Switch to using relative paths to the git repository.

This allows the git repository to be moved while git-annex is running in
it, with fewer problems.

On Windows, this avoids some of the problems with the absurdly small
MAX_PATH of 260 bytes. In particular, git-annex repositories should
work in deeper/longer directory structures than before. See
http://git-annex.branchable.com/bugs/__34__git-annex:_direct:_1_failed__34___on_Windows/

There are several possible ways this change could break git-annex:

1. If it changes its working directory while it's running, that would
   be Bad News. Good news everyone! git-annex never does so. It would also
   break thread safety, so all such things were stomped out long ago.

2. parentDir "." -> "" which is not a valid path. I had to fix one
   instace of this, and I should probably wipe all calls to parentDir out
   of the git-annex code base; it was never a good idea.

3. Things like relPathDirToFile require absolute input paths,
   and code assumes that the git repo path is absolute and passes it to it
   as-is. In the case of relPathDirToFile, I converted it to not make
   this assumption.

Currently, the test suite has 16 failures.

Git/CheckAttr.hs

@@ -84,7 +84,7 @@ checkAttr (h, attrs, oldgit, currdir) want file = do
 	 - so use relative filenames. -}
 	file'
 		| oldgit = absPathFrom currdir file
-		| otherwise = relPathDirToFile currdir $ absPathFrom currdir file
+		| otherwise = relPathDirToFileAbs currdir $ absPathFrom currdir file
 	oldattrvalue attr l = end bits !! 0
 	  where
 		bits = split sep l

Git/Command.hs

@@ -16,7 +16,7 @@ import qualified Utility.CoProcess as CoProcess
 
 {- Constructs a git command line operating on the specified repo. -}
 gitCommandLine :: [CommandParam] -> Repo -> [CommandParam]
-gitCommandLine params r@(Repo { location = l@(Local _ _ ) }) =
+gitCommandLine params r@(Repo { location = l@(Local { } ) }) =
 	setdir : settree ++ gitGlobalOpts r ++ params
   where
 	setdir = Param $ "--git-dir=" ++ gitdir l

Git/FilePath.hs

@@ -39,8 +39,7 @@ fromTopFilePath p repo = absPathFrom (repoPath repo) (getTopFilePath p)
 
 {- The input FilePath can be absolute, or relative to the CWD. -}
 toTopFilePath :: FilePath -> Git.Repo -> IO TopFilePath
-toTopFilePath file repo = TopFilePath <$>
-	relPathDirToFile (repoPath repo) <$> absPath file
+toTopFilePath file repo = TopFilePath <$> relPathDirToFile (repoPath repo) file
 
 {- The input FilePath must already be relative to the top of the git
  - repository -}

Git/LsFiles.hs

@@ -131,9 +131,9 @@ typeChanged' ps l repo = do
 	(fs, cleanup) <- pipeNullSplit (prefix ++ ps ++ suffix) repo
 	-- git diff returns filenames relative to the top of the git repo;
 	-- convert to filenames relative to the cwd, like git ls-files.
-	let top = repoPath repo
+	top <- absPath (repoPath repo)
 	currdir <- getCurrentDirectory
-	return (map (\f -> relPathDirToFile currdir $ top </> f) fs, cleanup)
+	return (map (\f -> relPathDirToFileAbs currdir $ top </> f) fs, cleanup)
   where
 	prefix = [Params "diff --name-only --diff-filter=T -z"]
 	suffix = Param "--" : (if null l then [File "."] else map File l)

Git/Repair.hs

@@ -225,10 +225,13 @@ badBranches missing r = filterM isbad =<< getAllRefs r
  - Relies on packed refs being exploded before it's called.
  -}
 getAllRefs :: Repo -> IO [Ref]
-getAllRefs r = map toref <$> dirContentsRecursive refdir
-  where
-	refdir = localGitDir r </> "refs"
-	toref = Ref . relPathDirToFile (localGitDir r)
+getAllRefs r = getAllRefs' (localGitDir r </> "refs")
+
+getAllRefs' :: FilePath -> IO [Ref]
+getAllRefs' refdir = do
+	let topsegs = length (splitPath refdir) - 1
+	let toref = Ref . joinPath . drop topsegs . splitPath
+	map toref <$> dirContentsRecursive refdir
 
 explodePackedRefsFile :: Repo -> IO ()
 explodePackedRefsFile r = do