Fix: Exclude .factory/ directory from git commits

Summary

Prevent Factory internal state files (logs, conversation history, state files) from being committed to project repositories by ensuring .factory/ is always excluded from git operations.

Problem (Bug #4 from #167)

During Stage 2 execution, PR #19 accidentally included 86 Factory internal files:

• .factory/logs/2025-11-04_21-49-13_sprint/prompts/msg_*.txt (65+ prompt/response files)
• .factory/current-sprint.json
• Full conversation history from all tickets

This caused Code Reviewer to review the wrong ticket - it read Ticket #1's conversation logs and echoed that instead of reviewing Ticket #3's actual code changes.

Impact:

• Code Reviewer sees incorrect context (other tickets' conversations)
• PRs become massive (1.5MB for simple config changes)
• Exposes internal Factory operations in public repos
• Token waste (Code Reviewer reads logs instead of code)

Root Cause

1. .factory/ directory NOT in project's .gitignore
2. git_add tool stages everything matching patterns without filtering
3. Developer agent doesn't validate staged files before committing

Solution

Primary Fix: git_add tool should auto-exclude .factory/

Update src/factory/agents/tools.py:

def git_add(files: list[str], project_path: str) -> dict:
    # ... existing validation ...

    # IMPORTANT: Never commit Factory internal state
    # Filter out .factory/ paths before staging
    filtered_files = []
    for file in files:
        if not file.startswith('.factory/') and '/.factory/' not in file:
            filtered_files.append(file)
        else:
            logger.warning(f"Skipping Factory internal file: {file}")

    if not filtered_files:
        return {"success": False, "error": "No files to add after filtering"}

    # Stage filtered files
    subprocess.run(["git", "add"] + filtered_files, cwd=project_path, ...)

Secondary Fix: CLI ensures .factory/ in .gitignore

At sprint start (Stage 2), verify .factory/ is in project's .gitignore:

# In cli.py, before execute_stage_2():
gitignore_path = project_dir / ".gitignore"
if gitignore_path.exists():
    content = gitignore_path.read_text()
    if '.factory/' not in content:
        # Append .factory/ to gitignore
        with open(gitignore_path, 'a') as f:
            f.write('\n# Factory internal state (do not commit)\n.factory/\n')

Test Plan

1. Unit test for git_add filtering:

• Create test files including .factory/logs/test.txt
• Call git_add(['.factory/logs/test.txt', 'src/index.ts'])
• Verify only src/index.ts staged
• Verify warning logged for .factory/ file

1. E2E test:

• Start fresh sprint with test project
• Let Developer complete one ticket
• Check staged files for PR: should NOT include .factory/*
• Check .gitignore: should contain .factory/

1. Verify existing repos:

• Run CLI on existing project without .factory/ in .gitignore
• Verify CLI adds it automatically
• Verify no Factory files in subsequent commits

Acceptance Criteria

• [ ] git_add tool filters out all .factory/ paths
• [ ] Warning logged when Factory files are skipped
• [ ] CLI verifies/adds .factory/ to .gitignore at sprint start
• [ ] Unit tests for git_add filtering
• [ ] E2E test verifies no Factory files in PRs
• [ ] Documentation: .factory/ should never be committed
• [ ] Test on existing repo without .factory/ in .gitignore

Related Issues

• Fixes Bug #4 in #167
• Prevents Code Reviewer from seeing wrong context
• Reduces PR size and token usage

Priority

High - This causes Code Reviewer to malfunction and review wrong tickets.