feat: Galaxy v6 physics engine, graph scene overhaul, and ledger UI improvements - #138

…mprovements

- Galaxy physics: orbital mechanics, leapfrog integration, black hole gravity,
  solar system hierarchy, evidence-mass sizing, drag velocity preservation
- Graph scene: ghost edge sort fix, connected_only+include_history interaction,
  set-wise visibility refactor, code overlay fallback correction
- Ledger UI: graph load caching fix, repo filter in cache key, accessibility
  improvements, Galaxy controls integration
- Store: schema migration, logical digest header zeroing fix, verification
  scope correction, context_savings workspace coercion
- Service: entity visibility filter, workspace N+1 query fix, history mode
  ghost flags, migration locking
- API: graph scene fallback narrowing, whitespace workspace validation
- E2E tests: Galaxy slider/half-step/orbital separation coverage
- Unit tests: graph engine assets, explorer v2, scene contracts, benchmarks
- Scripts: dashboard readiness probe, port conflict differentiation
- Docs: changelog, MCP tools reference, skill package update

Co-authored-by: review agents (16 parallel reviewers, 4 fix agents)

- Restore schema cookie (offset 40) normalization in _logical_digest:
  SQLite backup can reset this field, causing digest mismatch and
  aborting all v3-v16 migrations. Codex P1.
- Reserve edge capacity for historical ghost relations: when
  include_history=True, ghost edges covering historical nodes are
  selected first before applying the final edge_cap, preventing the
  time-travel view from losing all historical edges. Codex P2.
- Update test_store_class_integrity to validate the corrected digest
  offsets (24, 40, 92).

Prevents unbounded URL growth on persistent asset load failures.
The retry counter appends to asset URLs as a cache-buster; without a
cap, repeated failures produce increasingly long URLs and complicate
debugging. Ten retries provides ample recovery attempts before giving
up gracefully.

5 fixes for issues flagged by the Codex reviewer:

- P1 service.py: historical supports query now filters by
  memory.workspace_id so a cross-workspace support cannot leak into
  the include_history scene.
- P2 service.py: evidence facets (memory_types, time_from, time_to) are
  applied in history mode instead of being skipped by the live-only
  evidence_filter short-circuit.
- P2 service.py: entity candidate cap applies after session-scope
  pruning so private evidence cannot crowd out public entities.
- P1 engine.py: secure_erase re-checks successors after the potentially
  long index.delete and cleans up any new target IDs before calling
  store.secure_erase_memory.
- P2 graph_scene.py: ghost canonical nodes that collide with a live
  canonical_id are keyed as :ghost so the live node keeps its mass,
  community, and relations.

Co-authored-by: Codex review bot (addressed findings from d5dbcdb)

Move prune_entities assignment before its first reference in the
evidence_filter computation. Ruff F821 caught the UnboundLocalError
that broke all graph scene operations across every Python version.

The previous commit introduced a dependency on prune_entities in the
evidence_filter assignment that broke live-only evidence filtering
when memory_types/time facets were requested without include_history.
Restore the original 'not include_history' logic; the prune_entities
override for history mode is handled separately below.

Fixes test_graph_scene_filters_supporting_memory_type_and_time_window.

savingsQuery() returned empty string for the 'all' preset, producing
URLs like /context-savings? with a dangling query separator. Move the
? prefix into the returned string so the 'all' case produces a clean
/context-savings path with no query component.

Fixes one of the remaining low-severity review findings.