fix(integrations): strip UTF-8 BOM when reading agent context files (#2283)

* fix(integrations): strip UTF-8 BOM when reading agent context files

* test(integrations): add BOM regression tests for context file read/write

* test(workflows): mock shutil.which in tests that assume CLI is absent

* test(integrations): remove unused manifest variable in BOM test

Author: ayeshakhalid192007-dev

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,

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 +75,46 @@ 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")
+
+        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

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