Over Christmas, I'm working on making the assistant support direct
mode. I like to have a fairly detailed plan before starting this kind of
job, but in this case, I don't. (Also I have a cold so planning? Meh.)
This is a process of seeing what's broken in direct mode and fixing it.
I don't know if it'll be easy or hard. Let's find out..

* First, got direct mode adding of new files working. This was not hard, all the
  pieces I needed were there. For now, it uses the same method as in
  indirect mode to make sure nothing can modify the file while it's being
  added.

* An unexpected problem is that in its startup scan, the assistant runs
  `git add --update` to detect and stage any deletions that happened
  while it was not running. But in direct mode that also stages the full file
  contents, so can't be used. Had to switch to using git plumbing to only
  stage deleted files. Happily this also led to fixing a bug; deletions
  were not always committed at startup when using the old method; with the
  new method it can tell when there are deletions and trigger a commit.

* Next, got it to commit when direct mode files are modified. The Watcher
  thread gets a inotify event when this happens, so that was easy. (Although
  in doing that I had to disable a guard in direct mode that made annexed
  files co-exist with regular in-git files, so such mixed repositories
  probably won't work in direct mode yet.)

  However, naughty kqueue is another story, there are no kqueue events for
  file modifications. So this won't work on OSX or the BSDs yet. I tried
  setting some more kqueue flags in hope that one would make such events
  appear, but no luck. Seems I will need to find some other method to detect
  file modifications, possibly an OSX-specific API.

* Another unexpected problem: When an assistant receives new files from one
  of its remotes, in direct mode it still sets up symlinks to the content.
  This was because the Merger thread didn't use the `sync` command's direct
  mode aware merge code.. so fixed that.

* Finally there was some direct mode bookeeping the assistant has
  to get right. For example, when a file is modified, the old object has
  to be looked up, and be marked as not locally present any longer. That
  lookup relies on the already running `git cat-file --batch`, so it's
  not as fast as it could be, if I kept a local cache of the mapping
  between files and objects. But it seems fast enough for now.

At this point the assistant seems to work in direct mode on Linux!
Needs more testing..
