Worktree-aware agent execution: add cwd to run_agent()

[chanakyav]

Parent Epic

Part of #52 — Parallel stacked workstreams

Summary

Add a cwd parameter to run_agent() so the copilot agent runs inside a git worktree directory instead of the repo root. Update all prompts to stop instructing the agent to create branches (the worktree already has the branch checked out).

Context

Today, run_agent() in agent.py does not pass cwd to subprocess.Popen(), so the agent inherits the orchestrator's working directory. With git worktrees, each task gets its own directory — the agent must run inside it.

Additionally, prompts currently tell the agent to git checkout -b <branch>, which is wrong in a worktree context (the branch already exists).

Changes

agent.py

• Add cwd parameter to run_agent() signature
• Pass cwd=cwd to subprocess.Popen()
• Default to None (current behavior) for backward compatibility

orchestrator.py

• BaseOrchestrator stores worktree path (from task record)
• Pass cwd=self.worktree_path to run_agent() calls in _run_agent_with_retry()
• _get_workspace_dirs() updated to scan from worktree path, not os.getcwd()
• Fix os.getcwd() usage in _do_resolve_comments() for .autopilot-fix-summary.json path

prompts.py

• implement_prompt(): Remove git checkout -b instruction when worktree is active; add You are already on branch <branch> context
• implement_on_existing_branch_prompt(): Same adjustment
• plan_and_implement_prompt(): Same adjustment
• Replace hardcoded git diff main with git diff <base_branch> (uses get_default_branch())

persistence.py

• Add worktree_path column to tasks table (nullable TEXT)
• Schema version bump + migration

Depends On

• Use git worktrees for parallel task isolation #28 (git worktree creation/cleanup lifecycle)

Testing

• run_agent() with cwd parameter passes it to subprocess
• Prompts omit git checkout -b when worktree context is set
• Orchestrator reads worktree path from task record
• .autopilot-fix-summary.json read from worktree path, not os.getcwd()

[chanakyav]

Architecture Note: File Placement

The cwd parameter addition to run_agent() stays in agent.py (it's a simple parameter passthrough to subprocess.Popen).

Prompt updates (removing git checkout -b, using get_default_branch() instead of hardcoded main) stay in prompts.py.

Orchestrator changes (passing cwd=self.worktree_path) are minimal touches to _run_agent_with_retry() in orchestrator.py.

[chanakyav]

Status: Deferred (depends on #28)

Deferred along with #28 (git worktrees). Since V1 of the chain feature uses git checkout instead of worktrees, the agent doesn't need an explicit cwd parameter — it inherits the working directory from the tmux session, which is always the repo root.

Removed from epic #52 sub-issues. Will be implemented if/when #28 is picked up.