Make worktree isolation opt-in — default to simple branch strategy

[xliry]

Problem

Worktree isolation adds 289 lines of complexity (worktree.ts) and causes real problems:

• Agent gets confused about which directory it's in (worktree vs main workspace)
• lota-1 Task Phase 1: Vue 3 + Vite project scaffold with Tailwind CSS 4, Pinia, Vue Router #148 spent ~30 bash commands navigating between ~/kid-club-vue and ~/kid-club-vue/.worktrees/lota-1
• Merge conflicts leave conflict markers in files (Task Phase 5: Period detail view with KPI cards, monthly tabs, and transitions #152: TS1185: Merge conflict marker encountered)
• When agent times out, all worktree work is lost (cleanup deletes everything)
• For single-agent-per-repo (the common case), worktrees are pure overhead

Worktrees only help when multiple agents work on the same repo simultaneously. But logs show agents typically work on different repos (lota-1 on kid-club-vue, lota-3 on bosphorusIre).

What to do

In src/daemon.ts, runClaude() function:

1. Make worktree creation conditional — only use worktrees when --worktree flag is passed
2. Default behavior (no flag): agent works directly in the workspace on a branch task-{id}-{agent}
3. The agent creates the branch, does work, commits, pushes the branch
4. Daemon merges the branch to main after completion (simple git merge + git push)
5. No worktree creation, no worktree cleanup, no path confusion

New default flow (no worktree):

1. cd <workspace>
2. git checkout -b task-{id}-{agent}
3. [agent does work]
4. git commit + git push origin task-{id}-{agent}
5. [daemon merges branch to main]

Opt-in worktree flow (with --worktree flag):

1. createWorktree() in <workspace>/.worktrees/<agent>
2. [agent works in worktree]
3. [daemon merges + cleans up worktree]

Files

• src/daemon.ts — make worktree conditional in runClaude()
• src/worktree.ts — keep the code but only call it when opt-in
• Add --worktree flag to parseArgs()

Acceptance

• Default: no worktrees, agent works on branch in workspace directly
• --worktree flag enables worktree isolation
• Agent no longer confused about directory paths
• Timeout doesn't lose work (branch still exists on remote)
• Build passes: npm run build

[xliry]

Plan

Changes to src/daemon.ts:

1. Add useWorktree: boolean to AgentConfig interface
2. Add --worktree flag to parseArgs() switch + help text
3. Add useWorktree to parseArgs() return
4. Add mergeBranch() helper — merges task branch → main without worktrees
5. Modify buildPrompt(): use config (drop _ prefix), add branch checkout instruction for non-worktree mode
6. Modify runClaude(): wrap worktree creation in if (config.useWorktree), add default-branch post-completion merge

No changes to src/worktree.ts — keep it as-is, just call it only when opted in.

Acceptance:

• Default (lota-agent): agent works in workspace on branch task-{id}-{agent}, daemon merges after
• --worktree: old worktree isolation behavior preserved
• npm run build passes

[xliry]

Completion Report

Made worktree isolation opt-in. Default behavior now uses a simple branch strategy — agent works directly in the workspace on branch task-{id}-{agent}, daemon merges to main after completion. Pass --worktree flag to restore the old isolation behavior.

Build passes (npm run build).

Modified: src/daemon.ts