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.

Git/LsFiles.hs

@@ -1,6 +1,6 @@
 {- git ls-files interface
  -
- - Copyright 2010,2012 Joey Hess <id@joeyh.name>
+ - Copyright 2010-2018 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -8,6 +8,7 @@
 module Git.LsFiles (
 	inRepo,
 	notInRepo,
+	notInRepoIncludingEmptyDirectories,
 	allFiles,
 	deleted,
 	modified,
@@ -44,10 +45,14 @@ inRepo l = pipeNullSplit $
 
 {- Scans for files at the specified locations that are not checked into git. -}
 notInRepo :: Bool -> [FilePath] -> Repo -> IO ([FilePath], IO Bool)
-notInRepo include_ignored l repo = pipeNullSplit params repo
+notInRepo = notInRepo' []
+
+notInRepo' :: [CommandParam] -> Bool -> [FilePath] -> Repo -> IO ([FilePath], IO Bool)
+notInRepo' ps include_ignored l repo = pipeNullSplit params repo
   where
 	params = concat
 		[ [ Param "ls-files", Param "--others"]
+		, ps
 		, exclude
 		, [ Param "-z", Param "--" ]
 		, map File l
@@ -56,6 +61,11 @@ notInRepo include_ignored l repo = pipeNullSplit params repo
 		| include_ignored = []
 		| otherwise = [Param "--exclude-standard"]
 
+{- Scans for files at the specified locations that are not checked into
+ - git. Empty directories are included in the result. -}
+notInRepoIncludingEmptyDirectories :: Bool -> [FilePath] -> Repo -> IO ([FilePath], IO Bool)
+notInRepoIncludingEmptyDirectories = notInRepo' [Param "--directory"]
+
 {- Finds all files in the specified locations, whether checked into git or
  - not. -}
 allFiles :: [FilePath] -> Repo -> IO ([FilePath], IO Bool)