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.

Assistant/Threads/Committer.hs

@@ -352,7 +352,7 @@ handleAdds havelsof delayadd cs = returnWhen (null incomplete) $ do
 	done change mcache file key = liftAnnex $ do
 		logStatus key InfoPresent
 		link <- ifM isDirect
-			( inRepo $ gitAnnexLink file key
+			( calcRepo $ gitAnnexLink file key
 			, Command.Add.link file key mcache
 			)
 		whenM (pure DirWatcher.eventsCoalesce <||> isDirect) $

Assistant/Threads/Watcher.hs

@@ -232,7 +232,7 @@ onAddDirect symlinkssupported matcher file fs = do
 				 - so it symlink is restaged to make sure. -}
 				( ifM (shouldRestage <$> getDaemonStatus)
 					( do
-						link <- liftAnnex $ inRepo $ gitAnnexLink file key
+						link <- liftAnnex $ calcRepo $ gitAnnexLink file key
 						addLink file link (Just key)
 					, noChange
 					)
@@ -279,7 +279,7 @@ onAddSymlink' linktarget mk isdirect file filestatus = go mk
 	go (Just key) = do
 		when isdirect $
 			liftAnnex $ void $ addAssociatedFile key file
-		link <- liftAnnex $ inRepo $ gitAnnexLink file key
+		link <- liftAnnex $ calcRepo $ gitAnnexLink file key
 		if linktarget == Just link
 			then ensurestaged (Just link) =<< getDaemonStatus
 			else do