fix(persistence): atomic updates, durable writes and protected credentials - #418
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Gate & Scope
G3 persistence, findings A02/A07/A11. File writes acquire advisory locks, use owned temporary files, set permissions before fsync and sync the parent directory. Configuration transactions reload from disk under a lock and reject malformed YAML. Remove the redundant global cache; serialize disabled services deterministically. Repair existing secret permissions without rotating credentials. Compose files now use 0600 because they contain credentials.
Covered Requirements
REQ-SEC-003, REQ-SEC-004, REQ-OPS-001, REQ-TST-003.
Evidence
Six regression tests cover concurrent updates, corruption preservation and redaction, same-content timestamps, lock symlinks, secret permission repair, and independent config paths. git diff --check passed. Local build/test/clippy attempts are ongoing; GitHub CI must pass before merge. No local green result is asserted.
Risks / Visible Behavior
Compose becomes owner-readable only. Corrupt config is rejected instead of silently overwritten. Lockfiles remain alongside managed outputs. Parent directories must be trusted; this does not claim arbitrary symlink confinement.
Rollback
Revert this PR squash commit; permissions need not be loosened to revert code.
Out of Scope
Host deployment, web session lifecycle, operational error handling; handled separately.