docs: record PR #2 merge and local main synchronization

[zhenkun26]

Records the completed integration of PR #2 and synchronization of local main to merge commit d4820a2babfbbf8cd4022fad80bd6e6c81889ad7, and reconciles the status record with the actual Draft PR delivery.

Scope: only docs/REFACTOR_STATUS.md differs from main (12 insertions, 8 deletions). Current PR head: b661d8e732071c069b8f0fc7f858f631440c94c1. No application or R01 implementation is included.

Commit and delivery identities:

• PR docs: add refactoring plan and permission repair evidence #2 is merged; its source head at merge was 268e32fd3751477951dc776c6c245ae5befc515d. This is distinct from the later source-branch commits.
• bb8d43e9a3ed3ab4d9ad6aa8534df977f999d6e0 is the initial published PR docs: record PR #2 merge and local main synchronization #3 status-update checkpoint.
• b661d8e732071c069b8f0fc7f858f631440c94c1 is the published P3 follow-up and current PR head. It corrects the delivery state and separates the commit and CI checkpoints.
• The status document retains revision-specific CI evidence for bb8d43e and directs later revisions to their own checks; the results below apply to the current b661d8e head.

Verification:

• GitHub's comparison against main contains exactly docs/REFACTOR_STATUS.md; git diff --check passed.
• Local main, origin/main, and live remote main were verified at d4820a2babfbbf8cd4022fad80bd6e6c81889ad7; the worktree remained on codex/permission-repair-status.
• The completed local verification found all 148 tracked contents matched the index, the 144 repaired files remained 0600, the other four remained 0644, and existing local branches were preserved.
• Push CI completed successfully for b661d8e732071c069b8f0fc7f858f631440c94c1.
• PR CI completed successfully for the same head. Ruff, import checks, tests, and the evaluation smoke test passed.

The historical permission-repair record is unchanged. Only executable bits were removed from the 144 verified files (0700 -> 0600); other permission bits were retained. The original aggregate extended-attribute comparison remains recorded as FAIL, and exact historical reconstruction remains BLOCKED because pre-repair values and per-file differences were not retained. Later attribute stability checks do not prove historical attributes were unchanged. Retain current extended attributes without further handling.

CI does not certify workstation metadata, reconstruct historical attributes, establish full application runtime behavior, or complete R01. Implementation remains NOT_STARTED, with active increment NONE.

Keep this PR in Draft. Do not merge and do not start R01.