fix(cli): keep init recovery logs out of progress

[sunerpy]

Summary

• demote successful stale-index recovery events from INFO to DEBUG so normal codegraph init progress stays cohesive
• add black-box regressions for missing state slots and moved/copied project identities, while preserving opt-in DEBUG diagnostics
• update the bundled CodeGraph skill to follow explicit codegraph init recovery for missing slots or all-OwnerMismatch state without generalizing to other corruption

Validation

• make ci
• pre-push fmt, clippy, workspace tests, golden equivalence, and guardrail
• CodeGraph skill quick_validate.py

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

@@           Coverage Diff           @@
##             main     #240   +/-   ##
=======================================
  Coverage   95.35%   95.35%           
=======================================
  Files         141      141           
  Lines       79452    79452           
=======================================
  Hits        75765    75765           
  Misses       3687     3687           

Files with missing lines	Coverage Δ
crates/codegraph-store/src/rebuild.rs	92.87% <100.00%> (ø)

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