Directory-sync now writes/reads a git-keep marker file to detect prior sync state

Directory sync now reads and writes a small JSON marker file inside a synced directory, recording a version number and the time it was written. It's created exclusively so it can't silently overwrite an existing one, and failures to read or write it are logged. A companion piece of logic also maps the various reasons directory sync can detach from a folder (commit not held, not in history, on another branch, branch switched, switched off, diverged, machine stopped) to explanations shown to the user.