Add relationship indexing, graph traversal, and activity tracking

[mgoldsborough]

Summary

• Relationship index — write-time reverse index at _index/relations.json enables O(1) relationship lookups. Auto-rebuilds from entity files if missing or corrupt. Atomic writes via temp file + os.replace.
• Graph traversal — three new methods on UpjackApp: query_by_relationship, get_related (forward/reverse), get_composite (entity + all related in one call with _related key)
• Activity tracking — opt-in via "activities": true in manifest. Activities are regular entities (prefix act) with log_activity and get_activities convenience methods using the reverse index.
• CRUD hooks — on_relationships_changed callback on create/update/delete, auto-wired by UpjackApp to maintain the index
• MCP tools — per-entity: query_{plural}_by_relationship, get_related_{name}, get_{name}_composite. Global: rebuild_index, log_activity, get_activities

Test plan

• 374 tests pass (make check)
• 20 relation index tests (CRUD, rebuild, query, corrupt recovery)
• 21 graph traversal tests (prefix resolution, query_by_relationship, get_related, get_composite)
• 22 activity tests (schema, manifest parsing, log/get, indexing, lifecycle)
• 8 CRUD hook tests (create/update/delete callbacks, soft vs hard delete)
• 6 index wiring tests (UpjackApp auto-maintains index)
• 16 MCP tool tests (relationship + activity tools through server interface)
• 8 integration tests against real CRM/Todo example schemas

Closes #12