reuse hashes of dotfiles/dirs/submodules when entering view

This fixes a crash when a git submodule has a name starting with a dot.
Such a submodule might contain dotfiles that are intended to be used when
inside the view (since a dot-directory that's not a submodule was already
preserved when entering a view). So, rather than eliminating the submodule
from the view, its git ls-files --stage hash is copied over into the view.

dotfiles/dirs have their git ls-files --stage hashes similarly copied over
to the view. This is more efficient and simpler than the old method,
and also won't break if git ever adds a new type of tree item, like was
done with submodules.

Since the content of dotfiles in the working tree is no longer hashed
when entering a view, when there are unstaged modifications, they are
not included in the view branch. Entering the view branch still works,
but git checkout shows "M .dotfile", and git diff will show the unstaged
changes. This seems like an improvement over the old behavior.

Also made Command.View not delete empty directories that are submodules
when entering a view, while still deleting other empty directories.

This commit was supported by the NSF-funded DataLad project.

Command/View.hs

@@ -12,6 +12,8 @@ import qualified Git
 import qualified Git.Command
 import qualified Git.Ref
 import qualified Git.Branch
+import qualified Git.LsFiles as LsFiles
+import Git.FilePath
 import Types.View
 import Annex.View
 import Logs.View
@@ -65,15 +67,21 @@ checkoutViewBranch view mkbranch = do
 	when ok $ do
 		setView view
 		{- A git repo can easily have empty directories in it,
-		 - and this pollutes the view, so remove them. -}
-		top <- fromRepo Git.repoPath
-		liftIO $ removeemptydirs top
+		 - and this pollutes the view, so remove them.
+		 - (However, emptry directories used by submodules are not
+		 - removed.) -}
+		top <- liftIO . absPath =<< fromRepo Git.repoPath
+		(l, cleanup) <- inRepo $
+			LsFiles.notInRepoIncludingEmptyDirectories False [top]
+		forM_ l (removeemptydir top)
+		liftIO $ void cleanup
 		unlessM (liftIO $ doesDirectoryExist here) $ do
 			showLongNote (cwdmissing top)
 	return ok
   where
-	removeemptydirs top = mapM_ (tryIO . removeDirectory)
-		=<< dirTreeRecursiveSkipping (".git" `isSuffixOf`) top
+	removeemptydir top d = do
+		p <- inRepo $ toTopFilePath d
+		liftIO $ tryIO $ removeDirectory (top </> getTopFilePath p)
 	cwdmissing top = unlines
 		[ "This view does not include the subdirectory you are currently in."
 		, "Perhaps you should:  cd " ++ top