Avoid a crash if a mapping contains files that no longer exist.
This could happen because eg, one was deleted and a commit has not yet been
done to update the mapping.
Fix path calculation.
When a file is changed in direct mode, the old content is probably lost
(at least from the local repo), and bookeeping needs to be updated to
reflect this.
Also, synthetic add events are generated at assistant startup, so
make it detect when the file has not really changed, and avoid re-adding
it.
This does add the overhead of querying the runing git cat-file for the
key that's recorded in git for the file, each time a file is added or
modified in direct mode.
