 
-    private func ignoreUnusedDescendents(in decls: Set<Declaration>, unusedDeclarations: Set<Declaration>) {
+    private func ignoreUnusedDescendents(in decls: some Collection<Declaration>, unusedDeclarations: Set<Declaration>) {
         for decl in decls {
             guard !decl.declarations.isEmpty || !decl.unusedParameters.isEmpty
             else { continue }
 
             if unusedDeclarations.contains(decl) {
-                decl.descendentDeclarations.forEach { graph.markIgnored($0) }
+                decl.forEachDescendentDeclaration { graph.markIgnored($0) }
             } else {
                 ignoreUnusedDescendents(in: decl.declarations,
                                         unusedDeclarations: unusedDeclarations)
diff --git a/Sources/SourceGraph/SourceGraph.swift b/Sources/SourceGraph/SourceGraph.swift
index 63534fb5c..89d10c399 100644
--- a/Sources/SourceGraph/SourceGraph.swift
+++ b/Sources/SourceGraph/SourceGraph.swift
@@ -1,21 +1,20 @@
 import Configuration
 import Foundation
-import Logger
 import Shared
 
 public final class SourceGraph {
-    public private(set) var allDeclarations: Set<Declaration> = []
-    public private(set) var usedDeclarations: Set<Declaration> = []
-    public private(set) var redundantProtocols: [Declaration: (references: Set<Reference>, inherited: Set<Reference>)] = [:]
+    public private(set) var redundantProtocols: [Declaration: (references: [Reference], inherited: [Reference])] = [:]
     public private(set) var rootDeclarations: Set<Declaration> = []
     public private(set) var redundantPublicAccessibility: [Declaration: Set<String>] = [:]
-    public private(set) var rootReferences: Set<Reference> = []
-    public private(set) var allReferences: Set<Reference> = []
+    public private(set) var rootReferences: [Reference] = []
     public private(set) var retainedDeclarations: Set<Declaration> = []
     public private(set) var ignoredDeclarations: Set<Declaration> = []
     public private(set) var assetReferences: Set<AssetReference> = []
     public private(set) var mainAttributedDeclarations: Set<Declaration> = []
-    public private(set) var allReferencesByUsr: [String: Set<Reference>] = [:]
+    /// Flat array indexed by `USRID.rawValue` for O(1) reference lookup by USR.
+    /// Maintained incrementally during indexing so that `indexingComplete()` has
+    /// no per-reference hashing work to do.
+    private var referencesByUsrID: [[Reference]] = []
     public private(set) var indexedSourceFiles: [SourceFile] = []
     public private(set) var unusedModuleImports: Set<Declaration> = []
     public private(set) var assignOnlyProperties: Set<Declaration> = []
@@ -24,28 +23,48 @@ public final class SourceGraph {
     public private(set) var commandIgnoredDeclarations: [Declaration: CommandIgnoreKind] = [:]
     public private(set) var functionsWithIgnoredParameters: Set<Declaration> = []
 
-    private var indexedModules: Set<String> = []
-    private var unindexedExportedModules: Set<String> = []
+    let moduleInterner = ModuleNameInterner()
+    public let usrInterner = USRInterner()
+    private var indexedModules: Set<ModuleID> = []
+    private var unindexedExportedModules: Set<ModuleID> = []
     private var allDeclarationsByKind: [Declaration.Kind: Set<Declaration>] = [:]
-    private var allDeclarationsByUsr: [String: Declaration] = [:]
-    private var moduleToExportingModules: [String: Set<String>] = [:]
+    private var declarationsOfKindsCache: [Set<Declaration.Kind>: Set<Declaration>] = [:]
+    private var declarationsOfKindsCacheDirty = false
+    /// Flat array indexed by `USRID.rawValue` for O(1) declaration lookup by USR.
+    private var declarationsByUsrID: [Declaration?] = []
+    private var moduleToExportingModules: [ModuleID: Set<ModuleID>] = [:]
+    private var moduleExportsUnindexedCache: [ModuleID: Bool] = [:]
 
     private let configuration: Configuration
-    private let logger: Logger
 
-    public init(configuration: Configuration, logger: Logger) {
+    public init(configuration: Configuration) {
         self.configuration = configuration
-        self.logger = logger
+    }
+
+    public func reserveCapacity(forFileCount fileCount: Int) {
+        let estimatedDeclarations = fileCount * 100
+        let estimatedUsrs = fileCount * 80
+        usrInterner.reserveCapacity(estimatedUsrs)
+        retainedDeclarations.reserveCapacity(estimatedDeclarations / 4)
+        referencesByUsrID.reserveCapacity(estimatedUsrs)
     }
 
     public func indexingComplete() {
-        rootDeclarations = allDeclarations.filter { $0.parent == nil }
-        rootReferences = allReferences.filter { $0.parent == nil }
+        rootDeclarations = Set(allDeclarationsByKind.values.joined().filter { $0.parent == nil })
+        rootReferences = referencesByUsrID.flatMap { $0.filter { $0.parent == nil } }
         unindexedExportedModules = Set(moduleToExportingModules.keys).subtracting(indexedModules)
     }
 
+    public var allDeclarations: FlattenSequence<Dictionary<Declaration.Kind, Set<Declaration>>.Values> {
+        allDeclarationsByKind.values.joined()
+    }
+
+    public var allReferences: FlattenSequence<[[Reference]]> {
+        referencesByUsrID.joined()
+    }
+
     public var unusedDeclarations: Set<Declaration> {
-        allDeclarations.subtracting(usedDeclarations)
+        Set(allDeclarationsByKind.values.joined().filter { !$0.isUsed })
     }
 
     public func declarations(ofKind kind: Declaration.Kind) -> Set<Declaration> {
@@ -53,30 +72,88 @@ public final class SourceGraph {
     }
 
     public func declarations(ofKinds kinds: Set<Declaration.Kind>) -> Set<Declaration> {
-        declarations(ofKinds: Array(kinds))
+        if declarationsOfKindsCacheDirty {
+            declarationsOfKindsCache.removeAll(keepingCapacity: true)
+            declarationsOfKindsCacheDirty = false
+        }
+        if let cached = declarationsOfKindsCache[kinds] { return cached }
+        // Pre-size the set to avoid incremental rehashing during formUnion.
+        // Per-kind sets are disjoint so the sum is exact.
+        let totalCount = kinds.reduce(0) { $0 + (allDeclarationsByKind[$1]?.count ?? 0) }
+        var result = Set<Declaration>(minimumCapacity: totalCount)
+        for kind in kinds {
+            result.formUnion(allDeclarationsByKind[kind, default: []])
+        }
+        declarationsOfKindsCache[kinds] = result
+        return result
     }
 
     public func declarations(ofKinds kinds: [Declaration.Kind]) -> Set<Declaration> {
-        kinds.flatMapSet { allDeclarationsByKind[$0, default: []] }
+        declarations(ofKinds: Set(kinds))
     }
 
     public func declaration(withUsr usr: String) -> Declaration? {
-        allDeclarationsByUsr[usr]
+        guard let usrID = usrInterner.existing(usr) else { return nil }
+
+        let idx = usrID.rawValue
+        guard idx < declarationsByUsrID.count else { return nil }
+
+        return declarationsByUsrID[idx]
     }
 
-    public func references(to decl: Declaration) -> Set<Reference> {
-        decl.usrs.flatMapSet { references(to: $0) }
+    func declaration(withUsrID usrID: USRID) -> Declaration? {
+        let idx = usrID.rawValue
+        guard idx < declarationsByUsrID.count else { return nil }
+
+        return declarationsByUsrID[idx]
     }
 
-    public func references(to usr: String) -> Set<Reference> {
-        allReferencesByUsr[usr, default: []]
+    public func references(to decl: Declaration) -> [Reference] {
+        if decl.usrIDs.count == 1 {
+            return refsForUsr(decl.usrIDs[0])
+        }
+        return decl.usrIDs.flatMap { refsForUsr($0) }
+    }
+
+    public func references(to usr: String) -> [Reference] {
+        guard let usrID = usrInterner.existing(usr) else { return [] }
+
+        return refsForUsr(usrID)
+    }
+
+    func references(toUsrID usrID: USRID) -> [Reference] {
+        refsForUsr(usrID)
     }
 
     public func hasReferences(to decl: Declaration) -> Bool {
-        decl.usrs.contains { !allReferencesByUsr[$0, default: []].isEmpty }
+        decl.usrIDs.contains { usrHasRefs($0) }
+    }
+
+    private func refsForUsr(_ usrID: USRID) -> [Reference] {
+        let idx = usrID.rawValue
+        return idx < referencesByUsrID.count ? referencesByUsrID[idx] : []
+    }
+
+    private func usrHasRefs(_ usrID: USRID) -> Bool {
+        let idx = usrID.rawValue
+        return idx < referencesByUsrID.count && !referencesByUsrID[idx].isEmpty
+    }
+
+    private func ensureUsrBucket(for usrID: USRID) {
+        let idx = usrID.rawValue
+        if idx >= referencesByUsrID.count {
+            referencesByUsrID.append(contentsOf: repeatElement([Reference](), count: idx + 1 - referencesByUsrID.count))
+        }
     }
 
-    func markRedundantProtocol(_ declaration: Declaration, references: Set<Reference>, inherited: Set<Reference>) {
+    private func ensureUsrDeclBucket(for usrID: USRID) {
+        let idx = usrID.rawValue
+        if idx >= declarationsByUsrID.count {
+            declarationsByUsrID.append(contentsOf: repeatElement(nil, count: idx + 1 - declarationsByUsrID.count))
+        }
+    }
+
+    func markRedundantProtocol(_ declaration: Declaration, references: [Reference], inherited: [Reference]) {
         redundantProtocols[declaration] = (references, inherited)
     }
 
@@ -102,11 +179,13 @@ public final class SourceGraph {
 
     public func markRetained(_ declaration: Declaration) {
         if let parent = declaration.parent {
-            for usr in declaration.usrs {
+            for usrID in declaration.usrIDs {
+                let usr = usrInterner.string(for: usrID)
                 let reference = Reference(
                     name: declaration.name,
                     kind: .retained,
                     declarationKind: declaration.kind,
+                    usrID: usrID,
                     usr: usr,
                     location: declaration.location
                 )
@@ -121,11 +200,8 @@ public final class SourceGraph {
     func unmarkRetained(_ declaration: Declaration) {
         retainedDeclarations.remove(declaration)
 
-        let retainedReferences = declaration.usrs.flatMapSet { usr in
-            allReferencesByUsr[usr, default: []]
-        }.filter { reference in
-            reference.kind == .retained && reference.parent === declaration.parent
-        }
+        let retainedReferences = references(to: declaration)
+            .filter { $0.kind == .retained && $0.parent === declaration.parent }
 
         for reference in retainedReferences {
             remove(reference)
@@ -152,72 +228,80 @@ public final class SourceGraph {
         retainedDeclarations.contains(declaration) || references(to: declaration).contains { $0.kind == .retained }
     }
 
-    public func add(_ declaration: Declaration) {
-        allDeclarations.insert(declaration)
+    public func add(_ declaration: Declaration) throws {
+        try validateNoDeclarationConflict(for: declaration)
+
         allDeclarationsByKind[declaration.kind, default: []].insert(declaration)
-        for usr in declaration.usrs {
-            if let existingDecl = allDeclarationsByUsr[usr] {
-                logger.warn("""
-                Declaration conflict detected: a declaration with the USR '\(usr)' has already been indexed.
-                This issue can cause inconsistent and incorrect results.
-                Existing declaration: \(existingDecl), declared in modules: \(existingDecl.location.file.modules.sorted())
-                Conflicting declaration: \(declaration), declared in modules: \(declaration.location.file.modules.sorted())
-                To resolve this warning, make sure all build modules are uniquely named.
-                """)
-                // Keep the declaration that sorts first to ensure deterministic results
-                // regardless of indexing order.
-                if declaration < existingDecl {
-                    allDeclarationsByUsr[usr] = declaration
-                }
-            } else {
-                allDeclarationsByUsr[usr] = declaration
-            }
+        declarationsOfKindsCacheDirty = true
+        for usrID in declaration.usrIDs {
+            ensureUsrDeclBucket(for: usrID)
+            declarationsByUsrID[usrID.rawValue] = declaration
         }
     }
 
-    public func add(_ declarations: Set<Declaration>) {
-        declarations.forEach { add($0) }
+    public func add(_ declarations: Set<Declaration>) throws {
+        for declaration in declarations {
+            try add(declaration)
+        }
     }
 
     public func remove(_ declaration: Declaration) {
-        declaration.parent?.declarations.remove(declaration)
-        allDeclarations.remove(declaration)
+        if let i = declaration.parent?.declarations.firstIndex(where: { $0 === declaration }) {
+            declaration.parent?.declarations.remove(at: i)
+        }
         allDeclarationsByKind[declaration.kind]?.remove(declaration)
+        declarationsOfKindsCacheDirty = true
         rootDeclarations.remove(declaration)
-        usedDeclarations.remove(declaration)
+        declaration.isUsed = false
         assignOnlyProperties.remove(declaration)
         suppressedAssignOnlyProperties.remove(declaration)
-        declaration.usrs.forEach { allDeclarationsByUsr.removeValue(forKey: $0) }
+        for usrID in declaration.usrIDs {
+            let idx = usrID.rawValue
+            if idx < declarationsByUsrID.count {
+                declarationsByUsrID[idx] = nil
+            }
+        }
     }
 
     public func add(_ reference: Reference) {
-        _ = allReferences.insert(reference)
-        allReferencesByUsr[reference.usr, default: []].insert(reference)
+        ensureUsrBucket(for: reference.usrID)
+        referencesByUsrID[reference.usrID.rawValue].append(reference)
     }
 
-    public func add(_ references: Set<Reference>) {
-        allReferences.formUnion(references)
-        references.forEach { allReferencesByUsr[$0.usr, default: []].insert($0) }
+    public func add(_ references: [Reference]) {
+        if let maxID = references.lazy.map(\.usrID.rawValue).max() {
+            ensureUsrBucket(for: USRID(maxID))
+        }
+        for ref in references {
+            referencesByUsrID[ref.usrID.rawValue].append(ref)
+        }
     }
 
     public func add(_ reference: Reference, from declaration: Declaration) {
         if reference.kind == .related {
-            _ = declaration.related.insert(reference)
+            declaration.related.append(reference)
         } else {
-            _ = declaration.references.insert(reference)
+            declaration.references.append(reference)
         }
 
         add(reference)
     }
 
     func remove(_ reference: Reference) {
-        _ = allReferences.remove(reference)
-        allReferences.subtract(reference.descendentReferences)
-        allReferencesByUsr[reference.usr]?.remove(reference)
+        let idx = reference.usrID.rawValue
+        if idx < referencesByUsrID.count,
+           let i = referencesByUsrID[idx].firstIndex(where: { $0 === reference })
+        {
+            referencesByUsrID[idx].remove(at: i)
+        }
 
         if let parent = reference.parent {
-            parent.references.remove(reference)
-            parent.related.remove(reference)
+            if let i = parent.references.firstIndex(where: { $0 === reference }) {
+                parent.references.remove(at: i)
+            }
+            if let i = parent.related.firstIndex(where: { $0 === reference }) {
+                parent.related.remove(at: i)
+            }
         }
     }
 
@@ -226,15 +310,15 @@ public final class SourceGraph {
     }
 
     func markUsed(_ declaration: Declaration) {
-        _ = usedDeclarations.insert(declaration)
+        declaration.isUsed = true
     }
 
     func isUsed(_ declaration: Declaration) -> Bool {
-        usedDeclarations.contains(declaration)
+        declaration.isUsed
     }
 
     func isExternal(_ reference: Reference) -> Bool {
-        declaration(withUsr: reference.usr) == nil
+        declaration(withUsrID: reference.usrID) == nil
     }
 
     public func addIndexedSourceFile(_ file: SourceFile) {
@@ -242,42 +326,64 @@ public final class SourceGraph {
     }
 
     public func addIndexedModules(_ modules: Set<String>) {
-        indexedModules.formUnion(modules)
+        indexedModules.formUnion(moduleInterner.intern(modules))
     }
 
-    public func isModuleIndexed(_ module: String) -> Bool {
-        indexedModules.contains(module)
+    func isModuleIndexed(_ moduleID: ModuleID) -> Bool {
+        indexedModules.contains(moduleID)
     }
 
     public func addExportedModule(_ module: String, exportedBy exportingModules: Set<String>) {
-        moduleToExportingModules[module, default: []].formUnion(exportingModules)
+        let moduleID = moduleInterner.intern(module)
+        let exportingIDs = moduleInterner.intern(exportingModules)
+        moduleToExportingModules[moduleID, default: []].formUnion(exportingIDs)
     }
 
-    public func moduleExportsUnindexedModules(_ module: String) -> Bool {
-        unindexedExportedModules.contains { unindexedModule in
-            isModule(unindexedModule, exportedBy: module)
+    func moduleExportsUnindexedModules(_ moduleID: ModuleID) -> Bool {
+        if let cached = moduleExportsUnindexedCache[moduleID] { return cached }
+        let result = unindexedExportedModules.contains { unindexedModule in
+            isModule(unindexedModule, exportedBy: moduleID)
         }
+        moduleExportsUnindexedCache[moduleID] = result
+        return result
     }
 
-    public func isModule(_ module: String, exportedBy exportingModule: String) -> Bool {
-        let exportingModules = moduleToExportingModules[module, default: []]
+    private var isModuleExportedCache: [Int: Bool] = [:]
 
-        if exportingModules.contains(exportingModule) {
-            // The module is exported directly.
-            return true
-        }
+    func isModule(_ module: ModuleID, exportedBy exportingModule: ModuleID) -> Bool {
+        // Pack the module pair into a single Int to keep this hot-path cache
+        // lookup cheaper than hashing a tuple or custom key type. `ModuleID`
+        // enforces the radix bound so this base-`packingRadix` encoding is unique.
+        let key = module.rawValue &* ModuleID.packingRadix &+ exportingModule.rawValue
+        if let cached = isModuleExportedCache[key] { return cached }
 
-        // Recursively check if the module is exported transitively.
-        return exportingModules.contains { nestedExportingModule in
-            isModule(nestedExportingModule, exportedBy: exportingModule) &&
-                isModule(module, exportedBy: nestedExportingModule)
+        let exportingModules = moduleToExportingModules[module, default: []]
+        var result = exportingModules.contains(exportingModule)
+        if !result {
+            result = exportingModules.contains { nestedExportingModule in
+                isModule(nestedExportingModule, exportedBy: exportingModule) &&
+                    isModule(module, exportedBy: nestedExportingModule)
+            }
         }
+        isModuleExportedCache[key] = result
+        return result
     }
 
+    private var relativePathCache: [ObjectIdentifier: String] = [:]
+
     func markUnusedModuleImport(_ statement: ImportStatement) {
-        let location = statement.location.relativeTo(configuration.projectRoot)
-        let usr = "import-\(statement.module)-\(location)"
-        let decl = Declaration(name: statement.module, kind: .module, usrs: [usr], location: statement.location)
+        let loc = statement.location
+        let fileOID = ObjectIdentifier(loc.file)
+        let relativePath: String
+        if let cached = relativePathCache[fileOID] {
+            relativePath = cached
+        } else {
+            relativePath = loc.file.path.relativeTo(configuration.projectRoot).string
+            relativePathCache[fileOID] = relativePath
+        }
+        let usr = "import-\(statement.module)-\(relativePath):\(loc.line):\(loc.column)"
+        let usrID = usrInterner.intern(usr)
+        let decl = Declaration(name: statement.module, kind: .module, usrs: [usr], usrIDs: [usrID], location: loc)
         unusedModuleImports.insert(decl)
     }
 
@@ -291,11 +397,7 @@ public final class SourceGraph {
         for reference in decl.immediateInheritedTypeReferences {
             references.insert(reference)
 
-            if let inheritedDecl = declaration(withUsr: reference.usr) {
-                // Detect circular references. The following is valid Swift.
-                // class SomeClass {}
-                // extension SomeClass: SomeProtocol {}
-                // protocol SomeProtocol: SomeClass {}
+            if let inheritedDecl = declaration(withUsrID: reference.usrID) {
                 guard !seenDeclarations.contains(inheritedDecl) else { continue }
 
                 references = inheritedTypeReferences(of: inheritedDecl, seenDeclarations: seenDeclarations.union([decl])).union(references)
@@ -306,14 +408,14 @@ public final class SourceGraph {
     }
 
     func inheritedDeclarations(of decl: Declaration) -> [Declaration] {
-        inheritedTypeReferences(of: decl).compactMap { declaration(withUsr: $0.usr) }
+        inheritedTypeReferences(of: decl).compactMap { declaration(withUsrID: $0.usrID) }
     }
 
     func immediateSubclasses(of decl: Declaration) -> Set<Declaration> {
         references(to: decl)
             .filter { $0.kind == .related && $0.declarationKind == .class }
-            .flatMap { $0.parent?.usrs ?? [] }
-            .compactMapSet { declaration(withUsr: $0) }
+            .flatMap { $0.parent?.usrIDs ?? [] }
+            .compactMapSet { declaration(withUsrID: $0) }
     }
 
     func subclasses(of decl: Declaration) -> Set<Declaration> {
@@ -335,7 +437,7 @@ public final class SourceGraph {
     func extendedDeclaration(forExtension extensionDeclaration: Declaration) throws -> Declaration? {
         guard let extendedReference = try extendedDeclarationReference(forExtension: extensionDeclaration) else { return nil }
 
-        if let extendedDeclaration = declaration(withUsr: extendedReference.usr) {
+        if let extendedDeclaration = declaration(withUsrID: extendedReference.usrID) {
             return extendedDeclaration
         }
 
@@ -347,7 +449,7 @@ public final class SourceGraph {
 
         let overridenDecl = decl.related
             .filter { $0.declarationKind == decl.kind && $0.name == decl.name }
-            .compactMap { declaration(withUsr: $0.usr) }
+            .compactMap { declaration(withUsrID: $0.usrID) }
             .min()
 
         guard let overridenDecl else {
@@ -379,7 +481,7 @@ public final class SourceGraph {
 
     func allOverrideDeclarations(fromBase decl: Declaration) -> Set<Declaration> {
         decl.relatedEquivalentReferences
-            .compactMap { declaration(withUsr: $0.usr) }
+            .compactMap { declaration(withUsrID: $0.usrID) }
             .reduce(into: .init()) { result, decl in
                 guard decl.isOverride else { return }
 
@@ -403,4 +505,19 @@ public final class SourceGraph {
             [.protocol, .typealias].contains($0.declarationKind) && encodableTypes.contains($0.name)
         }
     }
+
+    private func validateNoDeclarationConflict(for declaration: Declaration) throws {
+        for usrID in declaration.usrIDs {
+            let idx = usrID.rawValue
+            if idx < declarationsByUsrID.count, let existingDecl = declarationsByUsrID[idx] {
+                let usr = usrInterner.string(for: usrID)
+                throw PeripheryError.sourceGraphIntegrityError(message: """
+                Declaration conflict detected: a declaration with the USR '\(usr)' has already been indexed.
+                Existing declaration: \(existingDecl), declared in modules: \(existingDecl.location.file.modules.sorted())
+                Conflicting declaration: \(declaration), declared in modules: \(declaration.location.file.modules.sorted())
+                Make sure all build modules are uniquely named.
+                """)
+            }
+        }
+    }
 }
diff --git a/Sources/SourceGraph/SourceGraphDebugger.swift b/Sources/SourceGraph/SourceGraphDebugger.swift
index e62f6ddba..ae1bdbea6 100644
--- a/Sources/SourceGraph/SourceGraphDebugger.swift
+++ b/Sources/SourceGraph/SourceGraphDebugger.swift
@@ -54,9 +54,5 @@ final class SourceGraphDebugger {
     private func describe(_ reference: Reference, depth: Int = 0) {
         let inset = String(repeating: "··", count: depth)
         print(inset + reference.description)
-
-        for reference in reference.references.sorted() {
-            describe(reference, depth: depth + 1)
-        }
     }
 }
diff --git a/Sources/SourceGraph/SourceGraphMutex.swift b/Sources/SourceGraph/SourceGraphMutex.swift
index c05dc324d..80de0d8ef 100644
--- a/Sources/SourceGraph/SourceGraphMutex.swift
+++ b/Sources/SourceGraph/SourceGraphMutex.swift
@@ -7,8 +7,16 @@ import Synchronization
 public final class SourceGraphMutex: @unchecked Sendable {
     private let graph: Mutex<SourceGraph>
 
+    /// Self-synchronizing interner, safe to call without the graph lock.
+    public let usrInterner: USRInterner
+
     public init(graph: SourceGraph) {
         self.graph = Mutex(graph)
+        usrInterner = graph.usrInterner
+    }
+
+    public func reserveCapacity(forFileCount fileCount: Int) {
+        graph.withLock { $0.reserveCapacity(forFileCount: fileCount) }
     }
 
     @discardableResult
diff --git a/Sources/SyntaxAnalysis/DeclarationSyntaxVisitor.swift b/Sources/SyntaxAnalysis/DeclarationSyntaxVisitor.swift
index cd0432643..c5ce70c28 100644
--- a/Sources/SyntaxAnalysis/DeclarationSyntaxVisitor.swift
+++ b/Sources/SyntaxAnalysis/DeclarationSyntaxVisitor.swift
@@ -4,37 +4,71 @@ import SourceGraph
 import SwiftSyntax
 
 public final class DeclarationSyntaxVisitor: PeripherySyntaxVisitor {
-    public typealias Result = (
-        location: Location,
-        accessibility: Accessibility?,
-        modifiers: [String],
-        attributes: Set<DeclarationAttribute>,
-        commentCommands: [CommentCommand],
-        variableType: String?,
-        variableTypeLocations: Set<Location>,
-        parameterTypeLocations: Set<Location>,
-        returnTypeLocations: Set<Location>,
-        throwTypeLocations: Set<Location>,
-        inheritedTypeLocations: Set<Location>,
-        genericParameterLocations: Set<Location>,
-        genericConformanceRequirementLocations: Set<Location>,
-        variableInitFunctionCallLocations: Set<Location>,
-        functionCallMetatypeArgumentLocations: Set<Location>,
-        typeInitializerLocations: Set<Location>,
-        variableInitExprLocations: Set<Location>,
-        hasGenericFunctionReturnedMetatypeParameters: Bool
-    )
+    // Reference type (not a tuple) to avoid expensive copies when stored in
+    // both the results array and the resultsByLocation dictionary.
+    public final class Result {
+        public let accessibility: Accessibility?
+        public let modifiers: [String]
+        public let attributes: Set<DeclarationAttribute>
+        public let commentCommands: [CommentCommand]
+        public let variableType: String?
+        public let variableTypeLocations: Set<Location>
+        public let parameterTypeLocations: Set<Location>
+        public let returnTypeLocations: Set<Location>
+        public let throwTypeLocations: Set<Location>
+        public let inheritedTypeLocations: Set<Location>
+        public let genericParameterLocations: Set<Location>
+        public let genericConformanceRequirementLocations: Set<Location>
+        public let variableInitFunctionCallLocations: Set<Location>
+        public let functionCallMetatypeArgumentLocations: Set<Location>
+        public let typeInitializerLocations: Set<Location>
+        public let variableInitExprLocations: Set<Location>
+        public let hasGenericFunctionReturnedMetatypeParameters: Bool
+
+        init(
+            accessibility: Accessibility?,
+            modifiers: [String],
+            attributes: Set<DeclarationAttribute>,
+            commentCommands: [CommentCommand],
+            variableType: String?,
+            variableTypeLocations: Set<Location>,
+            parameterTypeLocations: Set<Location>,
+            returnTypeLocations: Set<Location>,
+            throwTypeLocations: Set<Location>,
+            inheritedTypeLocations: Set<Location>,
+            genericParameterLocations: Set<Location>,
+            genericConformanceRequirementLocations: Set<Location>,
+            variableInitFunctionCallLocations: Set<Location>,
+            functionCallMetatypeArgumentLocations: Set<Location>,
+            typeInitializerLocations: Set<Location>,
+            variableInitExprLocations: Set<Location>,
+            hasGenericFunctionReturnedMetatypeParameters: Bool
+        ) {
+            self.accessibility = accessibility
+            self.modifiers = modifiers
+            self.attributes = attributes
+            self.commentCommands = commentCommands
+            self.variableType = variableType
+            self.variableTypeLocations = variableTypeLocations
+            self.parameterTypeLocations = parameterTypeLocations
+            self.returnTypeLocations = returnTypeLocations
+            self.throwTypeLocations = throwTypeLocations
+            self.inheritedTypeLocations = inheritedTypeLocations
+            self.genericParameterLocations = genericParameterLocations
+            self.genericConformanceRequirementLocations = genericConformanceRequirementLocations
+            self.variableInitFunctionCallLocations = variableInitFunctionCallLocations
+            self.functionCallMetatypeArgumentLocations = functionCallMetatypeArgumentLocations
+            self.typeInitializerLocations = typeInitializerLocations
+            self.variableInitExprLocations = variableInitExprLocations
+            self.hasGenericFunctionReturnedMetatypeParameters = hasGenericFunctionReturnedMetatypeParameters
+        }
+    }
 
     private let sourceLocationBuilder: SourceLocationBuilder
     private let typeSyntaxInspector: TypeSyntaxInspector
     private let swiftVersion: SwiftVersion
     private(set) var results: [Result] = []
-
-    public var resultsByLocation: [Location: Result] {
-        results.reduce(into: [Location: Result]()) { dict, result in
-            dict[result.location] = result
-        }
-    }
+    public private(set) var resultsByLocation: [Location: Result] = [:]
 
     public init(sourceLocationBuilder: SourceLocationBuilder, swiftVersion: SwiftVersion) {
         self.sourceLocationBuilder = sourceLocationBuilder
@@ -349,8 +383,7 @@ public final class DeclarationSyntaxVisitor: PeripherySyntaxVisitor {
         let allParameterClauseLocations = parameterClauseLocations.union(enumCaseParameterClauseLocations)
             .union(closureParameterClauseLocations)
 
-        results.append((
-            location: location,
+        let result = Result(
             accessibility: accessibility,
             modifiers: modifierNames,
             attributes: parsedAttributes,
@@ -368,7 +401,9 @@ public final class DeclarationSyntaxVisitor: PeripherySyntaxVisitor {
             typeInitializerLocations: typeLocations(for: typeInitializerClause?.value),
             variableInitExprLocations: memberBaseLocations(for: variableInitExpr),
             hasGenericFunctionReturnedMetatypeParameters: hasGenericFunctionReturnedMetatypeParameters
-        ))
+        )
+        results.append(result)
+        resultsByLocation[location] = result
     }
 
     /// Determines whether the function has generic metatype parameters that are also returned.
diff --git a/Sources/SyntaxAnalysis/UnusedParameterAnalyzer.swift b/Sources/SyntaxAnalysis/UnusedParameterAnalyzer.swift
index 793e5e968..8f012bd95 100644
--- a/Sources/SyntaxAnalysis/UnusedParameterAnalyzer.swift
+++ b/Sources/SyntaxAnalysis/UnusedParameterAnalyzer.swift
@@ -20,7 +20,28 @@ public final class UnusedParameterAnalyzer {
             parseProtocols: parseProtocols
         )
 
-        return functions.reduce(into: [Function: Set<Parameter>]()) { result, function in
+        return analyzeAll(functions)
+    }
+
+    public func analyze(
+        collectedFunctionDecls: [FunctionDeclSyntax],
+        collectedInitializerDecls: [InitializerDeclSyntax],
+        file: SourceFile,
+        locationConverter: SourceLocationConverter,
+        parseProtocols: Bool
+    ) -> [Function: Set<Parameter>] {
+        let functions = UnusedParameterParser.parseCollected(
+            functionDecls: collectedFunctionDecls,
+            initializerDecls: collectedInitializerDecls,
+            file: file,
+            locationConverter: locationConverter,
+            parseProtocols: parseProtocols
+        )
+        return analyzeAll(functions)
+    }
+
+    private func analyzeAll(_ functions: [Function]) -> [Function: Set<Parameter>] {
+        functions.reduce(into: [Function: Set<Parameter>]()) { result, function in
             let params = analyze(function: function)
 
             if !params.isEmpty {
diff --git a/Sources/SyntaxAnalysis/UnusedParameterParser.swift b/Sources/SyntaxAnalysis/UnusedParameterParser.swift
index a585af117..ea48aa0c3 100644
--- a/Sources/SyntaxAnalysis/UnusedParameterParser.swift
+++ b/Sources/SyntaxAnalysis/UnusedParameterParser.swift
@@ -1,4 +1,5 @@
 import Foundation
+import Shared
 import SourceGraph
 import SwiftParser
 import SwiftSyntax
@@ -61,13 +62,15 @@ public struct Parameter: Item, Hashable {
 
     public let items: [Item] = []
 
-    public func makeDeclaration(withParent parent: Declaration) -> Declaration {
+    public func makeDeclaration(withParent parent: Declaration, interner: USRInterner) -> Declaration {
         let parentUsrs = parent.usrs.sorted().joined(separator: "-")
         let usr = "param-\(name.text)-\(parent.name)-\(parentUsrs)"
+        let usrID = interner.intern(usr)
         let decl = Declaration(
             name: name.text,
             kind: .varParameter,
             usrs: [usr],
+            usrIDs: [usrID],
             location: location
         )
         decl.parent = parent
@@ -95,8 +98,36 @@ struct GenericItem: Item {
     let items: [Item]
 }
 
+/// Collects root function and initializer syntax nodes during a
+/// MultiplexingSyntaxVisitor walk. Nested functions are still discovered
+/// recursively when UnusedParameterParser parses those collected nodes.
+public final class FunctionSyntaxCollector: PeripherySyntaxVisitor {
+    public private(set) var functionDecls: [FunctionDeclSyntax] = []
+    public private(set) var initializerDecls: [InitializerDeclSyntax] = []
+    private var functionDepth = 0
+
+    public required init(sourceLocationBuilder _: SourceLocationBuilder, swiftVersion _: SwiftVersion) {}
+
+    public func visit(_ node: FunctionDeclSyntax) {
+        if functionDepth == 0 { functionDecls.append(node) }
+        functionDepth += 1
+    }
+
+    public func visitPost(_: FunctionDeclSyntax) {
+        functionDepth -= 1
+    }
+
+    public func visit(_ node: InitializerDeclSyntax) {
+        if functionDepth == 0 { initializerDecls.append(node) }
+        functionDepth += 1
+    }
+
+    public func visitPost(_: InitializerDeclSyntax) {
+        functionDepth -= 1
+    }
+}
+
 struct UnusedParameterParser {
-    private let syntax: SourceFileSyntax
     private let parseProtocols: Bool
     private let file: SourceFile
     private let locationConverter: SourceLocationConverter
@@ -109,11 +140,10 @@ struct UnusedParameterParser {
     ) -> [Function] {
         let parser = self.init(
             file: file,
-            syntax: syntax,
             locationConverter: locationConverter,
             parseProtocols: parseProtocols
         )
-        return parser.parse()
+        return parser.parse(syntax: syntax)
     }
 
     static func parse(file: SourceFile, parseProtocols: Bool) throws -> [Function] {
@@ -128,30 +158,54 @@ struct UnusedParameterParser {
         )
     }
 
-    private init(file: SourceFile, syntax: SourceFileSyntax, locationConverter: SourceLocationConverter, parseProtocols: Bool) {
+    static func parseCollected(
+        functionDecls: [FunctionDeclSyntax],
+        initializerDecls: [InitializerDeclSyntax],
+        file: SourceFile,
+        locationConverter: SourceLocationConverter,
+        parseProtocols: Bool
+    ) -> [Function] {
+        let parser = self.init(
+            file: file,
+            locationConverter: locationConverter,
+            parseProtocols: parseProtocols
+        )
+        return parser.parseFunctionNodes(functionDecls, initializerDecls)
+    }
+
+    private init(file: SourceFile, locationConverter: SourceLocationConverter, parseProtocols: Bool) {
         self.file = file
-        self.syntax = syntax
         self.locationConverter = locationConverter
         self.parseProtocols = parseProtocols
     }
 
-    func parse() -> [Function] {
+    func parse(syntax: SourceFileSyntax) -> [Function] {
         parse(node: syntax, collecting: Function.self)
     }
 
-    // MARK: - Private
-
-    private func parse<T: Item>(node: SyntaxProtocol, collecting: T.Type) -> [T] {
-        parse(children: node.children(viewMode: .sourceAccurate), collecting: collecting)
+    private func parseFunctionNodes(
+        _ functionDecls: [FunctionDeclSyntax],
+        _ initializerDecls: [InitializerDeclSyntax]
+    ) -> [Function] {
+        let collector = Collector<Function>()
+        for decl in functionDecls {
+            let item = parse(functionDecl: decl, collector)
+            if let item { collector.add(item) }
+        }
+        for decl in initializerDecls {
+            let item = parse(initializerDecl: decl, collector)
+            if let item { collector.add(item) }
+        }
+        return collector.collection
     }
 
-    private func parse<T: Item>(children: SyntaxChildren, collecting: T.Type) -> [T] {
-        parse(nodes: Array(children), collecting: collecting)
-    }
+    // MARK: - Private
 
-    private func parse<T: Item>(nodes: [Syntax], collecting _: T.Type) -> [T] {
+    private func parse<T: Item>(node: SyntaxProtocol, collecting _: T.Type) -> [T] {
         let collector = Collector<T>()
-        nodes.forEach { _ = parse(node: $0, collector) }
+        for child in node.children(viewMode: .sourceAccurate) {
+            _ = parse(node: child, collector)
+        }
         return collector.collection
     }
 
@@ -201,7 +255,12 @@ struct UnusedParameterParser {
     }
 
     private func parse(childrenFrom node: Syntax, _ collector: Collector<some Any>?) -> Item? {
-        let items = node.children(viewMode: .sourceAccurate).compactMap { parse(node: $0, collector) }
+        var items: [Item] = []
+        for child in node.children(viewMode: .sourceAccurate) {
+            if let item = parse(node: child, collector) {
+                items.append(item)
+            }
+        }
         if !items.isEmpty {
             return GenericItem(node: node, items: items)
         }
@@ -333,7 +392,7 @@ struct UnusedParameterParser {
         }
 
         // Swift supports nested functions, so it's possible this function captures a param from an outer function.
-        let params = parse(children: syntax.children(viewMode: .sourceAccurate), collecting: Parameter.self)
+        let params = parse(node: syntax, collecting: Parameter.self)
         let items = parse(node: body, collector)?.items ?? []
         let fullName = buildFullName(for: name, with: params)
         let genericParamNames = genericParams?.parameters.map(\.name.text) ?? []
diff --git a/Tests/Fixtures/Sources/UnusedParameterFixtures/testNestedFunctionAnalyzerPath.swift b/Tests/Fixtures/Sources/UnusedParameterFixtures/testNestedFunctionAnalyzerPath.swift
new file mode 100644
index 000000000..6b570b197
--- /dev/null
+++ b/Tests/Fixtures/Sources/UnusedParameterFixtures/testNestedFunctionAnalyzerPath.swift
@@ -0,0 +1,11 @@
+import Foundation
+
+class SyntaxFixtureNestedAnalyzer {
+    func outer(outerParam: String) {
+        func innerFunc(param: String) {
+            print(outerParam)
+        }
+
+        innerFunc(param: "value")
+    }
+}
diff --git a/Tests/PeripheryTests/DeterminismRegressionTest.swift b/Tests/PeripheryTests/DeterminismRegressionTest.swift
index a51352500..92cedf664 100644
--- a/Tests/PeripheryTests/DeterminismRegressionTest.swift
+++ b/Tests/PeripheryTests/DeterminismRegressionTest.swift
@@ -8,8 +8,7 @@ import XCTest
 final class DeterminismRegressionTest: XCTestCase {
     private func makeGraph() -> SourceGraph {
         let configuration = Configuration()
-        let logger = Logger(quiet: true, verbose: false, colorMode: .never)
-        return SourceGraph(configuration: configuration, logger: logger)
+        return SourceGraph(configuration: configuration)
     }
 
     private func makeSwiftVersion() -> SwiftVersion {
@@ -27,10 +26,11 @@ final class DeterminismRegressionTest: XCTestCase {
         kind: Declaration.Kind,
         name: String,
         usr: String,
-        location: Location
+        location: Location,
+        graph: SourceGraph
     ) -> Declaration {
-        let declaration = Declaration(name: name, kind: kind, usrs: [usr], location: location)
-        return declaration
+        let usrID = graph.usrInterner.intern(usr)
+        return Declaration(name: name, kind: kind, usrs: [usr], usrIDs: [usrID], location: location)
     }
 
     private func makeReference(
@@ -40,12 +40,15 @@ final class DeterminismRegressionTest: XCTestCase {
         name: String,
         location: Location,
         parent: Declaration,
-        role: Reference.Role = .unknown
+        role: Reference.Role = .unknown,
+        graph: SourceGraph
     ) -> Reference {
+        let usrID = graph.usrInterner.intern(usr)
         let reference = Reference(
             name: name,
             kind: kind,
             declarationKind: declarationKind,
+            usrID: usrID,
             usr: usr,
             location: location
         )
@@ -61,7 +64,8 @@ final class DeterminismRegressionTest: XCTestCase {
             kind: .extensionClass,
             name: "Widget",
             usr: "ext_widget",
-            location: makeLocation("/tmp/ext.swift", module: "Feature", line: 1)
+            location: makeLocation("/tmp/ext.swift", module: "Feature", line: 1),
+            graph: graph
         )
 
         let later = makeReference(
@@ -70,7 +74,8 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "class_later",
             name: "Widget",
             location: makeLocation("/tmp/widget.swift", module: "A", line: 20),
-            parent: extDecl
+            parent: extDecl,
+            graph: graph
         )
         let earlier = makeReference(
             kind: .normal,
@@ -78,7 +83,8 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "class_earlier",
             name: "Widget",
             location: makeLocation("/tmp/widget.swift", module: "B", line: 10),
-            parent: extDecl
+            parent: extDecl,
+            graph: graph
         )
 
         extDecl.references = [later, earlier]
@@ -87,14 +93,15 @@ final class DeterminismRegressionTest: XCTestCase {
         XCTAssertEqual(selected.usr, "class_earlier")
     }
 
-    func testBaseDeclarationUsesDeterministicSelection() {
+    func testBaseDeclarationUsesDeterministicSelection() throws {
         let graph = makeGraph()
 
         let overrideDecl = makeDeclaration(
             kind: .functionMethodInstance,
             name: "configure()",
             usr: "child_configure",
-            location: makeLocation("/tmp/child.swift", module: "Feature", line: 30)
+            location: makeLocation("/tmp/child.swift", module: "Feature", line: 30),
+            graph: graph
         )
         overrideDecl.modifiers.insert("override")
 
@@ -102,13 +109,15 @@ final class DeterminismRegressionTest: XCTestCase {
             kind: .functionMethodInstance,
             name: "configure()",
             usr: "base_later",
-            location: makeLocation("/tmp/later.swift", module: "BaseA", line: 50)
+            location: makeLocation("/tmp/later.swift", module: "BaseA", line: 50),
+            graph: graph
         )
         let baseEarlier = makeDeclaration(
             kind: .functionMethodInstance,
             name: "configure()",
             usr: "base_earlier",
-            location: makeLocation("/tmp/earlier.swift", module: "BaseB", line: 10)
+            location: makeLocation("/tmp/earlier.swift", module: "BaseB", line: 10),
+            graph: graph
         )
 
         let refToLater = makeReference(
@@ -117,7 +126,8 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "child_configure",
             name: "configure()",
             location: makeLocation("/tmp/ref_later.swift", module: "Feature", line: 1),
-            parent: baseLater
+            parent: baseLater,
+            graph: graph
         )
         let refToEarlier = makeReference(
             kind: .related,
@@ -125,18 +135,21 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "child_configure",
             name: "configure()",
             location: makeLocation("/tmp/ref_earlier.swift", module: "Feature", line: 2),
-            parent: baseEarlier
+            parent: baseEarlier,
+            graph: graph
         )
 
+        try graph.add(overrideDecl)
         graph.add(refToLater)
         graph.add(refToEarlier)
+        graph.indexingComplete()
 
         let (base, resolved) = graph.baseDeclaration(fromOverride: overrideDecl)
         XCTAssertTrue(resolved)
         XCTAssertEqual(base.usrs, ["base_earlier"])
     }
 
-    func testExternalOverrideRetainerRetainsWhenAnyMatchingRelatedReferenceIsExternal() {
+    func testExternalOverrideRetainerRetainsWhenAnyMatchingRelatedReferenceIsExternal() throws {
         let graph = makeGraph()
         let configuration = Configuration()
         let swiftVersion = makeSwiftVersion()
@@ -145,7 +158,8 @@ final class DeterminismRegressionTest: XCTestCase {
             kind: .functionMethodInstance,
             name: "configure()",
             usr: "feature_configure",
-            location: makeLocation("/tmp/feature.swift", module: "Feature", line: 100)
+            location: makeLocation("/tmp/feature.swift", module: "Feature", line: 100),
+            graph: graph
         )
         overrideDecl.modifiers.insert("override")
 
@@ -153,10 +167,11 @@ final class DeterminismRegressionTest: XCTestCase {
             kind: .functionMethodInstance,
             name: "configure()",
             usr: "internal_base",
-            location: makeLocation("/tmp/base.swift", module: "Core", line: 10)
+            location: makeLocation("/tmp/base.swift", module: "Core", line: 10),
+            graph: graph
         )
-        graph.add(internalBase)
-        graph.add(overrideDecl)
+        try graph.add(internalBase)
+        try graph.add(overrideDecl)
 
         let matchingInternal = makeReference(
             kind: .related,
@@ -164,7 +179,8 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "internal_base",
             name: "configure()",
             location: overrideDecl.location,
-            parent: overrideDecl
+            parent: overrideDecl,
+            graph: graph
         )
         let matchingExternal = makeReference(
             kind: .related,
@@ -172,7 +188,8 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "external_base",
             name: "configure()",
             location: overrideDecl.location,
-            parent: overrideDecl
+            parent: overrideDecl,
+            graph: graph
         )
         overrideDecl.related = [matchingInternal, matchingExternal]
 
@@ -180,7 +197,7 @@ final class DeterminismRegressionTest: XCTestCase {
         XCTAssertTrue(graph.isRetained(overrideDecl))
     }
 
-    func testAssetReferenceRetainerHandlesAllMatchingSourcesForClassName() {
+    func testAssetReferenceRetainerHandlesAllMatchingSourcesForClassName() throws {
         let graph = makeGraph()
         let configuration = Configuration()
 
@@ -188,20 +205,22 @@ final class DeterminismRegressionTest: XCTestCase {
             kind: .class,
             name: "FixtureController",
             usr: "fixture_controller",
-            location: makeLocation("/tmp/controller.swift", module: "UI", line: 1)
+            location: makeLocation("/tmp/controller.swift", module: "UI", line: 1),
+            graph: graph
         )
         let outletDecl = makeDeclaration(
             kind: .varInstance,
             name: "submitButton",
             usr: "fixture_controller_submit_button",
-            location: makeLocation("/tmp/controller.swift", module: "UI", line: 5)
+            location: makeLocation("/tmp/controller.swift", module: "UI", line: 5),
+            graph: graph
         )
         outletDecl.attributes.insert(DeclarationAttribute(name: "IBOutlet", arguments: nil))
         outletDecl.parent = classDecl
-        classDecl.declarations.insert(outletDecl)
+        classDecl.declarations.append(outletDecl)
 
-        graph.add(classDecl)
-        graph.add(outletDecl)
+        try graph.add(classDecl)
+        try graph.add(outletDecl)
         graph.markRedundantPublicAccessibility(classDecl, modules: ["UI"])
         graph.markRedundantPublicAccessibility(outletDecl, modules: ["UI"])
 
@@ -215,6 +234,7 @@ final class DeterminismRegressionTest: XCTestCase {
         )
         graph.add(xcDataModelRef)
         graph.add(ibRef)
+        graph.indexingComplete()
 
         AssetReferenceRetainer(graph: graph, configuration: configuration, swiftVersion: makeSwiftVersion()).mutate()
 
@@ -224,7 +244,7 @@ final class DeterminismRegressionTest: XCTestCase {
         XCTAssertNil(graph.redundantPublicAccessibility[outletDecl])
     }
 
-    func testProtocolConformanceReferenceBuilderDeterministicallySelectsSuperclassImplementation() {
+    func testProtocolConformanceReferenceBuilderDeterministicallySelectsSuperclassImplementation() throws {
         let graph = makeGraph()
         let configuration = Configuration()
 
@@ -232,61 +252,68 @@ final class DeterminismRegressionTest: XCTestCase {
             kind: .protocol,
             name: "Renderable",
             usr: "proto_renderable",
-            location: makeLocation("/tmp/proto.swift", module: "Core", line: 1)
+            location: makeLocation("/tmp/proto.swift", module: "Core", line: 1),
+            graph: graph
         )
         let requirement = makeDeclaration(
             kind: .functionMethodInstance,
             name: "configure()",
             usr: "proto_requirement_configure",
-            location: makeLocation("/tmp/proto.swift", module: "Core", line: 2)
+            location: makeLocation("/tmp/proto.swift", module: "Core", line: 2),
+            graph: graph
         )
         requirement.parent = proto
-        proto.declarations.insert(requirement)
+        proto.declarations.append(requirement)
 
         let conformingClass = makeDeclaration(
             kind: .class,
             name: "FeatureWidget",
             usr: "feature_widget",
-            location: makeLocation("/tmp/feature.swift", module: "Feature", line: 1)
+            location: makeLocation("/tmp/feature.swift", module: "Feature", line: 1),
+            graph: graph
         )
 
         let superLater = makeDeclaration(
             kind: .class,
             name: "BaseWidgetA",
             usr: "base_widget_a",
-            location: makeLocation("/tmp/base.swift", module: "BaseA", line: 40)
+            location: makeLocation("/tmp/base.swift", module: "BaseA", line: 40),
+            graph: graph
         )
         let superEarlier = makeDeclaration(
             kind: .class,
             name: "BaseWidgetB",
             usr: "base_widget_b",
-            location: makeLocation("/tmp/base.swift", module: "BaseB", line: 5)
+            location: makeLocation("/tmp/base.swift", module: "BaseB", line: 5),
+            graph: graph
         )
         let superLaterMethod = makeDeclaration(
             kind: .functionMethodInstance,
             name: "configure()",
             usr: "base_widget_a_configure",
-            location: makeLocation("/tmp/base_method.swift", module: "BaseA", line: 41)
+            location: makeLocation("/tmp/base_method.swift", module: "BaseA", line: 41),
+            graph: graph
         )
         superLaterMethod.parent = superLater
-        superLater.declarations.insert(superLaterMethod)
+        superLater.declarations.append(superLaterMethod)
 
         let superEarlierMethod = makeDeclaration(
             kind: .functionMethodInstance,
             name: "configure()",
             usr: "base_widget_b_configure",
-            location: makeLocation("/tmp/base_method.swift", module: "BaseB", line: 6)
+            location: makeLocation("/tmp/base_method.swift", module: "BaseB", line: 6),
+            graph: graph
         )
         superEarlierMethod.parent = superEarlier
-        superEarlier.declarations.insert(superEarlierMethod)
+        superEarlier.declarations.append(superEarlierMethod)
 
-        graph.add(proto)
-        graph.add(requirement)
-        graph.add(conformingClass)
-        graph.add(superLater)
-        graph.add(superEarlier)
-        graph.add(superLaterMethod)
-        graph.add(superEarlierMethod)
+        try graph.add(proto)
+        try graph.add(requirement)
+        try graph.add(conformingClass)
+        try graph.add(superLater)
+        try graph.add(superEarlier)
+        try graph.add(superLaterMethod)
+        try graph.add(superEarlierMethod)
 
         let conformsRef = makeReference(
             kind: .related,
@@ -294,7 +321,8 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "proto_renderable",
             name: "Renderable",
             location: makeLocation("/tmp/feature.swift", module: "Feature", line: 3),
-            parent: conformingClass
+            parent: conformingClass,
+            graph: graph
         )
         let inheritsLater = makeReference(
             kind: .related,
@@ -302,7 +330,8 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "base_widget_a",
             name: "BaseWidgetA",
             location: makeLocation("/tmp/feature.swift", module: "Feature", line: 4),
-            parent: conformingClass
+            parent: conformingClass,
+            graph: graph
         )
         let inheritsEarlier = makeReference(
             kind: .related,
@@ -310,12 +339,14 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "base_widget_b",
             name: "BaseWidgetB",
             location: makeLocation("/tmp/feature.swift", module: "Feature", line: 5),
-            parent: conformingClass
+            parent: conformingClass,
+            graph: graph
         )
 
         graph.add(conformsRef, from: conformingClass)
         graph.add(inheritsLater, from: conformingClass)
         graph.add(inheritsEarlier, from: conformingClass)
+        graph.indexingComplete()
 
         ProtocolConformanceReferenceBuilder(graph: graph, configuration: configuration, swiftVersion: makeSwiftVersion()).mutate()
 
@@ -331,26 +362,30 @@ final class DeterminismRegressionTest: XCTestCase {
             kind: .protocol,
             name: "BaseWidget",
             usr: "base_protocol",
-            location: makeLocation("/tmp/base_protocol.swift", module: "Core", line: 1)
+            location: makeLocation("/tmp/base_protocol.swift", module: "Core", line: 1),
+            graph: graph
         )
         let constrainingProtocol = makeDeclaration(
             kind: .protocol,
             name: "Configurable",
             usr: "constraining_protocol",
-            location: makeLocation("/tmp/configurable.swift", module: "Core", line: 1)
+            location: makeLocation("/tmp/configurable.swift", module: "Core", line: 1),
+            graph: graph
         )
         let requirementLater = makeDeclaration(
             kind: .functionMethodInstance,
             name: "configure()",
             usr: "requirement_later",
-            location: makeLocation("/tmp/configurable.swift", module: "A", line: 40)
+            location: makeLocation("/tmp/configurable.swift", module: "A", line: 40),
+            graph: graph
         )
         requirementLater.parent = constrainingProtocol
         let requirementEarlier = makeDeclaration(
             kind: .functionMethodInstance,
             name: "configure()",
             usr: "requirement_earlier",
-            location: makeLocation("/tmp/configurable.swift", module: "B", line: 5)
+            location: makeLocation("/tmp/configurable.swift", module: "B", line: 5),
+            graph: graph
         )
         requirementEarlier.parent = constrainingProtocol
         constrainingProtocol.declarations = [requirementLater, requirementEarlier]
@@ -359,16 +394,18 @@ final class DeterminismRegressionTest: XCTestCase {
             kind: .extensionProtocol,
             name: "BaseWidget",
             usr: "base_protocol_extension",
-            location: makeLocation("/tmp/base_protocol_ext.swift", module: "Feature", line: 1)
+            location: makeLocation("/tmp/base_protocol_ext.swift", module: "Feature", line: 1),
+            graph: graph
         )
         let member = makeDeclaration(
             kind: .functionMethodInstance,
             name: "configure()",
             usr: "extension_member_configure",
-            location: makeLocation("/tmp/base_protocol_ext.swift", module: "Feature", line: 2)
+            location: makeLocation("/tmp/base_protocol_ext.swift", module: "Feature", line: 2),
+            graph: graph
         )
         member.parent = extensionDecl
-        extensionDecl.declarations.insert(member)
+        extensionDecl.declarations.append(member)
 
         let extendsBaseProtocolRef = makeReference(
             kind: .normal,
@@ -376,7 +413,8 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "base_protocol",
             name: "BaseWidget",
             location: makeLocation("/tmp/base_protocol_ext.swift", module: "Feature", line: 1),
-            parent: extensionDecl
+            parent: extensionDecl,
+            graph: graph
         )
         let whereConstraintRef = makeReference(
             kind: .normal,
@@ -385,16 +423,17 @@ final class DeterminismRegressionTest: XCTestCase {
             name: "Configurable",
             location: makeLocation("/tmp/base_protocol_ext.swift", module: "Feature", line: 1),
             parent: extensionDecl,
-            role: .genericRequirementType
+            role: .genericRequirementType,
+            graph: graph
         )
         extensionDecl.references = [extendsBaseProtocolRef, whereConstraintRef]
 
-        graph.add(baseProtocol)
-        graph.add(constrainingProtocol)
-        graph.add(requirementLater)
-        graph.add(requirementEarlier)
-        graph.add(extensionDecl)
-        graph.add(member)
+        try graph.add(baseProtocol)
+        try graph.add(constrainingProtocol)
+        try graph.add(requirementLater)
+        try graph.add(requirementEarlier)
+        try graph.add(extensionDecl)
+        try graph.add(member)
         graph.add(extendsBaseProtocolRef, from: extensionDecl)
         graph.add(whereConstraintRef, from: extensionDecl)
 
@@ -406,63 +445,74 @@ final class DeterminismRegressionTest: XCTestCase {
 
     // MARK: - USR Conflict Resolution
 
-    func testDuplicateUSRResolutionKeepsEarlierDeclaration() {
+    func testDuplicateUSRResolutionThrowsOnConflict() throws {
         let graph = makeGraph()
 
         let earlier = makeDeclaration(
             kind: .class,
             name: "MyClass",
             usr: "shared_usr",
-            location: makeLocation("/tmp/a.swift", module: "A", line: 10)
+            location: makeLocation("/tmp/a.swift", module: "A", line: 10),
+            graph: graph
         )
         let later = makeDeclaration(
             kind: .class,
             name: "MyClass",
             usr: "shared_usr",
-            location: makeLocation("/tmp/b.swift", module: "B", line: 20)
+            location: makeLocation("/tmp/b.swift", module: "B", line: 20),
+            graph: graph
         )
 
-        // Add earlier first, then later. Before the fix, SourceGraph.add always
-        // overwrote allDeclarationsByUsr unconditionally, so `later` would win.
-        // After the fix, the declaration that sorts first is kept.
-        graph.add(earlier)
-        graph.add(later)
+        try graph.add(earlier)
+
+        XCTAssertThrowsError(try graph.add(later)) { error in
+            guard case let PeripheryError.sourceGraphIntegrityError(message) = error else {
+                return XCTFail("Unexpected error: \(error)")
+            }
+
+            XCTAssertTrue(message.contains("shared_usr"))
+        }
 
         XCTAssertIdentical(graph.declaration(withUsr: "shared_usr"), earlier)
     }
 
-    func testDuplicateUSRResolutionIsDeterministicRegardlessOfInsertionOrder() {
-        let earlier = makeDeclaration(
-            kind: .class,
-            name: "MyClass",
-            usr: "shared_usr",
-            location: makeLocation("/tmp/a.swift", module: "A", line: 10)
-        )
-        let later = makeDeclaration(
-            kind: .class,
-            name: "MyClass",
-            usr: "shared_usr",
-            location: makeLocation("/tmp/b.swift", module: "B", line: 20)
-        )
+    func testDuplicateUSRResolutionThrowsRegardlessOfInsertionOrder() throws {
+        let locA = makeLocation("/tmp/a.swift", module: "A", line: 10)
+        let locB = makeLocation("/tmp/b.swift", module: "B", line: 20)
 
         let graph1 = makeGraph()
-        graph1.add(earlier)
-        graph1.add(later)
+        let earlier1 = makeDeclaration(kind: .class, name: "MyClass", usr: "shared_usr", location: locA, graph: graph1)
+        let later1 = makeDeclaration(kind: .class, name: "MyClass", usr: "shared_usr", location: locB, graph: graph1)
+        try graph1.add(earlier1)
+
+        XCTAssertThrowsError(try graph1.add(later1)) { error in
+            guard case let PeripheryError.sourceGraphIntegrityError(message) = error else {
+                return XCTFail("Unexpected error: \(error)")
+            }
+
+            XCTAssertTrue(message.contains("shared_usr"))
+        }
 
         let graph2 = makeGraph()
-        graph2.add(later)
-        graph2.add(earlier)
-
-        // Both graphs should resolve to the same declaration (the earlier-sorting one),
-        // regardless of insertion order. Before the fix, graph1 would have `later` and
-        // graph2 would have `earlier`, producing different results from the same input.
-        XCTAssertIdentical(graph1.declaration(withUsr: "shared_usr"), earlier)
-        XCTAssertIdentical(graph2.declaration(withUsr: "shared_usr"), earlier)
+        let later2 = makeDeclaration(kind: .class, name: "MyClass", usr: "shared_usr", location: locB, graph: graph2)
+        let earlier2 = makeDeclaration(kind: .class, name: "MyClass", usr: "shared_usr", location: locA, graph: graph2)
+        try graph2.add(later2)
+
+        XCTAssertThrowsError(try graph2.add(earlier2)) { error in
+            guard case let PeripheryError.sourceGraphIntegrityError(message) = error else {
+                return XCTFail("Unexpected error: \(error)")
+            }
+
+            XCTAssertTrue(message.contains("shared_usr"))
+        }
+
+        XCTAssertIdentical(graph1.declaration(withUsr: "shared_usr"), earlier1)
+        XCTAssertIdentical(graph2.declaration(withUsr: "shared_usr"), later2)
     }
 
     // MARK: - AncestralReferenceEliminator with Same-Location Declarations
 
-    func testAncestralReferenceEliminatorWithSameLocationDeclarations() {
+    func testAncestralReferenceEliminatorWithSameLocationDeclarations() throws {
         // Models the real-world scenario: a struct and a macro-generated class exist at
         // the same source location. If a dangling reference (to the struct's own USR) is
         // associated with the struct itself (instead of the class), it becomes a
@@ -477,24 +527,27 @@ final class DeterminismRegressionTest: XCTestCase {
             kind: .struct,
             name: "FeatureRunner",
             usr: "feature_runner_struct",
-            location: makeLocation("/tmp/feature.swift", module: "Feature", line: 7)
+            location: makeLocation("/tmp/feature.swift", module: "Feature", line: 7),
+            graph: graph
         )
 
         let classDecl = makeDeclaration(
             kind: .class,
             name: "$FeatureRunner",
             usr: "feature_runner_class",
-            location: makeLocation("/tmp/feature.swift", module: "Feature", line: 7)
+            location: makeLocation("/tmp/feature.swift", module: "Feature", line: 7),
+            graph: graph
         )
         classDecl.parent = structDecl
-        structDecl.declarations.insert(classDecl)
+        structDecl.declarations.append(classDecl)
 
         // A reference TO the struct from an external declaration (the correct scenario).
         let externalParent = makeDeclaration(
             kind: .class,
             name: "AppRunner",
             usr: "app_runner",
-            location: makeLocation("/tmp/app.swift", module: "App", line: 1)
+            location: makeLocation("/tmp/app.swift", module: "App", line: 1),
+            graph: graph
         )
         let externalRef = makeReference(
             kind: .normal,
@@ -502,24 +555,26 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "feature_runner_struct",
             name: "FeatureRunner",
             location: makeLocation("/tmp/app.swift", module: "App", line: 5),
-            parent: externalParent
+            parent: externalParent,
+            graph: graph
         )
 
-        graph.add(structDecl)
-        graph.add(classDecl)
-        graph.add(externalParent)
+        try graph.add(structDecl)
+        try graph.add(classDecl)
+        try graph.add(externalParent)
         graph.add(externalRef, from: externalParent)
 
+        graph.indexingComplete()
+
         XCTAssertTrue(graph.hasReferences(to: structDecl))
 
-        graph.indexingComplete()
         AncestralReferenceEliminator(graph: graph, configuration: configuration, swiftVersion: makeSwiftVersion()).mutate()
 
         // The external reference should survive since it's not a self-reference.
         XCTAssertTrue(graph.hasReferences(to: structDecl))
     }
 
-    func testAncestralReferenceEliminatorRemovesSelfReferences() {
+    func testAncestralReferenceEliminatorRemovesSelfReferences() throws {
         // When a dangling reference is incorrectly associated with the declaration it
         // references (creating a self-reference), AncestralReferenceEliminator correctly
         // removes it. This test verifies the eliminator's behavior is correct — the fix
@@ -532,7 +587,8 @@ final class DeterminismRegressionTest: XCTestCase {
             kind: .struct,
             name: "FeatureRunner",
             usr: "feature_runner_struct",
-            location: makeLocation("/tmp/feature.swift", module: "Feature", line: 7)
+            location: makeLocation("/tmp/feature.swift", module: "Feature", line: 7),
+            graph: graph
         )
 
         // Self-reference: a reference to the struct's own USR, parented by the struct.
@@ -542,15 +598,17 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "feature_runner_struct",
             name: "FeatureRunner",
             location: makeLocation("/tmp/feature.swift", module: "Feature", line: 7),
-            parent: structDecl
+            parent: structDecl,
+            graph: graph
         )
 
-        graph.add(structDecl)
+        try graph.add(structDecl)
         graph.add(selfRef, from: structDecl)
 
+        graph.indexingComplete()
+
         XCTAssertTrue(graph.hasReferences(to: structDecl))
 
-        graph.indexingComplete()
         AncestralReferenceEliminator(graph: graph, configuration: configuration, swiftVersion: makeSwiftVersion()).mutate()
 
         // Self-reference should be eliminated, leaving the struct unreferenced.
@@ -559,7 +617,7 @@ final class DeterminismRegressionTest: XCTestCase {
 
     // MARK: - Protocol Conformance Inversion with Multiple Conformances
 
-    func testProtocolConformanceInversionHandlesMultipleConformances() {
+    func testProtocolConformanceInversionHandlesMultipleConformances() throws {
         // When multiple classes conform to the same protocol, the inversion must
         // process all conformances correctly. Before the batch mutation fix, graph
         // mutations during iteration could cause order-dependent skipping.
@@ -570,53 +628,59 @@ final class DeterminismRegressionTest: XCTestCase {
             kind: .protocol,
             name: "Runnable",
             usr: "proto_runnable",
-            location: makeLocation("/tmp/proto.swift", module: "Core", line: 1)
+            location: makeLocation("/tmp/proto.swift", module: "Core", line: 1),
+            graph: graph
         )
         let requirement = makeDeclaration(
             kind: .functionMethodInstance,
             name: "run()",
             usr: "proto_run",
-            location: makeLocation("/tmp/proto.swift", module: "Core", line: 2)
+            location: makeLocation("/tmp/proto.swift", module: "Core", line: 2),
+            graph: graph
         )
         requirement.parent = proto
-        proto.declarations.insert(requirement)
+        proto.declarations.append(requirement)
 
         let classA = makeDeclaration(
             kind: .class,
             name: "RunnerA",
             usr: "class_a",
-            location: makeLocation("/tmp/a.swift", module: "A", line: 1)
+            location: makeLocation("/tmp/a.swift", module: "A", line: 1),
+            graph: graph
         )
         let implA = makeDeclaration(
             kind: .functionMethodInstance,
             name: "run()",
             usr: "impl_a_run",
-            location: makeLocation("/tmp/a.swift", module: "A", line: 2)
+            location: makeLocation("/tmp/a.swift", module: "A", line: 2),
+            graph: graph
         )
         implA.parent = classA
-        classA.declarations.insert(implA)
+        classA.declarations.append(implA)
 
         let classB = makeDeclaration(
             kind: .class,
             name: "RunnerB",
             usr: "class_b",
-            location: makeLocation("/tmp/b.swift", module: "B", line: 1)
+            location: makeLocation("/tmp/b.swift", module: "B", line: 1),
+            graph: graph
         )
         let implB = makeDeclaration(
             kind: .functionMethodInstance,
             name: "run()",
             usr: "impl_b_run",
-            location: makeLocation("/tmp/b.swift", module: "B", line: 2)
+            location: makeLocation("/tmp/b.swift", module: "B", line: 2),
+            graph: graph
         )
         implB.parent = classB
-        classB.declarations.insert(implB)
+        classB.declarations.append(implB)
 
-        graph.add(proto)
-        graph.add(requirement)
-        graph.add(classA)
-        graph.add(implA)
-        graph.add(classB)
-        graph.add(implB)
+        try graph.add(proto)
+        try graph.add(requirement)
+        try graph.add(classA)
+        try graph.add(implA)
+        try graph.add(classB)
+        try graph.add(implB)
 
         // Related references from conforming implementations to the protocol requirement.
         let relatedA = makeReference(
@@ -625,7 +689,8 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "proto_run",
             name: "run()",
             location: implA.location,
-            parent: implA
+            parent: implA,
+            graph: graph
         )
         let relatedB = makeReference(
             kind: .related,
@@ -633,7 +698,8 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "proto_run",
             name: "run()",
             location: implB.location,
-            parent: implB
+            parent: implB,
+            graph: graph
         )
 
         // Conformance references from classes to protocol.
@@ -643,7 +709,8 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "proto_runnable",
             name: "Runnable",
             location: classA.location,
-            parent: classA
+            parent: classA,
+            graph: graph
         )
         let conformsB = makeReference(
             kind: .related,
@@ -651,7 +718,8 @@ final class DeterminismRegressionTest: XCTestCase {
             usr: "proto_runnable",
             name: "Runnable",
             location: classB.location,
-            parent: classB
+            parent: classB,
+            graph: graph
         )
 
         graph.add(relatedA, from: implA)
diff --git a/Tests/PeripheryTests/ObjcAccessibleRetentionTest.swift b/Tests/PeripheryTests/ObjcAccessibleRetentionTest.swift
index f4b895279..8062ee70b 100644
--- a/Tests/PeripheryTests/ObjcAccessibleRetentionTest.swift
+++ b/Tests/PeripheryTests/ObjcAccessibleRetentionTest.swift
@@ -1,8 +1,9 @@
 import SystemPackage
-@testable import TestShared
 import XCTest
 
 #if os(macOS)
+    @testable import TestShared
+
     final class ObjcAccessibleRetentionTest: FixtureSourceGraphTestCase {
         func testRetainsOptionalProtocolMethodImplementedInSubclass() throws {
             try XCTSkipIf(Self.swiftVersion.version.isVersion(lessThan: "6.3"), "Requires Swift >= 6.3")
diff --git a/Tests/PeripheryTests/ObjcAnnotatedRetentionTest.swift b/Tests/PeripheryTests/ObjcAnnotatedRetentionTest.swift
index a2f344343..bbf60631b 100644
--- a/Tests/PeripheryTests/ObjcAnnotatedRetentionTest.swift
+++ b/Tests/PeripheryTests/ObjcAnnotatedRetentionTest.swift
@@ -1,8 +1,9 @@
 import SystemPackage
-@testable import TestShared
 import XCTest
 
 #if os(macOS)
+    @testable import TestShared
+
     final class ObjcAnnotatedRetentionTest: FixtureSourceGraphTestCase {
         func testRetainsAnnotatedExtensionDeclarations() {
             analyze(retainObjcAnnotated: true) {
diff --git a/Tests/PeripheryTests/SourceGraphConflictTests.swift b/Tests/PeripheryTests/SourceGraphConflictTests.swift
new file mode 100644
index 000000000..eb7716f3f
--- /dev/null
+++ b/Tests/PeripheryTests/SourceGraphConflictTests.swift
@@ -0,0 +1,61 @@
+import Configuration
+import Shared
+@testable import SourceGraph
+import SystemPackage
+import XCTest
+
+final class SourceGraphConflictTests: XCTestCase {
+    func testAddThrowsOnUsrConflict() throws {
+        let graph = SourceGraph(
+            configuration: Configuration()
+        )
+        let usr = "s:4Test3fooyyF"
+
+        let firstDeclaration = makeDeclaration(
+            in: graph,
+            name: "foo",
+            usr: usr,
+            path: "/tmp/First.swift",
+            modules: ["FirstModule"]
+        )
+        let conflictingDeclaration = makeDeclaration(
+            in: graph,
+            name: "foo",
+            usr: usr,
+            path: "/tmp/Second.swift",
+            modules: ["SecondModule"]
+        )
+
+        try graph.add(firstDeclaration)
+
+        XCTAssertThrowsError(try graph.add(conflictingDeclaration)) { error in
+            guard case let PeripheryError.sourceGraphIntegrityError(message) = error else {
+                return XCTFail("Unexpected error: \(error)")
+            }
+
+            XCTAssertTrue(message.contains(usr))
+            XCTAssertTrue(message.contains("FirstModule"))
+            XCTAssertTrue(message.contains("SecondModule"))
+        }
+
+        XCTAssertTrue(graph.declaration(withUsr: usr) === firstDeclaration)
+    }
+
+    private func makeDeclaration(
+        in graph: SourceGraph,
+        name: String,
+        usr: String,
+        path: String,
+        modules: Set<String>
+    ) -> Declaration {
+        let file = SourceFile(path: FilePath(path), modules: modules)
+        let usrID = graph.usrInterner.intern(usr)
+        return Declaration(
+            name: name,
+            kind: .functionFree,
+            usrs: [usr],
+            usrIDs: [usrID],
+            location: Location(file: file, line: 1, column: 1)
+        )
+    }
+}
diff --git a/Tests/PeripheryTests/Syntax/UnusedParameterTest.swift b/Tests/PeripheryTests/Syntax/UnusedParameterTest.swift
index 5d9ad3a84..b533d8c72 100644
--- a/Tests/PeripheryTests/Syntax/UnusedParameterTest.swift
+++ b/Tests/PeripheryTests/Syntax/UnusedParameterTest.swift
@@ -1,5 +1,7 @@
 import Foundation
 @testable import SourceGraph
+import SwiftParser
+import SwiftSyntax
 @testable import SyntaxAnalysis
 @testable import TestShared
 import XCTest
@@ -114,6 +116,23 @@ final class UnusedParameterTest: XCTestCase {
         assertUsed(label: "param", name: "param", in: "myFunc(param:)")
     }
 
+    func testNestedFunctionAnalyzerPath() {
+        let sourceFile = SourceFile(path: testFixturePath, modules: ["UnusedParameterFixtures"])
+        let source = try! String(contentsOf: sourceFile.path.url, encoding: .utf8)
+        let syntax = Parser.parse(source: source)
+        let converter = SourceLocationConverter(fileName: sourceFile.path.string, tree: syntax)
+        let analyzer = UnusedParameterAnalyzer()
+        let paramsByFunction = analyzer.analyze(
+            file: sourceFile,
+            syntax: syntax,
+            locationConverter: converter,
+            parseProtocols: false
+        )
+
+        let unusedParams = paramsByFunction.first { $0.key.fullName == "innerFunc(param:)" }?.value
+        XCTAssertEqual(unusedParams?.map(\.name.text), ["param"])
+    }
+
     func testNestedVariable() {
         analyze()
         assertUsed(label: "param", name: "param", in: "myFunc(param:)")
diff --git a/Tests/Shared/SourceGraphTestCase.swift b/Tests/Shared/SourceGraphTestCase.swift
index 1177ed682..73b105f3e 100644
--- a/Tests/Shared/SourceGraphTestCase.swift
+++ b/Tests/Shared/SourceGraphTestCase.swift
@@ -26,7 +26,7 @@ open class SourceGraphTestCase: XCTestCase {
         swiftVersion = SwiftVersion(shell: shell)
         let configuration = Configuration()
         configuration.quiet = true
-        graph = SourceGraph(configuration: configuration, logger: logger)
+        graph = SourceGraph(configuration: configuration)
     }
 
     override open func tearDown() {
@@ -56,7 +56,7 @@ open class SourceGraphTestCase: XCTestCase {
             )
         }
 
-        graph = SourceGraph(configuration: configuration, logger: logger)
+        graph = SourceGraph(configuration: configuration)
         let pipeline = IndexPipeline(
             plan: newPlan,
             graph: SourceGraphMutex(graph: graph),
@@ -66,7 +66,7 @@ open class SourceGraphTestCase: XCTestCase {
         )
         try! pipeline.perform()
 
-        allIndexedDeclarations = graph.allDeclarations
+        allIndexedDeclarations = Set(graph.allDeclarations)
         try! SourceGraphMutatorRunner(
             graph: graph,
             logger: logger,
@@ -84,7 +84,7 @@ open class SourceGraphTestCase: XCTestCase {
         } else {
             guard let declaration = materialize(description, file: file, line: line) else { return }
 
-            if !Self.graph.usedDeclarations.contains(declaration) {
+            if !declaration.isUsed {
                 XCTFail("Expected declaration to be referenced: \(declaration)", file: file, line: line)
             }
 
@@ -303,7 +303,7 @@ open class SourceGraphTestCase: XCTestCase {
             switch scope {
             case let .declaration(declaration):
                 if result.contains(declaration) {
-                    result = declaration.declarations.union(declaration.unusedParameters)
+                    result = Set(declaration.declarations + declaration.unusedParameters)
                 }
             case let .module(module):
                 result = result.filter { $0.location.file.modules.contains(module) }
@@ -333,7 +333,7 @@ private extension [ScanResult] {
         }
     }
 
-    var redundantProtocolDeclarations: [Declaration: (references: Set<Reference>, inherited: Set<String>)] {
+    var redundantProtocolDeclarations: [Declaration: (references: [Reference], inherited: Set<String>)] {
         reduce(into: .init()) { result, scanResult in
             if case let .redundantProtocol(references, inherited) = scanResult.annotation {
                 result[scanResult.declaration] = (references, inherited)
diff --git a/baselines/bazel.json b/baselines/bazel.json
index 835493c5d..c9939d635 100644
--- a/baselines/bazel.json
+++ b/baselines/bazel.json
@@ -4,6 +4,9 @@
       "s:11SourceGraph0aB8DebuggerC",
       "s:13SystemPackage8FilePathV10ExtensionsE5chdir7closureyyyKXE_tKF",
       "s:14SyntaxAnalysis21UnusedParameterParserV5parse4file0F9ProtocolsSayAA8FunctionVG11SourceGraph0J4FileC_SbtKFZ",
+      "s:14SyntaxAnalysis21UnusedParameterParserV5parse4file6syntax17locationConverter0F9ProtocolsSayAA8FunctionVG11SourceGraph0M4FileC_05SwiftA00moA0VAO0m8LocationJ0CSbtFZ",
+      "s:14SyntaxAnalysis21UnusedParameterParserV5parse6syntaxSayAA8FunctionVG05SwiftA0010SourceFileA0V_tF",
+      "s:14SyntaxAnalysis23UnusedParameterAnalyzerC7analyze4file6syntax17locationConverter14parseProtocolsSDyAA8FunctionVShyAA0D0VGG11SourceGraph0N4FileC_05SwiftA00npA0VAR0n8LocationJ0CSbtF",
       "s:14SyntaxAnalysis8FunctionV8fullNameSSvp"
     ]
   }
diff --git a/baselines/linux-bazel.json b/baselines/linux-bazel.json
index f55df1d7e..f8df136df 100644
--- a/baselines/linux-bazel.json
+++ b/baselines/linux-bazel.json
@@ -7,6 +7,9 @@
       "s:13SystemPackage8FilePathV10ExtensionsE4globyShyACGSSFZ",
       "s:13SystemPackage8FilePathV10ExtensionsE5chdir7closureyyyKXE_tKF",
       "s:14SyntaxAnalysis21UnusedParameterParserV5parse4file0F9ProtocolsSayAA8FunctionVG11SourceGraph0J4FileC_SbtKFZ",
+      "s:14SyntaxAnalysis21UnusedParameterParserV5parse4file6syntax17locationConverter0F9ProtocolsSayAA8FunctionVG11SourceGraph0M4FileC_05SwiftA00moA0VAO0m8LocationJ0CSbtFZ",
+      "s:14SyntaxAnalysis21UnusedParameterParserV5parse6syntaxSayAA8FunctionVG05SwiftA0010SourceFileA0V_tF",
+      "s:14SyntaxAnalysis23UnusedParameterAnalyzerC7analyze4file6syntax17locationConverter14parseProtocolsSDyAA8FunctionVShyAA0D0VGG11SourceGraph0N4FileC_05SwiftA00npA0VAR0n8LocationJ0CSbtF",
       "s:14SyntaxAnalysis8FunctionV8fullNameSSvp",
       "s:6Shared14SetupSelectionO",
       "s:6Shared17SetupGuideHelpersC6select8multipleAA0B9SelectionOSaySSG_tF",
diff --git a/baselines/linux.json b/baselines/linux.json
index 13418f45e..ee4ccd627 100644
--- a/baselines/linux.json
+++ b/baselines/linux.json
@@ -1,8 +1,6 @@
 {
   "v1": {
     "usrs": [
-      "import-TestShared-Tests/PeripheryTests/ObjcAccessibleRetentionTest.swift:2:1",
-      "import-TestShared-Tests/PeripheryTests/ObjcAnnotatedRetentionTest.swift:2:1",
       "s:11SourceGraph15ProjectFileKindO10extensionsSaySSGvp",
       "s:6Shared14SetupSelectionO",
       "s:6Shared17SetupGuideHelpersC6select8multipleAA0B9SelectionOSaySSG_tF",