notmuch new: Detect deleted (renamed) files and directories.

This takes advantage of the notmuch_directory_t interfaces added
recently (with cooresponding storage of directory documents in the
database) to detect when files or entire directories are deleted or
renamed within the mail store.

This also fixes the recent regression where *all* files would be
processed by every run of "notmuch new", (now only new files are
processed once again).

The deleted files and directories are only detected so far. They
aren't properly removed from the database.