Automatically convert direct mode repositories to v7 with adjusted unlocked branches

* Automatically convert direct mode repositories to v7 with adjusted
  unlocked branches and set annex.thin.
* init: When run on a crippled filesystem with --version=5,
  will error out, since version 7 is needed for adjusted unlocked branch.
* direct: This command always errors out as direct mode is no longer
  supported.
* indirect: This command has become a deprecated noop.
* proxy: This command is deprecated because it was only needed in direct
  mode. (But it continues to work.)

Also removed mentions of direct mode throughough the documentation.

I have not removed all the direct mode code yet.

Command/Indirect.hs

@@ -8,89 +8,14 @@
 module Command.Indirect where
 
 import Command
-import qualified Git
-import qualified Git.Branch
-import qualified Git.LsFiles
-import Git.FileMode
-import Config
-import qualified Annex
-import Annex.Direct
-import Annex.Content
-import Annex.Content.Direct
-import Annex.CatFile
-import Annex.Init
-import Annex.Ingest
 
 cmd :: Command
 cmd = notBareRepo $ noDaemonRunning $
-	command "indirect" SectionSetup "switch repository to indirect mode"
+	command "indirect" SectionSetup "switch repository to indirect mode (deprecated)"
 		paramNothing (withParams seek)
 
 seek :: CmdParams -> CommandSeek
 seek = withNothing (commandAction start)
 
 start :: CommandStart
-start = ifM isDirect
-	( do
-		unlessM (coreSymlinks <$> Annex.getGitConfig) $
-			giveup "Git is configured to not use symlinks, so you must use direct mode."
-		whenM probeCrippledFileSystem $
-			giveup "This repository seems to be on a crippled filesystem, you must use direct mode."
-		starting "indirect" (ActionItemOther Nothing) 
-			perform
-	, stop
-	)
-
-perform :: CommandPerform
-perform = do
-	whenM stageDirect $ do
-		showOutput
-		void $ inRepo $ Git.Branch.commitCommand Git.Branch.ManualCommit
-			[ Param "-m"
-			, Param "commit before switching to indirect mode"
-			]
-
-	-- Note that we set indirect mode early, so that we can use
-	-- moveAnnex in indirect mode.
-	setDirect False
-
-	top <- fromRepo Git.repoPath
-	(l, clean) <- inRepo $ Git.LsFiles.stagedOthersDetails [top]
-	forM_ l go
-	void $ liftIO clean
-	next $ return True
-  where
-	{- Walk tree from top and move all present direct mode files into
-	 - the annex, replacing with symlinks. Also delete direct mode
-	 - caches and mappings. -}
-	go (f, Just sha, Just mode) | isSymLink mode = do
-		r <- liftIO $ catchMaybeIO $ getSymbolicLinkStatus f
-		case r of
-			Just s
-				| isSymbolicLink s -> void $ flip whenAnnexed f $
-					\_ k -> do
-						removeInodeCache k
-						removeAssociatedFiles k
-						return Nothing
-				| otherwise -> 
-					maybe noop (fromdirect f)
-						=<< catKey sha
-			_ -> noop
-	go _ = noop
-
-	fromdirect f k = do
-		removeInodeCache k
-		removeAssociatedFiles k
-		whenM (liftIO $ not . isSymbolicLink <$> getSymbolicLinkStatus f) $ do
-			v <- tryNonAsync (moveAnnex k f)
-			case v of
-				Right True -> do 
-					l <- calcRepo $ gitAnnexLink f k
-					liftIO $ createSymbolicLink l f
-				Right False -> warnlocked "Failed to move file to annex"
-				Left e -> catchNonAsync (restoreFile f k e) $
-					warnlocked . show
-
-	warnlocked msg = do
-		warning msg
-		warning "leaving this file as-is; correct this problem and run git annex add on it"
+start = stop