PR #TBD — Phase 4: synlynk doctor --fix agy

The Broader Goal at the End of the Previous PR

Phase 3 established the remediation audit log as the durable record for confirmed config writes. Phase 4 uses that foundation to close the Agy-specific pre-flight manifest gap.

Strategic Shifts in This PR (if any)

No broad strategy change. This phase narrows remediation to Agy only because the confirmed failure mode is a pre-dispatch permissions gap in ~/.gemini/antigravity-cli/settings.json, not a runtime prompt loop.

What This PR Shipped

synlynk doctor --fix agy now computes the exact JSON diff for ~/.gemini/antigravity-cli/settings.json, prints the proposed change, and writes only when the operator passes --yes or confirms interactively. On every write, synlynk appends a remediation_actions row with the timestamp, target file, exact diff, and confirmation mode, so the write is auditable even when the fix is applied headless.

Brainstorm Visuals Used

None.

What This Achieved on the Path to Autonomy

Agy can now be pre-seeded with the needed permission rules before dispatch rather than failing inside the job. That moves the system one step closer to a pre-flight, operator-visible remediation loop instead of a silent runtime permission failure.

Strategic Note: The Goal at the End of This PR

The next step is wiring this pre-flight remediation into the broader dispatch workflow without turning it into an auto-triggered runtime prompt.