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
+		( mergeDirect currbranch old branch (resolveMerge old branch)
-			d <- fromRepo gitAnnexMergeDir
-			r <- inRepo (mergeDirect d branch)
-				<||> resolveMerge old branch
-			mergeDirectCleanup d (fromMaybe Git.Sha.emptyTree old) Git.Ref.headRef
-			return r
 		, 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 
+ - tree. The resolution is committed.
- - staged to the index, and written to the gitAnnexMergeDir, and later
+ -
- - mergeDirectCleanup handles updating the work tree.
+ - 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 $
+		unlessM isDirect $ do
-			void preCommitDirect
+			void $ inRepo $ Git.Command.runBool
-		void $ inRepo $ Git.Command.runBool
+				[ Param "commit"
-			[ Param "commit"
+				, Param "--no-verify"
-			, Param "--no-verify"
+				, Param "-m"
-			, Param "-m"
+				, Param "git-annex automatic merge conflict fix"
-			, Param "git-annex automatic merge conflict fix"
+				]
-			]
 		showLongNote "Merge conflict was automatically resolved; you may want to examine the result."
 	return merged
 

Annex/Direct.hs

@@ -34,6 +34,8 @@ import Annex.Perms
 import Annex.ReplaceFile
 import Annex.Exception
 import Annex.VariantFile
+import Git.Index
+import Annex.Index
 
 {- Uses git ls-files to find files that need to be committed, and stages
  - them into the index. Returns True if some changes were staged. -}
@@ -141,21 +143,63 @@ addDirect file cache = do
 		)
 
 {- In direct mode, git merge would usually refuse to do anything, since it
- - sees present direct mode files as type changed files. To avoid this,
+ - sees present direct mode files as type changed files.
- - merge is run with the work tree set to a temp directory.
+ -
+ - So, to handle a merge, it's run with the work tree set to a temp
+ - directory, and the merge is staged into a copy of the index.
+ - Then the work tree is updated to reflect the merge, and
+ - finally, the merge is committed and the real index updated.
  -}
-mergeDirect :: FilePath -> Git.Ref -> Git.Repo -> IO Bool
+mergeDirect :: Maybe Git.Ref -> Maybe Git.Ref -> Git.Branch -> Annex Bool -> Annex Bool
-mergeDirect d branch g = do
+mergeDirect startbranch oldref branch resolvemerge = do
-	whenM (doesDirectoryExist d) $
+	-- Use the index lock file as the temp index file.
-		removeDirectoryRecursive d
+	-- This is actually what git does when updating the index,
-	createDirectoryIfMissing True d
+	-- and so it will prevent other git processes from making
-	let g' = g { location = Local { gitdir = Git.localGitDir g, worktree = Just d } }
+	-- any changes to the index while our merge is in progress.
-	Git.Merge.mergeNonInteractive branch g'
+	reali <- fromRepo indexFile
+	tmpi <- fromRepo indexFileLock
+	liftIO $ copyFile reali tmpi
 
-{- Cleans up after a direct mode merge. The merge must have been committed,
+	d <- fromRepo gitAnnexMergeDir
- - and the commit sha passed in, along with the old sha of the tree
+	liftIO $ do
- - before the merge. Uses git diff-tree to find files that changed between
+		whenM (doesDirectoryExist d) $
- - the two shas, and applies those changes to the work tree.
+			removeDirectoryRecursive d
+		createDirectoryIfMissing True d
+
+	withIndexFile tmpi $ do
+		r <- inRepo (mergein d) <||> resolvemerge
+		mergeDirectCleanup d (fromMaybe Git.Sha.emptyTree oldref)
+		mergeDirectCommit startbranch branch
+		liftIO $ rename tmpi reali
+		return r
+  where
+	mergein d g = Git.Merge.stageMerge branch $
+		g { location = Local { gitdir = Git.localGitDir g, worktree = Just d } }
+
+{- Commits after a direct mode merge is complete, and after the work
+ - tree has been updated by mergeDirectCleanup.
+ -}
+mergeDirectCommit :: Maybe Git.Ref -> Git.Branch -> Annex ()
+mergeDirectCommit old branch = do
+	void preCommitDirect
+	gitdir <- fromRepo Git.localGitDir
+	let merge_head = gitdir </> "MERGE_HEAD"
+	let merge_msg = gitdir </> "MERGE_MSG"
+	let merge_mode = gitdir </> "MERGE_MODE"
+	ifM (maybe (return False) (\o -> inRepo $ Git.Branch.fastForwardable o branch) old)
+		( inRepo $ Git.Branch.update Git.Ref.headRef branch -- fast forward
+		, do
+			msg <- liftIO $
+				catchDefaultIO ("merge " ++ fromRef branch) $
+					readFile merge_msg
+			void $ inRepo $ Git.Branch.commit False msg
+				Git.Ref.headRef [Git.Ref.headRef, branch]
+		)
+	liftIO $ mapM_ nukeFile [merge_head, merge_msg, merge_mode]
+
+{- Cleans up after a direct mode merge. The merge must have been staged
+ - in the index. Uses diff-index to compare the staged changes with
+ - the tree before the merge, and applies those changes to the work tree.
  -
  - There are really only two types of changes: An old item can be deleted,
  - or a new item added. Two passes are made, first deleting and then
@@ -164,9 +208,9 @@ mergeDirect d branch g = do
  - order, but we cannot add the directory until the file with the
  - same name is removed.)
  -}
-mergeDirectCleanup :: FilePath -> Git.Ref -> Git.Ref -> Annex ()
+mergeDirectCleanup :: FilePath -> Git.Ref -> Annex ()
-mergeDirectCleanup d oldsha newsha = do
+mergeDirectCleanup d oldref = do
-	(items, cleanup) <- inRepo $ DiffTree.diffTreeRecursive oldsha newsha
+	(items, cleanup) <- inRepo $ DiffTree.diffIndex oldref
 	makeabs <- flip fromTopFilePath <$> gitRepo
 	let fsitems = zip (map (makeabs . DiffTree.file) items) items
 	forM_ fsitems $
@@ -194,12 +238,12 @@ mergeDirectCleanup d oldsha newsha = do
 	 - key, it's left alone. 
 	 -
 	 - If the file is already present, and does not exist in the
-	 - oldsha branch, preserve this local file.
+	 - oldref, preserve this local file.
 	 -
 	 - Otherwise, create the symlink and then if possible, replace it
 	 - with the content. -}
 	movein item makeabs k f = unlessM (goodContent k f) $ do
-		preserveUnannexed item makeabs f oldsha
+		preserveUnannexed item makeabs f oldref
 		l <- inRepo $ gitAnnexLink f k
 		replaceFile f $ makeAnnexLink l
 		toDirect k f
@@ -207,13 +251,13 @@ mergeDirectCleanup d oldsha newsha = do
 	{- Any new, modified, or renamed files were written to the temp
 	 - directory by the merge, and are moved to the real work tree. -}
 	movein_raw item makeabs f = do
-		preserveUnannexed item makeabs f oldsha
+		preserveUnannexed item makeabs f oldref
 		liftIO $ do
 			createDirectoryIfMissing True $ parentDir f
 			void $ tryIO $ rename (d </> getTopFilePath (DiffTree.file item)) f
 
 {- If the file that's being moved in is already present in the work
- - tree, but did not exist in the oldsha branch, preserve this
+ - tree, but did not exist in the oldref, preserve this
  - local, unannexed file (or directory), as "variant-local".
  -
  - It's also possible that the file that's being moved in
@@ -221,7 +265,7 @@ mergeDirectCleanup d oldsha newsha = do
  - file (not a directory), which should be preserved.
  -}
 preserveUnannexed :: DiffTree.DiffTreeItem -> (TopFilePath -> FilePath) -> FilePath -> Ref -> Annex ()
-preserveUnannexed item makeabs absf oldsha = do
+preserveUnannexed item makeabs absf oldref = do
 	whenM (liftIO (collidingitem absf) <&&> unannexed absf) $
 		liftIO $ findnewname absf 0
 	checkdirs (DiffTree.file item)
@@ -241,7 +285,7 @@ preserveUnannexed item makeabs absf oldsha = do
 		<$> catchMaybeIO (getSymbolicLinkStatus f)
 
 	unannexed f = (isNothing <$> isAnnexLink f)
-		<&&> (isNothing <$> catFileDetails oldsha f)
+		<&&> (isNothing <$> catFileDetails oldref f)
 
 	findnewname :: FilePath -> Int -> IO ()
 	findnewname f n = do

Git/Branch.hs

@@ -52,7 +52,22 @@ changed origbranch newbranch repo
 	diffs = pipeReadStrict
 		[ Param "log"
 		, Param (fromRef origbranch ++ ".." ++ fromRef newbranch)
-		, Params "--oneline -n1"
+		, Param "-n1"
+		, Param "--pretty=%H"
+		] repo
+
+{- Check if it's possible to fast-forward from the old
+ - ref to the new ref.
+ -
+ - This requires there to be a path from the old to the new. -}
+fastForwardable :: Ref -> Ref -> Repo -> IO Bool
+fastForwardable old new repo = not . null <$>
+	pipeReadStrict
+		[ Param "log"
+		, Param $ fromRef old ++ ".." ++ fromRef new
+		, Param "-n1"
+		, Param "--pretty=%H"
+		, Param "--ancestry-path"
 		] repo
 
 {- Given a set of refs that are all known to have commits not
@@ -74,7 +89,7 @@ fastForward branch (first:rest) repo =
   where
 	no_ff = return False
 	do_ff to = do
-		run [Param "update-ref", Param $ fromRef branch, Param $ fromRef to] repo
+		update branch to repo
 		return True
 	findbest c [] = return $ Just c
 	findbest c (r:rs)

Git/DiffTree.hs

@@ -49,7 +49,7 @@ diffIndex :: Ref -> Repo -> IO ([DiffTreeItem], IO Bool)
 diffIndex ref = diffIndex' ref [Param "--cached"]
 
 {- Diffs between a tree and the working tree. Does nothing if there is not
- - yet a commit in the repository, of if the repository is bare. -}
+ - yet a commit in the repository, or if the repository is bare. -}
 diffWorkTree :: Ref -> Repo -> IO ([DiffTreeItem], IO Bool)
 diffWorkTree ref repo =
 	ifM (Git.Ref.headExists repo)

Git/Index.hs

@@ -30,3 +30,7 @@ override index = do
 
 indexFile :: Repo -> FilePath
 indexFile r = localGitDir r </> "index"
+
+{- Git locks the index by creating this file. -}
+indexFileLock :: Repo -> FilePath
+indexFileLock r = indexFile r ++ ".lock"

Git/Merge.hs

@@ -1,6 +1,6 @@
 {- git merging
  -
- - Copyright 2012 Joey Hess <joey@kitenet.net>
+ - Copyright 2012, 2014 Joey Hess <joey@kitenet.net>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -19,3 +19,15 @@ mergeNonInteractive branch
 	| otherwise = merge [Param "--no-edit", Param $ fromRef branch]
   where
 	merge ps = runBool $ Param "merge" : ps
+
+{- Stage the merge into the index, but do not commit it.-}
+stageMerge :: Ref -> Repo -> IO Bool
+stageMerge branch = runBool
+	[ Param "merge"
+	, Param "--quiet"
+	, Param "--no-commit"
+	-- Without this, a fast-forward merge is done, since it involves no
+	-- commit.
+	, Param "--no-ff"
+	, Param $ fromRef branch
+	]

debian/changelog

@@ -3,6 +3,11 @@ git-annex (5.20140607) UNRELEASED; urgency=medium
   * Ignore setsid failures.
   * Avoid leaving behind .tmp files when failing in some cases, including
     importing files to a disk that is full.
+  * direct mode: Avoid committing a merge until after the work tree is
+    updated. This avoids an interrupted merge leaving the work tree out
+    of sync with the last commit, which could result in the wrong thing
+    being committed later, and files appearing to get deleted.
+    (They could be recovered by reverting the bad commit.)
 
  -- Joey Hess <joeyh@debian.org>  Mon, 09 Jun 2014 14:44:09 -0400
 

doc/bugs/direct_mode_merge_interrupt.mdwn

@@ -17,10 +17,30 @@ mode repo can get them back.
 To fix this, direct mode merge would need to avoid updating the current
 branch when merging the remote branch into it (how?). It should first
 update the whole work tree, and only after it's updated should it update
-the current branch to reflect the merge. (I assume this is how `git merge`
+the index and the current branch to reflect the merge.  
-normally works.) --[[Joey]]
+
+This way, if the merge is interrupted, the work tree may have uncommitted
+changed -- but it's fine if they get accidentially committed, since when
+the merge is re-done, those changes will by the same ones made by the
+merge. (I assume this is how `git merge` normally works.) --[[Joey]]
 
 > Implemented that. And then realized that even updating the index
 > as part of a merge results in the work tree being out of sync with the
 > index. Which will cause the next sync to again delete any files that
-> are in the index but not the work tree. Urgh. --[[Joey]]
+> are in the index but not the work tree. Urgh. 
+> 
+> Seems that a direct mode
+> merge also needs to use a different index file to stage its changes?
+> (Ugh)
+> > [[done]] --[[Joey]]
+> 
+> Or could perhaps use `git-merge-tree`
+> and avoid staging the merge in the index until the work-tree is updated.
+> 
+> Alternatively, could use another strategy.. Add a lock file which is held while 
+> the merge is in progress and contains the pre-merge sha.
+> If the lock file is present but not held, state is inconsistent.
+> `git-annex sync` and the SanityChecker should
+> then run mergeDirectCleanup to recover, before any commits can be made
+> from the inconsistent state. This approach seems to get complicated
+> quickly.. --[[Joey]]