Loki Mode

Queued bug-hunt tail (wave-9) + CI test-isolation repair

A file-sharded verify-then-fix fleet cleared the WAVE8 queued MED/LOW findings.
Each finding was reproduced before fixing; STALE findings were refuted with
evidence rather than "fixed". Reviewed by a 3-reviewer council (2 Opus + 1
Sonnet) to unanimous approve. local-ci 84/84 on a quiet box.

CI / test-isolation:

• The two loki internal phase1-hooks H2 batch-abort tests stubbed
  learnings_writer via Bun's mock.module, a GLOBAL registry with no reliable
  per-test revert (mock.restore() does not touch it). Under cross-file test
  discovery ordering on Linux the throwing stub leaked into the learnings_writer
  suite, producing a nondeterministic CI red on the Tests and Coverage workflows
  (green on macOS where readdir order differs). Replaced with a module-local
  test seam reset deterministically in afterEach. Production behavior unchanged.

Memory subsystem:

• Consolidation no longer inflates pattern confidence on idempotent re-runs: the
  +0.05 merge boost is now gated on genuinely new source_episodes, so
  re-running consolidate() over an unchanged episode set is a no-op for
  confidence (was ratcheting +0.05 per run).
• Retrieval-time importance boost is now persisted to disk via a lock-spanning
  read-mutate-write keyed by id+source (mirrors the decay path), closing the
  "use it or lose it" asymmetry where decay persisted but the boost never did.
  Persistence is opt-in (persist_boost): only the autonomous RARV loop reinforces
  importance; manual surfaces (loki memory CLI, dashboard, MCP) do not silently
  inflate it. A failed boost-write never breaks retrieval.

Dashboard / migration:

• The terminal migration phase (verify) can now be advanced and completed via
  POST /api/migration/{id}/advance with only from_phase (it has no successor, so
  to_phase and the phase gate are meaningless for it). Previously the endpoint
  required to_phase and ran the gate for every phase, so verify could never be
  completed via the API and overall_status could never reach "completed". The
  409/idempotency semantics for already-advanced phases are preserved.

CLI / runtime (bash):

• loki status --json no longer crashes on a malformed status file: the
  JSON-error fallback was dead under set -e (a bare python3 call aborted the
  function before the fallback ran); it is now guarded so a parse error degrades
  to an honest error object.
• loki explain --json, loki heal, and loki onboard pass values to their
  python helpers via the environment instead of interpolating raw bash values
  into python3 -c heredocs, fixing a quote/apostrophe-injection class that
  silently degraded output (e.g. a project path containing an apostrophe).
• Removed the dead invoke_with_timeout helper and its unused spawn-config vars
  from run.sh (never wired to the provider invocation; kept route parity with
  the Bun side, which has no such wrapper).
• Checkpoint pruning now deletes the matching refs/loki/cp/<id> git refs (and
  their anchored stash commits) for pruned checkpoints, which previously leaked
  unbounded.

Refuted (verified STALE, no change): a PERPETUAL_MODE gate in run.sh (compounding
it would disable the completion council on every default run) and the crash.ts
global unhandledRejection handler (intentional, documented fail-fast).