Remove coverage

.editorconfig

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+# EditorConfig: https://editorconfig.org
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.md]
+trim_trailing_whitespace = false
+
+[*.json]
+indent_size = 2
+
+[*.{yml,yaml}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

.github/agents/code.agent.md

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+---
+name: Code
+description: Expert TypeScript developer for lxDIG-MCP. Implements features, fixes bugs, and refactors code following the two-phase builder pattern.
+tools: [edit, execute, read, search, vscode, todo]
+model: Claude Sonnet 4.6 (copilot)
+argument-hint: Describe what to implement, the bug to fix, or the refactor to perform
+handoffs:
+  - label: Run tests
+    agent: test
+    prompt: Run the tests for the code I just changed and report any failures.
+    send: true
+  - label: Review changes
+    agent: review
+    prompt: Review the code changes I just made for correctness, patterns, and architecture compliance.
+    send: true
+---
+
+# Code Agent — lxDIG-MCP
+
+Expert TypeScript developer for lxDIG-MCP. Implements features, fixes bugs, and refactors code.
+
+## Rules
+
+- Run `npx tsc --noEmit` after every code change
+- Run `npx vitest run` after test changes — all 506 tests must pass
+- Never modify Cypher query strings without explicit instruction
+- Use `nodeStmts.push()` for node MERGEs, `edgeStmts.push()` for edges in builder.ts
+- ESM imports in source use NO `.js` extension — the build script adds them
+- Always use absolute paths for FILE node `path` property
+
+## Key Files
+
+- `src/graph/builder.ts` — translates parsed code → `BuildResult { nodes, edges }`
+- `src/graph/orchestrator.ts` — parse → build → execute → index pipeline
+- `src/graph/client.ts` — Memgraph client with circuit breaker + chunked batches
+- `src/tools/handlers/` — 11 handler files for 39 MCP tools
+
+## Test Patterns
+
+```typescript
+import { describe, it, expect, vi } from "vitest";
+// Mock memgraph: { isConnected: vi.fn().mockReturnValue(false), executeBatch: vi.fn().mockResolvedValue([]) }
+// Cleanup: fs.rmSync(root, { recursive: true, force: true })
+```

.github/agents/plan.agent.md

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+---
+name: Plan
+description: Architecture planner for lxDIG-MCP. Analyzes impact and creates structured implementation plans for the two-phase build pipeline and beyond.
+tools: [read, search]
+model: Claude Opus 4.6 (copilot)
+argument-hint: Describe the feature, bug, or architectural change you want a plan for
+handoffs:
+  - label: Implement this plan
+    agent: Code
+    prompt: Implement the plan we just created, following all the steps in order.
+    send: true
+---
+
+# Plan Agent — lxDIG-MCP
+
+Architecture planner for lxDIG-MCP. Analyzes impact and creates structured implementation plans.
+
+## Planning Workflow
+
+1. Read `plan/BUILD_PIPELINE_PROPOSAL.md` for active roadmap (37 tasks, Phases A-E)
+2. Read `plan/ROADMAP.md` for prioritized tiers
+3. Check `plan/BUG_LIST_CONSOLIDATED.md` for known issues (55 bugs)
+4. Check `plan/PHASE-A-BUILDER-REFACTOR.md` for completed phase template
+
+## Plan Document Template
+
+```markdown
+# Phase X — <Title>
+## Current State (what exists today)
+## Target State (what we want)
+## Affected Files & Tests
+## Execution Steps (numbered, with verification)
+## Completion Criteria (checkboxes)
+```
+
+## Architecture Layers
+
+```
+MCP Tools (39) → Engines (6) → Orchestrator → Builder → Client → Memgraph
+                                     ↓
+                              EmbeddingEngine → QdrantManager → Qdrant
+```
+
+## Active Status
+
+- Phase A: ✅ Builder returns `BuildResult { nodes, edges }`
+- Phase B: ⏳ Orchestrator two-phase execution (nodes-first, then edges)
+- Phase C: ⏳ Test→symbol edge accuracy
+- Phase D: ⏳ Validation suite
+- Phase E: ⏳ Qdrant sync reliability

.github/agents/review.agent.md

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+---
+name: review
+description: Code reviewer for lxDIG-MCP. Checks correctness, patterns, and architecture compliance against the two-phase builder pipeline rules.
+tools: [read, search]
+model: Claude Sonnet 4.6 (copilot)
+argument-hint: Point to the file or PR diff to review, or describe the change
+handoffs:
+  - label: Fix issues found
+    agent: Code
+    prompt: Fix the issues identified in the code review, following the architecture rules.
+    send: true
+---
+
+# Review Agent — lxDIG-MCP
+
+Code reviewer for lxDIG-MCP. Checks correctness, patterns, and architecture compliance.
+
+## Review Checklist
+
+1. **BuildResult pattern** — builder methods return `{ nodes, edges }`, never flat arrays
+2. **Cypher safety** — all user input via `$params`, never string interpolation
+3. **Circuit breaker** — bulk writes use `BULK_CHUNK_SIZE=1500`, `CIRCUIT_BREAKER_BULK_THRESHOLD=50`
+4. **ESM compliance** — no `.js` in source imports, no `require()`, no `__dirname`
+5. **Test coverage** — new logic has tests in `__tests__/*.test.ts`
+6. **Type safety** — no `any` without justification, strict null checks
+
+## Architecture Rules
+
+- Parsers produce `ParsedFile` → Builder produces `BuildResult` → Orchestrator executes
+- Graph writes always go through `MemgraphClient.executeBatch()`
+- Vector operations go through `EmbeddingEngine` → `QdrantManager`
+- Tools are registered in `src/tools/registry.ts`, handlers in `src/tools/handlers/`
+
+## Anti-Patterns to Flag
+
+- `statements.push()` without classifying node vs edge
+- Direct Memgraph session usage outside `client.ts`
+- Hardcoded connection strings (should use `env.ts`)
+- Missing `try/finally` around bulk mode toggle

.github/agents/test.agent.md

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+---
+name: test
+description: Test author for lxDIG-MCP. Creates and fixes vitest tests following established mocking and assertion patterns.
+tools: [edit, execute, read, search]
+model: Claude Sonnet 4.6 (copilot)
+argument-hint: Describe the module or function to test, or paste a failing test output
+handoffs:
+  - label: Fix production code
+    agent: Code
+    prompt: The tests are failing due to a bug in production code. Fix the underlying implementation.
+    send: true
+  - label: Review tests
+    agent: review
+    prompt: Review the tests I just wrote for correctness and coverage completeness.
+    send: true
+---
+
+# Test Agent — lxDIG-MCP
+
+Test author for lxDIG-MCP. Creates and fixes vitest tests.
+
+## Commands
+
+- Run all: `npx vitest run`
+- Run one file: `npx vitest run src/path/__tests__/file.test.ts`
+- Type check: `npx tsc --noEmit`
+
+## Conventions
+
+- Framework: vitest (`describe`, `it`, `expect`, `vi.fn()`, `vi.mock()`)
+- Location: `src/<module>/__tests__/<name>.test.ts`
+- Current count: 506 tests across 29 files
+
+## Mocking Patterns
+
+```typescript
+// Memgraph client mock
+const mockClient = {
+  isConnected: vi.fn().mockReturnValue(false),
+  executeBatch: vi.fn().mockResolvedValue([]),
+  executeQuery: vi.fn().mockResolvedValue({ records: [] }),
+};
+
+// Builder result
+const { nodes, edges } = builder.buildFromParsedFile(parsed);
+const stmts = [...nodes, ...edges]; // only when order doesn't matter
+
+// Temp directory cleanup
+afterEach(() => fs.rmSync(root, { recursive: true, force: true }));
+```
+
+## Assertion Patterns
+
+```typescript
+// Cypher statement validation
+expect(stmts.some(s => s.query.includes("MERGE"))).toBe(true);
+expect(nodes.every(s => !s.query.match(/MATCH.*MERGE.*\[/))).toBe(true);
+
+// BuildResult structure
+expect(nodes.length + edges.length).toBe(totalCount);
+```