Prevents two bugs in the resumeForCommit flow:
1. Agent navigated to main repo instead of worktree due to relative paths
in commit prompt — now uses absolute paths from getDirtyWorktreePaths
2. git add -A staged unrelated files (screenshots, other agents' work) —
now uses git add -u to only stage tracked modified files
- Track worktree removal success in autoCleanupAfterCompletion() instead of
always returning removed:true when removeAgentWorktrees() throws
- Add removeAgentBranches() call to auto-cleanup path (agent/* branches were
never cleaned after completion)
- Add filesystem cleanup (worktrees, branches, logs) to dismiss() to prevent
resource leaks until next server restart
Move src/ → apps/server/ and packages/web/ → apps/web/ to adopt
standard monorepo conventions (apps/ for runnable apps, packages/
for reusable libraries). Update all config files, shared package
imports, test fixtures, and documentation to reflect new paths.
Key fixes:
- Update workspace config to ["apps/*", "packages/*"]
- Update tsconfig.json rootDir/include for apps/server/
- Add apps/web/** to vitest exclude list
- Update drizzle.config.ts schema path
- Fix ensure-schema.ts migration path detection (3 levels up in dev,
2 levels up in dist)
- Fix tests/integration/cli-server.test.ts import paths
- Update packages/shared imports to apps/server/ paths
- Update all docs/ files with new paths
