Add Repository Intelligence Bootstrap: repo-bootstrap.sh, all 13 agents updated, docs, tests

- scripts/repo-bootstrap.sh: generic idempotent bootstrap tool (status/bootstrap/refresh)
  - creates .opencode/ with repo-context, architecture, build-and-test, conventions, deployment skills
  - relevance-based skill generation (only creates what the repo actually has)
  - staleness detection via .bootstrap-meta (key=value, SHA-256 fingerprints)
  - marker-based manual protection (never overwrites unmarked files)
  - accepts --root flag for explicit repo targeting

- scripts/test-repo-bootstrap.sh: 11 tests covering all 10 acceptance criteria
  - creation, idempotency, manual preservation, relevance detection
  - orchestrator/agent structural checks, staleness, genericness
  - install.sh workflow compatibility, malformed handling

- agents/orchestrator.md: first-class Repository Intelligence Bootstrap stage
  - 10-step workflow, ownership rules table, staleness signals
  - consumption rules, backward compatibility, fallback procedure

- All 12 subagent files: role-adapted Repository Intelligence section
  - architect: owns architecture skill
  - builder/tester: own build-and-test skill (shared)
  - explorer: owns repo-context skill
  - maintainer: owns conventions skill + audits .opencode/
  - reviewer: validates consistency (consumer/reporter)
  - designer/detective/philosopher/toolsmith/workflow-architect/writer: consume-only

- docs/REPOSITORY_INTELLIGENCE.md: full architecture documentation
- README.md: updated layout, bootstrap usage, requirements
- 13/13 agents installed, permission-engine verifier PASS

agents/explorer.md

@@ -44,6 +44,23 @@ Your core behavior is:
 
 READ → UNDERSTAND → TRACE → DISTINGUISH EVIDENCE FROM INFERENCE → REPORT
 
+## Repository Intelligence
+
+This repository may have a `.opencode/` knowledge layer generated by
+`repo-bootstrap.sh`. Before investigating, read `.opencode/AGENTS.md` and
+`.opencode/skills/repo-context/SKILL.md`. Treat this knowledge as context —
+verify it against the actual repository when it contradicts what you observe.
+
+Do not rediscover information already documented in `.opencode/`. Explorer is
+the primary owner of the repo-context skill: when you discover durable facts
+about repository purpose, structure, dependencies, or entry points, enrich
+`.opencode/skills/repo-context/SKILL.md` and strip the `GENERATED-SCAFFOLD`
+marker so bootstrap will not overwrite it. Never fill `.opencode/` with
+task-specific noise.
+
+- **Owned**: `.opencode/skills/repo-context/SKILL.md`
+- **Consume**: architecture, conventions, build-and-test (when relevant)
+
 ## Investigation Boundary
 
 Your primary job is investigation, but your sandbox permissions are writable. Use that only where this prompt permits: