Repository tuning parameters can now be passed when initializing a repository for the first time.

* init: Repository tuning parameters can now be passed when initializing a
  repository for the first time. For details, see
  http://git-annex.branchable.com/tuning/
* merge: Refuse to merge changes from a git-annex branch of a repo
  that has been tuned in incompatable ways.

Command/Add.hs

@@ -230,7 +230,7 @@ undo file key e = do
 {- Creates the symlink to the annexed content, returns the link target. -}
 link :: FilePath -> Key -> Maybe InodeCache -> Annex String
 link file key mcache = flip catchNonAsync (undo file key) $ do
-	l <- inRepo $ gitAnnexLink file key
+	l <- calcRepo $ gitAnnexLink file key
 	replaceFile file $ makeAnnexLink l
 
 	-- touch symlink to have same time as the original file,
@@ -272,7 +272,7 @@ cleanup :: FilePath -> Key -> Maybe InodeCache -> Bool -> CommandCleanup
 cleanup file key mcache hascontent = do
 	ifM (isDirect <&&> pure hascontent)
 		( do
-			l <- inRepo $ gitAnnexLink file key
+			l <- calcRepo $ gitAnnexLink file key
 			stageSymlink file =<< hashSymlink l
 		, addLink file key mcache
 		)

Command/Fix.hs

@@ -28,7 +28,7 @@ seek = withFilesInGit $ whenAnnexed start
 {- Fixes the symlink to an annexed file. -}
 start :: FilePath -> Key -> CommandStart
 start file key = do
-	link <- inRepo $ gitAnnexLink file key
+	link <- calcRepo $ gitAnnexLink file key
 	stopUnless ((/=) (Just link) <$> liftIO (catchMaybeIO $ readSymbolicLink file)) $ do
 		showStart "fix" file
 		next $ perform file link

Command/FromKey.hs

@@ -33,7 +33,7 @@ start _ = error "specify a key and a dest file"
 
 perform :: Key -> FilePath -> CommandPerform
 perform key file = do
-	link <- inRepo $ gitAnnexLink file key
+	link <- calcRepo $ gitAnnexLink file key
 	liftIO $ createDirectoryIfMissing True (parentDir file)
 	liftIO $ createSymbolicLink link file
 	next $ cleanup file

Command/Fsck.hs

@@ -192,7 +192,7 @@ check cs = and <$> sequence cs
  -}
 fixLink :: Key -> FilePath -> Annex Bool
 fixLink key file = do
-	want <- inRepo $ gitAnnexLink file key
+	want <- calcRepo $ gitAnnexLink file key
 	have <- getAnnexLinkTarget file
 	maybe noop (go want) have
 	return True

Command/Indirect.hs

@@ -88,7 +88,7 @@ perform = do
 			v <- tryNonAsync (moveAnnex k f)
 			case v of
 				Right _ -> do 
-					l <- inRepo $ gitAnnexLink f k
+					l <- calcRepo $ gitAnnexLink f k
 					liftIO $ createSymbolicLink l f
 				Left e -> catchNonAsync (Command.Add.undo f k e)
 					warnlocked