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The skill SKILL.md files are hardlinked across .agents/skills/ and .claude/skills/ (same inode, two paths), but git had committed divergent blobs: the .agents/ copies carried an "Extended reference: AGENTS.md" note that the .claude/ copies lacked. Because one physical file cannot match two different blobs, the working tree was permanently dirty on the three .claude/skills paths. Stage the .claude copies so both paths commit identical content (with the AGENTS.md reference note, the fuller intended version). Restores a clean git status and keeps it clean across checkouts. Affected skills: flux-best-practices, vercel-composition-patterns, vercel-react-best-practices.