avoid bad commits after interrupted direct mode sync (or merge)

It was possible for a interrupted sync or merge in direct mode to
leave the work tree out of sync with the last recorded commit.
This would result in the next commit seeing files missing from the work
tree, and committing their removal.

Now, a direct mode merge happens not only in a throwaway work tree, but using
a temporary index file, and without any commits or index changes
being made until the real work tree has been updated. If the merge is
interrupted, the work tree may have some updated files, but worst case a
commit will redundantly commit changes that come from the merge.

This commit was sponsored by Tony Cantor.

Annex/AutoMerge.hs

@@ -17,7 +17,6 @@ import qualified Git.LsFiles as LsFiles
 import qualified Git.UpdateIndex as UpdateIndex
 import qualified Git.Merge
 import qualified Git.Ref
-import qualified Git.Sha
 import qualified Git
 import Git.Types (BlobType(..))
 import Config
@@ -38,12 +37,7 @@ autoMergeFrom branch currbranch = do
 		Just b -> go =<< inRepo (Git.Ref.sha b)
   where
 	go old = ifM isDirect
-		( do
-			d <- fromRepo gitAnnexMergeDir
-			r <- inRepo (mergeDirect d branch)
-				<||> resolveMerge old branch
-			mergeDirectCleanup d (fromMaybe Git.Sha.emptyTree old) Git.Ref.headRef
-			return r
+		( mergeDirect currbranch old branch (resolveMerge old branch)
 		, inRepo (Git.Merge.mergeNonInteractive branch)
 			<||> resolveMerge old branch
 		)
@@ -70,9 +64,11 @@ autoMergeFrom branch currbranch = do
  -
  - In indirect mode, the merge is resolved in the work tree and files
  - staged, to clean up from a conflicted merge that was run in the work
- - tree. In direct mode, the work tree is not touched here; files are 
- - staged to the index, and written to the gitAnnexMergeDir, and later
- - mergeDirectCleanup handles updating the work tree.
+ - tree. The resolution is committed.
+ -
+ - In direct mode, the work tree is not touched here, and no commit is made;
+ - files are  staged to the index, and written to the gitAnnexMergeDir, and
+ - later mergeDirectCleanup handles updating the work tree.
  -}
 resolveMerge :: Maybe Git.Ref -> Git.Ref -> Annex Bool
 resolveMerge us them = do
@@ -92,14 +88,13 @@ resolveMerge us them = do
 		unlessM isDirect $
 			cleanConflictCruft mergedfs top
 		Annex.Queue.flush
-		whenM isDirect $
-			void preCommitDirect
-		void $ inRepo $ Git.Command.runBool
-			[ Param "commit"
-			, Param "--no-verify"
-			, Param "-m"
-			, Param "git-annex automatic merge conflict fix"
-			]
+		unlessM isDirect $ do
+			void $ inRepo $ Git.Command.runBool
+				[ Param "commit"
+				, Param "--no-verify"
+				, Param "-m"
+				, Param "git-annex automatic merge conflict fix"
+				]
 		showLongNote "Merge conflict was automatically resolved; you may want to examine the result."
 	return merged