docs: add refactoring plan and permission repair evidence

[zhenkun26]

Add the refactoring plan, its consistency review, and a status record of completed local permission maintenance. This is a documentation-only PR: application implementation remains NOT_STARTED, with R01–R08 still PLANNED.

Scope

GitHub's base-to-head comparison was verified to contain exactly these three files:

• REFACTOR_INTEGRATION_PLAN.md
• docs/REFACTOR_STATUS.md
• docs/reviews/2026-10-02-refactor-plan-consistency.md

The source branch incorporates the existing main history so already-merged README changes do not appear in this PR. Existing local and published commits were preserved.

Recorded inspection results

• PASS: Removed only executable bits from the 144 verified baseline files, changing local filesystem permissions from 0700 to 0600 while retaining owner-only read/write permissions. These local permission changes are evidence recorded in this PR, not a 144-file Git diff.
• PASS: At the completed maintenance baseline, all 148 tracked file contents matched their indexed blobs. Ownership and recorded stat fields were preserved, no extended ACL entries were present on the repaired files, and Git refs/index entries were preserved.
• PASS: Git object integrity checking completed successfully. Repeated read-only attribute inspection across 1,114 files/directories, including .git, found only com.apple.provenance and no changes during that investigation.

Historical attribute limitation and disposition

• FAIL: The original aggregate xattr CLI output comparison differed before and after permission repair.
• BLOCKED: The checker did not retain the pre-repair attribute values or a per-file difference, and no available local snapshots could reconstruct them. Exact affected paths and old/new attribute bytes therefore cannot be reported reliably.
• The strongly supported explanation is a macOS provenance update triggered by changing permissions: current file markers match the executing ChatGPT/Codex process lineage and matching markers appear in contemporaneous system logs. This does not prove every repaired file's attribute changed or that all attributes were preserved.
• The owner accepted retaining the current extended attributes with no further handling. No content damage, unexpected final permission/ACL state, or Git integrity problem was found. Full application execution, cross-application writes, and all macOS security-policy effects were not tested.

PR validation and review boundary

Passed: UTF-8/Markdown structure, 33 local documentation links, whitespace checks, preservation of the 144 files' 0600 permissions, and the exact three-file GitHub comparison. No application code changed; local application tests were not rerun for this documentation-only update.

On 2026-10-17, the owner explicitly authorized marking this PR ready for review and merging into main after CI passes for the current head, while retaining existing branches and local commits. R01 remains outside this authorization.