C:/Program Files/Git/compact does not clean up subagent directory, causing stale agent state in compacted sessions

Summary

When a session is compacted via /compact, the subagents/ directory (containing agent-*.meta.json and agent-*.jsonl files from all previously spawned agents) is not cleaned up. On session re-initialization, the harness loads these stale agent entries into an in-memory registry, causing cascading failures including the stop hook infinite loop reported in #58637.

Environment

• Windows 10, Claude Code v2.1.131
• Session that spawned 18 subagents across ~12 turns before compaction

Steps to Reproduce

1. Spawn ≥6 background subagents across multiple turns (e.g., a large ingest pipeline)
2. Wait for all subagents to complete successfully
3. Run /compact
4. Observe: subagents/ directory still contains all 18 agent-*.meta.json + agent-*.jsonl files
5. After compaction, the stop hook permanently reports "Background subagents are still running"

Expected Behavior

/compact should either:

1. Delete all files in subagents/ (since the session state is being reset), OR
2. Mark all agent entries with "status": "completed" or "status": "discarded"

Actual Behavior

• All agent-*.meta.json files persist unchanged with no status field
• All agent-*.jsonl transcript files persist
• The harness loads these into an in-memory registry on session init and never re-reads from disk
• Disk cleanup post-compaction has zero effect because the registry is memory-resident

Impact

Combined with the registry state-sync bug (#58637), this means a session that hits the subagent limit becomes permanently broken — even /compact cannot recover it. Users must kill the process and restart.

Related

• #58637 — Stop hook false positive from zombie agent IDs
• #48470 — Stop hook false-positive: stale subagent IDs

Suggested fix priority

This is a smaller, more targeted fix than the full registry sync issue. Cleaning subagents/ on compaction (or adding a "discarded" status) would prevent the compacted-session variant of #58637 even without fixing the underlying registry.