Observer writes observations.jsonl relative to cwd instead of git root

[marcoamtz]

When a subagent changes the working directory (e.g., during file moves with cd), the observer agent creates .claude/homunculus/observations.jsonl relative to the current directory instead of the git root. This results in stray .claude/ directories nested inside source code folders.

Steps to reproduce:

Run a session that uses cd into a subdirectory (e.g., during a file reorganization)
The background observer creates .claude/homunculus/observations.jsonl in that subdirectory

Expected:

The observer should resolve the .claude/ path using git rev-parse --show-toplevel (or equivalent) to always write to the project root.

Version: 2.0.0-alpha (commit 59b6520)

[proofoftom]

Hit a related symptom on Claude Code (macOS). Spawned an observer subagent pointed at a chunk file with a project-relative path (.claude/homunculus/chunks/chunk-06.jsonl). The subagent ran from a working directory it didn't recognize and concluded:

The chunk file doesn't exist either. Since the homunculus observer system and the chunk-06.jsonl file don't exist in this environment, I cannot complete this task. The infrastructure for processing observations and creating instincts hasn't been set up yet.
Expected directory structure:

• /Users/proofoftom/.claude/homunculus/ (does not exist)

It looked at ~/.claude/homunculus/ (user home) instead of <project>/.claude/homunculus/. After re-spawning with the absolute project path baked into the prompt, it worked fine.

Same root cause as this issue: the observer agent's view of "where homunculus lives" doesn't pin to git root (or the parent's cwd) reliably across spawn contexts. Worth pinning to git rev-parse --show-toplevel || pwd early in the agent so subagents inherit the right base path.

(Plugin 2.0.0-alpha, Claude Code on Darwin 24.6.0.)