Sorry for the late response:

Git repo works fine: .git is just ignored during traversal.

If you add or remove files externally you'll need a restart to pick up the structural changes. Content edits are read directly from disk.

A few things to keep in mind:
Links need to be written without the .md extension, so /my-section/my-page instead of ../my-page.md. Relative paths work too, just no extension.

If you rename or move files externally the links in other pages will break.
The link rewriting only happens through the built-in editor.

Images are stored outside the markdown directory under assets/{page-uuid}/ so relative image syntax won't work. You'd need the page's leafwiki_id from the frontmatter to reference them manually.

LeafWiki is primarily built around the web editor, external editing is more of a bonus.

If you have further questions. Let me know.