Startup Conflict Prompt ("Uncommitted changes detected")¶

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Problem¶

Every time amplihack starts, you see this prompt:

Uncommitted changes detected in .claude/
The following files have uncommitted changes:
  .claude/context/PROJECT.md
  .claude/context/PROJECT.md.bak
How to proceed? [Y/t/n]:

Cause¶

This happens when framework-generated files (PROJECT.md, PROJECT.md.bak) have uncommitted changes in your ~/.amplihack repository. These files are auto-generated by the framework on each startup, so the prompt fires every time.

Fix¶

Option 1: Set auto_update preference to "always" (recommended)

Run this in a Claude Code session:

/amplihack:customize set auto_update always

Or manually edit ~/.amplihack/.claude/context/USER_PREFERENCES.md and set:

### Auto Update

always

This tells amplihack to skip all startup prompts and auto-approve overwrites.

Option 2: Commit the generated files

cd ~/.amplihack
git add .claude/context/PROJECT.md .claude/context/PROJECT.md.bak
git commit -m "chore: commit auto-generated PROJECT.md files"

Option 3: Add to .gitignore

echo ".claude/context/PROJECT.md" >> ~/.amplihack/.gitignore
echo ".claude/context/PROJECT.md.bak" >> ~/.amplihack/.gitignore

Background¶

The auto_update preference controls two behaviors:

1. Version mismatch updates: Auto-updates .claude/ directory when a new amplihack version is installed
2. Conflict prompt: Auto-approves overwrites when uncommitted changes are detected in .claude/ essential directories

See Issue #2256 for details.