Persisted isolated subagents created their fresh JSONL session through
SessionManager.open(), which fell back to getProjectDir() when the file had no
header. createAgentSession still received the isolated worktree cwd, but built-in
tools resolve paths through sessionManager.getCwd(), so file tools could target
the parent repository while patch capture saw no isolated delta.
Allow SessionManager.open() to take an initial cwd for empty/missing session
files and pass the isolated worktree cwd from task execution. Non-empty resumes
still use the persisted header cwd. Add regression coverage asserting persisted
isolated subagent sessions expose the worktree cwd through their session
manager.
Bin Jin
41b9567525