always check with ls-files before adding new files

Makes it safe to use git annex unlock with the watcher/assistant.
And also to mix use of the watcher/assistant with regular files stored in git.

Long ago, I had avoided doing this check, except during the startup scan,
because it would be slow to run ls-files repeatedly.

But then I added the lsof check, and to make that fast, got it to detect
batch file adds. So let's move the ls-files check to also occur when it'll
have a batch, and can check them all with one call.

This does slow down adding a single file by just a bit, but really only
a little bit. (The lsof check is probably more expensive.) It also
speeds up the startup scan, especially when there are lots of new files
found by the scan.

Also, fixed the sleep for annex.delayadd to not run while the threadstate
lock is held, so it doesn't unnecessarily freeze everything else.

Also, --force no longer makes it skip the lsof check, which was not
documented, and seems never a good idea.

debian/changelog

@@ -3,6 +3,9 @@ git-annex (3.20121002) UNRELEASED; urgency=low
   * group, ungroup: New commands to indicate groups of repositories.
   * --copies=group:number can now be used to match files that are present
     in a specified number of repositories in a group.
+  * watch, assistant: It's now safe to git annex unlock files while
+    the watcher is running, as well as modify files checked into git
+    as normal files.
 
  -- Joey Hess <joeyh@debian.org>  Mon, 01 Oct 2012 15:09:49 -0400