docs: update TODO.md to reflect completed implementation status

Check off all implemented and tested items across Hippocampus (HierarchyBuilder,
FastNeighborInsert, Ingest), Cortex (Ranking, MetroidBuilder, KnowledgeGapDetector,
OpenTSPSolver, Query, QueryResult), Daydreamer (ExperienceReplay, ClusterStability),
integration tests, benchmarks, CI hardening, documentation, and product surfaces.

Update section headings with ✅ COMPLETE markers and refresh the summary table
to reflect v0.1/v0.5/v1.0 phases as complete. Only P3-A (WebGL provider) and
P3-H (GitHub sync smoke test) remain pending.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: Copilot