bugfix: avoid staging but not committing changes to git-annex branch

Branch.get is not able to see changes that have been staged to the index
but not committed. This is a limitation of git cat-file --batch; when
reading from the index, as opposed to from a branch, it does not notice
changes made after the first time it reads the index.

So, had to revert the changes made in 1f73db3469
to make annex.alwayscommit=false stage changes.

Also, ensure that Branch.change and Branch.get always see changes
at all points during a commit, by not deleting journal files when
staging to the index. Delete them only after committing the branch.
Before, there was a race during commits where a different git-annex
could see out-of-date info from the branch while a commit was in progress.

That's also done when updating the branch to merge in remote branches.

In the case where the local git-annex branch has had changes pushed into it
that are not yet reflected in the index, and there are journalled changes
as well, a merge commit has to be done.

Annex/Content.hs

@@ -301,8 +301,8 @@ saveState :: Bool -> Annex ()
 saveState oneshot = doSideAction $ do
 	Annex.Queue.flush
 	unless oneshot $
-		ifM alwayscommit
-			( Annex.Branch.commit "update" , Annex.Branch.stage)
+		whenM alwayscommit $
+			Annex.Branch.commit "update"
 	where
 		alwayscommit = fromMaybe True . Git.Config.isTrue
 			<$> getConfig (annexConfig "alwayscommit") ""