pre-commit: Update direct mode mappings.

Making the pre-commit hook look at git diff-index to find changed direct
mode files and update the mappings works pretty well.

One case where it does not work is when a file is git annex added, and then
git rmed, and then this is committed. That's a no-op commit, so the hook
probably doesn't even run, and it certianly never notices that the file
was deleted, so the mapping will still have the original filename in it.

For this and other reasons, it's important that the mappings still be
treated as possibly inconsistent.

Also, the assistant now allows the pre-commit hook to run when in direct
mode, so the mappings also get updated there.

Assistant/Threads/Committer.hs

@@ -82,12 +82,16 @@ commitStaged = do
 	case v of
 		Left _ -> return False
 		Right _ -> do
-			void $ inRepo $ Git.Command.runBool "commit" $ nomessage
-				[ Param "--quiet"
-				{- Avoid running the usual git-annex pre-commit hook;
-				 - watch does the same symlink fixing, and we don't want
-				 - to deal with unlocked files in these commits. -}
-				, Param "--no-verify"
+			direct <- isDirect
+			void $ inRepo $ Git.Command.runBool "commit" $ nomessage $
+				catMaybes
+				[ Just $ Param "--quiet"
+				{- In indirect mode, avoid running the
+				 - usual git-annex pre-commit hook;
+				 - watch does the same symlink fixing,
+				 - and we don't want to deal with unlocked
+				 - files in these commits. -}
+				, if direct then Nothing else Just $ Param "--no-verify"
 				]
 			{- Empty commits may be made if tree changes cancel
 			 - each other out, etc. Git returns nonzero on those,