Finish remaining TODO items: bake hand CCs for adapted files + reconc…

[glloq]

…ile resolved items

Bake gate (behavioral fix):

• PlaybackAssignmentCommands.applyAssignments no longer skips baking hand-position CCs (CC22/23/24) when creating an adapted file. The gate blobMatchesAdapted = !createAdaptedFile was left behind after its blocking bug (the adapted buffer never reaching disk) was fixed: the adapted bytes are now persisted via FileManager.replaceFileBytes / createDerivedFile before the bake step, so targetFileId's blob is always correct and the editor CC pane is populated for adapted files too.
• Add tests/apply-assignments-bake-adapted-hand-cc.test.js (3 cases).

Stale-comment cleanup (commands verified already-implemented):

• PlaybackControlCommands: playback_transpose is a real live global transpose (setGlobalTranspose), not a placeholder; set_tempo/set_volume are likewise implemented. Fix the file header and the transpose JSDoc.
• SystemCommands: system_restore is fully implemented. Fix header.
• MidiCommands: midi_reset is fully implemented. Fix header.

Contract coverage:

• Add executed playback_transpose contract tests (5 cases) and rewrite the orphan stub fixture to match the real live-offset behavior.

TODO.md reconciliation (per audit Meta-constat #0 - stop re-triaging):

• Mark ScoringConfig weight-sum and DelayCalibrator carte-regex resolved, with file:line evidence.
• Record the octave-wrap collision decision: keep warning-only, because a nearest-free remap would break pitch-class preservation.
• Note the adapted-file bake gate is lifted; correct stale dependency version numbers (better-sqlite3 is 11.x, not 9.x).

Claude-Session: https://claude.ai/code/session_01GPPovNdv6SbTBkx48QkVv1