chore: sync core lib and CLAUDE.md from agent-core

[avifenesh]

Automated sync of lib/ and CLAUDE.md from agent-core.

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Note

Medium Risk
Changes how applyFixes and restoreFromBackup read/write files by blocking symlinks, which could affect workflows that legitimately rely on symlinked files and introduces new error paths during fixing/restoring.

Overview
Adds a new assertNotSymlink guard and wires it into the auto-fixer’s read/backup/write and backup-restore paths to refuse operating on symlinked targets (including .backup files), mitigating symlink-based overwrite attacks.

The fixer now records a structured error and skips applying fixes when the target path is a symlink, and re-checks immediately before writes to narrow TOCTOU exposure; assertNotSymlink is also exported.

^{Reviewed by Cursor Bugbot for commit 4602b17. Configure here.}

[gemini-code-assist]

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