improve alwayscommit=false mode

Now changes are staged into the branch's index, but not committed,
which avoids growing a large journal. And sync and merge always
explicitly commit, ensuring that even when they do nothing else,
they commit the staged changes.

Added a flag file to indicate that the branch's journal contains
uncommitted changes. (Could use git ls-files, but don't want to run
that every time.)

In the future, this ability to have uncommitted changes staged in the
journal might be used on remotes after a series of oneshot commands.

Locations.hs

@@ -22,6 +22,7 @@ module Locations (
 	gitAnnexJournalLock,
 	gitAnnexIndex,
 	gitAnnexIndexLock,
+	gitAnnexIndexDirty,
 	gitAnnexSshDir,
 	isLinkToAnnex,
 	annexHashes,
@@ -143,6 +144,10 @@ gitAnnexIndex r = gitAnnexDir r </> "index"
 gitAnnexIndexLock :: Git.Repo -> FilePath
 gitAnnexIndexLock r = gitAnnexDir r </> "index.lck"
 
+{- Flag file for .git/annex/index. -}
+gitAnnexIndexDirty :: Git.Repo -> FilePath
+gitAnnexIndexDirty r = gitAnnexDir r </> "index.dirty"
+
 {- .git/annex/ssh/ is used for ssh connection caching -}
 gitAnnexSshDir :: Git.Repo -> FilePath
 gitAnnexSshDir r = addTrailingPathSeparator $ gitAnnexDir r </> "ssh"