For files that don't need transformation (AGENTS.md, skills, most rules), LNAI creates symlinks. .claude/CLAUDE.md → ../.ai/AGENTS.md. Edit the source, all tools see it immediately.

For transformed files (Cursor's .mdc frontmatter, GEMINI.md sub-directory rules), you re-run lnai sync. LNAI maintains a manifest tracking of every generated file with content hashes, so it knows what changed and cleans up orphans automatically.

So it's not really "sync once", it's "symlink for instant propagation, regenerate-on-demand for transforms." The manifest ensures LNAI always knows its downstream state.

This system can also break down if you create new skills/rules in the specific tool directories (.claude, .codex, etc.) but that is against LNAI's philosophy. If you need per-tool overrides you put them in `.ai/.{claude/codex/etc.}` sub-directories and LNAI manages them for you.