more core.sharedRepository perm fixes

Fix more places where files in .git/annex/ were written with modes that
did not take the core.sharedRepository config into account.

This commit was sponsored by Jeff Goeke-Smith on Patreon.

Annex/Branch.hs

@@ -57,6 +57,7 @@ import Annex.CatFile
 import Annex.Perms
 import Logs
 import Logs.Transitions
+import Logs.File
 import Logs.Trust.Pure
 import Logs.Difference.Pure
 import Annex.ReplaceFile
@@ -420,8 +421,7 @@ needUpdateIndex branchref = do
 setIndexSha :: Git.Ref -> Annex ()
 setIndexSha ref = do
 	f <- fromRepo gitAnnexIndexStatus
-	liftIO $ writeFile f $ fromRef ref ++ "\n"
-	setAnnexFilePerm f
+	writeLogFile f $ fromRef ref ++ "\n"
 	runAnnexHook postUpdateAnnexHook
 
 {- Stages the journal into the index and returns an action that will
@@ -583,7 +583,7 @@ ignoreRefs rs = do
 	old <- getIgnoredRefs
 	let s = S.unions [old, S.fromList rs]
 	f <- fromRepo gitAnnexIgnoredRefs
-	replaceFile f $ \tmp -> liftIO $ writeFile tmp $
+	writeLogFile f $
 		unlines $ map fromRef $ S.elems s
 
 getIgnoredRefs :: Annex (S.Set Git.Sha)
@@ -600,7 +600,7 @@ addMergedRefs new = do
 	-- Keep only the newest sha for each branch.
 	let l = nubBy ((==) `on` snd) (new ++ old)
 	f <- fromRepo gitAnnexMergedRefs
-	replaceFile f $ \tmp -> liftIO $ writeFile tmp $
+	writeLogFile f $
 		unlines $ map (\(s, b) -> fromRef s ++ '\t' : fromRef b) l
 
 getMergedRefs :: Annex (S.Set Git.Sha)

Annex/Content/Direct.hs

@@ -34,6 +34,7 @@ import Annex.Perms
 import qualified Git
 import Utility.Tmp
 import Logs.Location
+import Logs.File
 import Utility.InodeCache
 import Utility.CopyFile
 import Annex.ReplaceFile
@@ -67,7 +68,7 @@ changeAssociatedFiles key transform = do
 	let files' = transform files
 	when (files /= files') $
 		modifyContent mapping $
-			liftIO $ viaTmp writeFile mapping $ unlines files'
+			writeLogFile mapping $ unlines files'
 	top <- fromRepo Git.repoPath
 	return $ map (top </>) files'
 

Logs/File.hs

@@ -11,6 +11,9 @@ import Annex.Common
 import Annex.Perms
 import Utility.Tmp
 
+-- | Writes content to a file, replacing the file atomically, and
+-- making the new file have whatever permissions the git repository is
+-- configured to use. Creates the parent directory when necessary.
 writeLogFile :: FilePath -> String -> Annex ()
 writeLogFile f c = go `catchNonAsync` \_e -> do
 	-- Most of the time, the directory will exist, so this is only