v5.6.1

Bug-fix release: restores local-mode operation broken on the 4.28→5.6.0 upgrade
path, plus the RDR-141 single-writer hardening. Promotes develop (#1055, #1056,
#1063) to main.

Added

• nx hooks update-all (#1056). Refreshes the nexus stanza in already-managed
  git hooks across all catalog-registered repos, bringing every repo to the
  current stanza after an upgrade. Unmanaged/uninstalled hooks are untouched; also
  run automatically by nx upgrade.

Fixed

• RDR-108 orphan-migration error message (#1056). The high-volume orphan gate
  pointed at a non-existent nx catalog mark-superseded command; it now references
  the real nx catalog rename-collection.

• Local-mode search restored (#1058). The local bge embedding function
  pre-converted fastembed's numpy arrays to Python lists; chromadb ≥1.x calls
  .tolist() on each element itself, so every local-mode (bge) search raised
  'list' object has no attribute 'tolist'. The embedding function now returns
  numpy arrays. Added a chromadb<2 upper bound — the unbounded >=0.6 silently
  resolved the contract-tightening 1.5.9.

• Collection renames restored (#1057). rename_collection_cascade referenced
  the document_aspects.source_path column dropped at 4.31.0, so every rename
  failed with no such column: source_path on migrated databases. The
  collision-defense now resolves the live primary-key column (doc_id when
  migrated, else source_path) for both the document_aspects and
  aspect_extraction_queue cascades.

• nx mineru start on a stock install (#1059). mineru-api (a bundled
  dependency's console script) is not linked onto PATH by uv tool install.
  Resolution now tries the interpreter's venv bin, then a module-anchored venv
  walk (fixes the MCP/daemon auto-restart path under a different interpreter),
  then PATH.

• Collection-name overflow guidance (#1060). Relabeling to the longer bge
  token could exceed ChromaDB's 63-char cap; the error now points at the
  canonical repo-id name via nx catalog collection-name instead of a bare
  ValueError.

• Daemon-unreachable log spam (#1048). t2_index_write logged a fallback
  warning on every write while the daemon was alive-but-busy; it now
  distinguishes daemon-absent from alive-but-unresponsive and rate-limits the
  warning per event.

• Version-skew double-writer (RDR-141, #1055). t2_index_write split its
  conflated except: a schema-version mismatch (a stale daemon still serving)
  now re-asserts the supervisor instead of opening a second direct writer on
  memory.db.

Changed

• nx doctor (#1061 E1). Now fails (instead of false-green "could not
  query") when the active embedder's dimension does not match the stored
  collections' — a total search outage is a failure with remediation.
• nx upgrade --dry-run (#1061 E2). Reports deferred/gated RDR-108 migrations
  (both aspect tables) instead of "no pending migrations" when a gated step would
  still run on the next daemon bootstrap.
• T2-backed commands (#1061 E3). Print a clean one-liner when the T2 daemon is
  down instead of a raw DaemonNotRunningError traceback.