bug: daemon unresponsive after index completes on macOS — gortex daemon stop and MCP tools hang

[lijiacheng-jc]

Describe the bug

After gortex daemon start --detach + gortex track completes indexing on a large workspace (~100 services, 20,000+ source files), the daemon becomes unresponsive:

• gortex daemon stop hangs indefinitely (tested up to 5 minutes)
• All MCP tools and gortex call CLI commands hang
• ~/.gortex/cache/daemon.sock exists but is 0 bytes — no listener
• Process shows state UN (uninterruptible sleep) in ps aux

To Reproduce

1. macOS 26.5 arm64 (Apple M1 Pro, 16 GB RAM)
2. Gortex v0.61.4+447e66c (go1.26.4)
3. gortex daemon start --detach
4. gortex track /path/to/workspace (~20,000 source files)
5. Wait for indexing to finish (~10-15 min)
6. gortex daemon stop → hangs
7. gortex call search_text --arg query="test" --arg limit=5 → hangs

Expected behavior

gortex daemon stop responds within seconds. CLI and MCP tools return results normally.

Environment

• OS: macOS 26.5 arm64 (Apple M1 Pro, 16 GB RAM)
• Gortex: v0.61.4+447e66c (go1.26.4)

Additional context

• Reproduced 5+ times with a clean store each time
• Cannot confirm whether this is a v0.61.4 regression — we were debugging other issues on earlier versions and may never have completed a full index before upgrading
• kill -9 + restart leads to store corruption, compounding the problem
• Similar to Windows: MCP tools hang after index reports ready #300 (reported on Windows) but observed on macOS
• Related: bug: index_health reports 100% while the graph holds orphan nodes, a deleted-repo ghost, and ~30% purgeable edges #311, bug: per-repo .gortex.yaml changes require a full daemon restart — daemon reload drops the workspace-config cache but nothing re-reads it; re-track short-circuits #320, log noise: periodic PASSIVE WAL checkpoint reports "checkpoint incomplete ... context deadline exceeded" with all-zero stats during bulk indexing #325