Fix: Preserve user content when generating rules

[MS-Jahan]

Fix: Preserve user content when generating rules

Problem

The codegenome rules command was destructively overwriting existing files, causing loss of user customizations:

• .windsurfrules: Users' Windsurf IDE rules replaced completely
• AGENTS.md: Important agent instructions lost
• .github/copilot-instructions.md: Custom Copilot settings overwritten
• .cursor/rules/codegenome-knowledge-graph.mdc: Cursor rules reset

This made the rules command unsafe to run more than once and prevented users from adding their own customizations alongside CodeGenome instructions.

Solution

Modified write_rule() in src/codegenome/rules.py to use section markers for non-destructive content management:

<!-- BEGIN CODEGENOME MCP INTEGRATION -->
[CodeGenome-managed content here]
<!-- END CODEGENOME MCP INTEGRATION -->

Behavior

1. New files: Creates file with CodeGenome content wrapped in markers
2. Existing files without section: Appends CodeGenome section with markers (preserves all existing content)
3. Existing files with section: Replaces only the CodeGenome section (preserves user content before and after)

Example

Before (destructive):

# My Custom Rules
User content here

Running codegenome rules would replace everything with CodeGenome content.

After (non-destructive):

# My Custom Rules
User content here

<!-- BEGIN CODEGENOME MCP INTEGRATION -->
# CodeGenome Knowledge Graph (MCP)
[CodeGenome instructions]
<!-- END CODEGENOME MCP INTEGRATION -->

User content preserved! Running the command again only updates the CodeGenome section.

Benefits

✓ Safe to run multiple times - updates don't destroy customizations
✓ Users can add custom rules - above or below CodeGenome section
✓ Backwards compatible - works with existing files
✓ Automatic backup - creates .backup if file is unreadable

Testing

Added comprehensive test suite in tests/test_rules_append.py:

• ✓ New file creation with markers
• ✓ Appending to existing files (preserves user content)
• ✓ Replacing existing CodeGenome section
• ✓ Multiple updates to same file
• ✓ Whitespace preservation

All tests pass ✓

Files Changed

• src/codegenome/rules.py - Modified write_rule() function (42 lines added)
• tests/test_rules_append.py - New test suite (134 lines)

Migration

No migration needed. Existing generated files will work as-is. Next time users run codegenome rules, it will append the section with markers instead of overwriting.