From 49803c1f6938e5168b2cbfd223692539f1fc1297 Mon Sep 17 00:00:00 2001
From: ayeshakhalid192007-dev <ayeshakhalid192007@gmail.com>
Date: Mon, 20 Apr 2026 22:42:17 +0500
Subject: [PATCH 1/4] fix(integrations): strip UTF-8 BOM when reading agent
 context files

---
 src/specify_cli/integrations/base.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/specify_cli/integrations/base.py b/src/specify_cli/integrations/base.py
index 4c71b165e5..a3d8a42aa2 100644
--- a/src/specify_cli/integrations/base.py
+++ b/src/specify_cli/integrations/base.py
@@ -482,7 +482,7 @@ def upsert_context_section(
         )
 
         if ctx_path.exists():
-            content = ctx_path.read_text(encoding="utf-8")
+            content = ctx_path.read_text(encoding="utf-8-sig")
             start_idx = content.find(self.CONTEXT_MARKER_START)
             end_idx = content.find(
                 self.CONTEXT_MARKER_END,
@@ -547,7 +547,7 @@ def remove_context_section(self, project_root: Path) -> bool:
         if not ctx_path.exists():
             return False
 
-        content = ctx_path.read_text(encoding="utf-8")
+        content = ctx_path.read_text(encoding="utf-8-sig")
         start_idx = content.find(self.CONTEXT_MARKER_START)
         end_idx = content.find(
             self.CONTEXT_MARKER_END,

From 26eda3e0aca18214b1770c0037b53b7e18122d17 Mon Sep 17 00:00:00 2001
From: ayeshakhalid192007-dev <ayeshakhalid192007@gmail.com>
Date: Tue, 21 Apr 2026 01:23:30 +0500
Subject: [PATCH 2/4] test(integrations): add BOM regression tests for context
 file read/write

---
 tests/integrations/test_integration_claude.py | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/tests/integrations/test_integration_claude.py b/tests/integrations/test_integration_claude.py
index 153983dcf4..973a7a4e4a 100644
--- a/tests/integrations/test_integration_claude.py
+++ b/tests/integrations/test_integration_claude.py
@@ -1,5 +1,6 @@
 """Tests for ClaudeIntegration."""
 
+import codecs
 import json
 import os
 from unittest.mock import patch
@@ -74,6 +75,47 @@ def test_setup_upserts_context_section(self, tmp_path):
         assert "<!-- SPECKIT END -->" in content
         assert "read the current plan" in content
 
+    def test_upsert_context_section_strips_bom(self, tmp_path):
+        """Existing context file with UTF-8 BOM must be cleaned up on upsert."""
+        integration = get_integration("claude")
+        ctx_path = tmp_path / integration.context_file
+
+        # Write a file that starts with a UTF-8 BOM (as the old PowerShell script did)
+        bom = codecs.BOM_UTF8
+        ctx_path.write_bytes(bom + b"# CLAUDE.md\n\nSome existing content.\n")
+
+        manifest = IntegrationManifest("claude", tmp_path)
+        integration.upsert_context_section(tmp_path)
+
+        result = ctx_path.read_bytes()
+        assert not result.startswith(bom), "BOM must be stripped after upsert"
+        content = result.decode("utf-8")
+        assert "<!-- SPECKIT START -->" in content
+        assert "Some existing content." in content
+
+    def test_remove_context_section_strips_bom(self, tmp_path):
+        """remove_context_section must clean BOM from context file on Windows-authored files."""
+        integration = get_integration("claude")
+        ctx_path = tmp_path / integration.context_file
+
+        marker_content = (
+            "# CLAUDE.md\n\n"
+            "<!-- SPECKIT START -->\n"
+            "For additional context about technologies to be used, project structure,\n"
+            "shell commands, and other important information, read the current plan\n"
+            "<!-- SPECKIT END -->\n"
+        )
+        ctx_path.write_bytes(codecs.BOM_UTF8 + marker_content.encode("utf-8"))
+
+        result = integration.remove_context_section(tmp_path)
+
+        assert result is True
+        assert ctx_path.exists(), "File should exist (non-empty content remains)"
+        remaining = ctx_path.read_bytes()
+        assert not remaining.startswith(codecs.BOM_UTF8), "BOM must be stripped after remove"
+        assert b"<!-- SPECKIT" not in remaining
+        assert b"# CLAUDE.md" in remaining
+
     def test_ai_flag_auto_promotes_and_enables_skills(self, tmp_path):
         from typer.testing import CliRunner
         from specify_cli import app

From 02d550ab7ca31a3b1fc2c4ad02e0996ef3f64b95 Mon Sep 17 00:00:00 2001
From: ayeshakhalid192007-dev <ayeshakhalid192007@gmail.com>
Date: Tue, 21 Apr 2026 01:30:01 +0500
Subject: [PATCH 3/4] test(workflows): mock shutil.which in tests that assume
 CLI is absent

---
 tests/test_workflows.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/tests/test_workflows.py b/tests/test_workflows.py
index c972945d04..04477015c0 100644
--- a/tests/test_workflows.py
+++ b/tests/test_workflows.py
@@ -400,6 +400,7 @@ class TestCommandStep:
     """Test the command step type."""
 
     def test_execute_basic(self):
+        from unittest.mock import patch
         from specify_cli.workflows.steps.command import CommandStep
         from specify_cli.workflows.base import StepContext, StepStatus
 
@@ -413,7 +414,8 @@ def test_execute_basic(self):
             "command": "speckit.specify",
             "input": {"args": "{{ inputs.name }}"},
         }
-        result = step.execute(config, ctx)
+        with patch("specify_cli.workflows.steps.command.shutil.which", return_value=None):
+            result = step.execute(config, ctx)
         assert result.status == StepStatus.FAILED
         assert result.output["command"] == "speckit.specify"
         assert result.output["integration"] == "claude"
@@ -474,6 +476,7 @@ def test_options_merge(self):
 
     def test_dispatch_not_attempted_without_cli(self):
         """When the CLI tool is not installed, step should fail."""
+        from unittest.mock import patch
         from specify_cli.workflows.steps.command import CommandStep
         from specify_cli.workflows.base import StepContext, StepStatus
 
@@ -488,7 +491,8 @@ def test_dispatch_not_attempted_without_cli(self):
             "command": "speckit.specify",
             "input": {"args": "{{ inputs.name }}"},
         }
-        result = step.execute(config, ctx)
+        with patch("specify_cli.workflows.steps.command.shutil.which", return_value=None):
+            result = step.execute(config, ctx)
         assert result.status == StepStatus.FAILED
         assert result.output["dispatched"] is False
         assert result.error is not None
@@ -566,6 +570,7 @@ class TestPromptStep:
     """Test the prompt step type."""
 
     def test_execute_basic(self):
+        from unittest.mock import patch
         from specify_cli.workflows.steps.prompt import PromptStep
         from specify_cli.workflows.base import StepContext, StepStatus
 
@@ -579,7 +584,8 @@ def test_execute_basic(self):
             "type": "prompt",
             "prompt": "Review {{ inputs.file }} for security issues",
         }
-        result = step.execute(config, ctx)
+        with patch("specify_cli.workflows.steps.prompt.shutil.which", return_value=None):
+            result = step.execute(config, ctx)
         assert result.status == StepStatus.FAILED
         assert result.output["prompt"] == "Review auth.py for security issues"
         assert result.output["integration"] == "claude"
@@ -1311,6 +1317,7 @@ def test_load_not_found(self, project_dir):
             engine.load_workflow("nonexistent")
 
     def test_execute_simple_workflow(self, project_dir):
+        from unittest.mock import patch
         from specify_cli.workflows.engine import WorkflowEngine, WorkflowDefinition
         from specify_cli.workflows.base import RunStatus
 
@@ -1333,7 +1340,8 @@ def test_execute_simple_workflow(self, project_dir):
 """
         definition = WorkflowDefinition.from_string(yaml_str)
         engine = WorkflowEngine(project_dir)
-        state = engine.execute(definition, {"name": "login"})
+        with patch("specify_cli.workflows.steps.command.shutil.which", return_value=None):
+            state = engine.execute(definition, {"name": "login"})
 
         assert state.status == RunStatus.FAILED
         assert "step-one" in state.step_results

From 7d88b8a8224294d68fabcff32356f7571b6b7011 Mon Sep 17 00:00:00 2001
From: ayeshakhalid192007-dev <ayeshakhalid192007@gmail.com>
Date: Tue, 21 Apr 2026 01:37:45 +0500
Subject: [PATCH 4/4] test(integrations): remove unused manifest variable in
 BOM test

---
 tests/integrations/test_integration_claude.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/integrations/test_integration_claude.py b/tests/integrations/test_integration_claude.py
index 973a7a4e4a..72e73bb02b 100644
--- a/tests/integrations/test_integration_claude.py
+++ b/tests/integrations/test_integration_claude.py
@@ -84,7 +84,6 @@ def test_upsert_context_section_strips_bom(self, tmp_path):
         bom = codecs.BOM_UTF8
         ctx_path.write_bytes(bom + b"# CLAUDE.md\n\nSome existing content.\n")
 
-        manifest = IntegrationManifest("claude", tmp_path)
         integration.upsert_context_section(tmp_path)
 
         result = ctx_path.read_bytes()