Dhanji R. Prasanna 39e586982c feat: Externalize research tool as embedded skill ...

Replaces the built-in research/research_status tools with a portable
skill-based approach:

- Add embedded skills infrastructure (skills compiled into binary)
- Add repo-local skills/ directory support (highest priority)
- Create research skill with SKILL.md and g3-research shell script
- Script extraction to .g3/bin/ with version tracking
- Filesystem-based handoff via .g3/research/<id>/status.json
- Remove PendingResearchManager and all research tool code
- Update system prompt to reference skill instead of tool

Benefits:
- No special tool infrastructure needed (just shell + read_file)
- Context-efficient (reports stay on disk until needed)
- Crash-resilient (state persisted to filesystem)
- Portable (skill can be overridden per-workspace)

Breaking change: research tool calls now return a deprecation message
pointing to the research skill.

2026-02-05 13:23:26 +11:00

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