Preserve execute bits of unlocked files in v6 mode.

When annex.thin is set, adding an object will add the execute bits to the
work tree file, and this does mean that the annex object file ends up
executable.

This doesn't add any complexity that wasn't already present, because git
annex add of an executable file has always ingested it so that the annex
object ends up executable.

But, since an annex object file can be executable or not, when populating
an unlocked file from one, the executable bit is always added or removed
to match the mode of the pointer file.

Command/Fix.hs

@@ -67,7 +67,8 @@ start fixwhat file key = do
 breakHardLink :: FilePath -> Key -> FilePath -> CommandPerform
 breakHardLink file key obj = do
 	replaceFile file $ \tmp -> do
-		unlessM (checkedCopyFile key obj tmp) $
+		mode <- liftIO $ catchMaybeIO $ fileMode <$> getFileStatus file
+		unlessM (checkedCopyFile key obj tmp mode) $
 			error "unable to break hard link"
 		thawContent tmp
 		modifyContent obj $ freezeContent obj
@@ -77,7 +78,8 @@ breakHardLink file key obj = do
 makeHardLink :: FilePath -> Key -> CommandPerform
 makeHardLink file key = do
 	replaceFile file $ \tmp -> do
-		r <- linkFromAnnex key tmp
+		mode <- liftIO $ catchMaybeIO $ fileMode <$> getFileStatus file
+		r <- linkFromAnnex key tmp mode
 		case r of
 			LinkAnnexFailed -> error "unable to make hard link"
 			_ -> noop

Command/Fsck.hs

@@ -301,12 +301,13 @@ verifyWorkTree key file = do
 		case mk of
 			Just k | k == key -> whenM (inAnnex key) $ do
 				showNote "fixing worktree content"
-				replaceFile file $ \tmp -> 
+				replaceFile file $ \tmp -> do
+					mode <- liftIO $ catchMaybeIO $ fileMode <$> getFileStatus file
 					ifM (annexThin <$> Annex.getGitConfig)
-						( void $ linkFromAnnex key tmp
+						( void $ linkFromAnnex key tmp mode
 						, do
 							obj <- calcRepo $ gitAnnexLocation key
-							void $ checkedCopyFile key obj tmp
+							void $ checkedCopyFile key obj tmp mode
 							thawContent tmp
 						)
 				Database.Keys.storeInodeCaches key [file]

Command/Lock.hs

@@ -78,7 +78,7 @@ performNew file key filemodified = do
 		mfc <- withTSDelta (liftIO . genInodeCache file)
 		unlessM (sameInodeCache obj (maybeToList mfc)) $ do
 			modifyContent obj $ replaceFile obj $ \tmp -> do
-				unlessM (checkedCopyFile key obj tmp) $
+				unlessM (checkedCopyFile key obj tmp Nothing) $
 					error "unable to lock file"
 			Database.Keys.storeInodeCaches key [obj]
 
@@ -92,7 +92,7 @@ performNew file key filemodified = do
 			liftIO $ nukeFile obj
 			case mfile of
 				Just unmodified ->
-					unlessM (checkedCopyFile key unmodified obj)
+					unlessM (checkedCopyFile key unmodified obj Nothing)
 						lostcontent
 				Nothing -> lostcontent
 		| otherwise = modifyContent obj $ 

Command/ReKey.hs

@@ -61,7 +61,7 @@ linkKey file oldkey newkey = ifM (isJust <$> isAnnexLink file)
 	 - and vulnerable to corruption. -}
 	( getViaTmp' DefaultVerify newkey $ \tmp -> unVerified $ do
 		oldobj <- calcRepo (gitAnnexLocation oldkey)
-		linkOrCopy' (return True) newkey oldobj tmp
+		linkOrCopy' (return True) newkey oldobj tmp Nothing
 	, do
 		ic <- withTSDelta (liftIO . genInodeCache file)
 	 	{- The file being rekeyed is itself an unlocked file, so if
@@ -69,7 +69,7 @@ linkKey file oldkey newkey = ifM (isJust <$> isAnnexLink file)
 		oldobj <- calcRepo (gitAnnexLocation oldkey)
 		v <- tryNonAsync $ modifyContent oldobj $ do
 			replaceFile oldobj $ \tmp ->
-				unlessM (checkedCopyFile oldkey file tmp) $
+				unlessM (checkedCopyFile oldkey file tmp Nothing) $
 					error "can't lock old key"
 			freezeContent oldobj
 			oldic <- withTSDelta (liftIO . genInodeCache oldobj)
@@ -95,9 +95,10 @@ cleanup file oldkey newkey = do
 			liftIO $ removeFile file
 			addLink file newkey Nothing
 		, do
+			mode <- liftIO $ catchMaybeIO $ fileMode <$> getFileStatus file
 			liftIO $ whenM (isJust <$> isPointerFile file) $
-				writeFile file (formatPointer newkey)
-			stagePointerFile file =<< hashPointerFile newkey
+				writePointerFile file newkey mode
+			stagePointerFile file mode =<< hashPointerFile newkey
 			Database.Keys.removeAssociatedFile oldkey 
 				=<< inRepo (toTopFilePath file)
 		)

Command/Unlock.hs

@@ -15,6 +15,7 @@ import Annex.Version
 import Annex.Link
 import Annex.ReplaceFile
 import Utility.CopyFile
+import Utility.FileMode
 
 cmd :: Command
 cmd = mkcmd "unlock" "unlock files for modification"
@@ -50,16 +51,17 @@ start file key = ifM (isJust <$> isAnnexLink file)
 
 performNew :: FilePath -> Key -> CommandPerform
 performNew dest key = do
+	destmode <- liftIO $ catchMaybeIO $ fileMode <$> getFileStatus dest
 	replaceFile dest $ \tmp -> do
-		r <- linkFromAnnex key tmp
+		r <- linkFromAnnex key tmp destmode
 		case r of
 			LinkAnnexOk -> return ()
 			_ -> error "unlock failed"
-	next $ cleanupNew dest key
+	next $ cleanupNew dest key destmode
 
-cleanupNew ::  FilePath -> Key -> CommandCleanup
-cleanupNew dest key = do
-	stagePointerFile dest =<< hashPointerFile key
+cleanupNew ::  FilePath -> Key -> Maybe FileMode -> CommandCleanup
+cleanupNew dest key destmode = do
+	stagePointerFile dest destmode =<< hashPointerFile key
 	return True
 
 startOld :: FilePath -> Key -> CommandStart