chore: housekeeping — rm dead code, consolidate MCP tools, add tests, clean docs (#50)
* implemented stubbed IGraphContextService methods
* feat: wire graph communication updates in ipc, mcp and cli
* fix: fix call graph recall and add profiling coverage to graph calls sites
* fix: fixes for work where we added agent navigation to graph tooling
* fix(corpus): clean FTS and KG orphans on document delete
* fix(repair): clean orphans, honor cancellation, surface stats
* fix(rm): order content removal before metadata/KG delete. keep manifest while content is still referenced
* fix(daemon): seed built-in content extractor for readiness
* chore(cli): remove dead stubs and unwired helpers
* feat(search): named-collection scoping + provable relevance gate
* fix(refactor): rm dead stubs, inline simd, add proto/metrics tests
* chore: rm dead interfaces/enums, consolidate guards, add tests
* refactor: rm dr vaporware, collapse download handlers, clean list flags
* docs: rm stale testing investigation logs
* fix: address Copilot review findings from PR #50
- relationship_ops: return existing id when INSERT OR IGNORE skips
- document_crud_ops: propagate FTS5 cleanup error (was silent skip)
- builtin_text_content_extractor: unsigned char cast for tolower, add cctype
- mcp_server download_jobs: validate job_id for status/cancel actions
- list_command tests: unsigned char cast for isspace, add cctype include
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