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Three fix families, all mirrored in node + python:
- Corrupt or misshapen .harness/config.json now fails gently everywhere (doctor, skill add/update/remove, optimize, instinct toggles), no tracebacks.
- Staged-file secret scans report true line numbers (hunk-header aware), tolerate non-UTF-8 staged files, and the auditor skips its own deploy copies so fresh installs do not self-flag on their first git add -A.
- One run at a time in the GUI run endpoint; hook toggles record disabled hooks in the manifest so doctor --fix no longer re-enables them; --harness/--port flag values fail loudly; memory prune and optimize are separate commands; fixes for animated install deadlocks, escape-key handling, and frontmatter ending at the closing fence.
- Dev dependency refresh: npm audit clean (vite 8.3.5, vitest 5.0.5).
Full sweep green: tsc, eslint, 30 vitest, 24 pytest, audit clean, ci + security + CodeQL workflows.