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.

Annex/Content/Direct.hs

@@ -114,7 +114,7 @@ addAssociatedFile key file = do
 normaliseAssociatedFile :: FilePath -> Annex FilePath
 normaliseAssociatedFile file = do
 	top <- fromRepo Git.repoPath
-	liftIO $ relPathDirToFile top <$> absPath file
+	liftIO $ relPathDirToFile top file
 
 {- Checks if a file in the tree, associated with a key, has not been modified.
  -

Annex/Direct/Fixup.hs

@@ -10,16 +10,17 @@ module Annex.Direct.Fixup where
 import Git.Types
 import Git.Config
 import qualified Git.Construct as Construct
-import Utility.Path
 import Utility.SafeCommand
 
+import System.FilePath
+
 {- Direct mode repos have core.bare=true, but are not really bare.
  - Fix up the Repo to be a non-bare repo, and arrange for git commands
  - run by git-annex to be passed parameters that override this setting. -}
 fixupDirect :: Repo -> IO Repo
 fixupDirect r@(Repo { location = l@(Local { gitdir = d, worktree = Nothing }) }) = do
 	let r' = r
-		{ location = l { worktree = Just (parentDir d) }
+		{ location = l { worktree = Just (takeDirectory d) }
 		, gitGlobalOpts = gitGlobalOpts r ++
 			[ Param "-c"
 			, Param $ coreBare ++ "=" ++ boolConfig False