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.

Test.hs

@@ -79,9 +79,11 @@ import qualified Remote.Helper.Encryptable
 import qualified Types.Crypto
 import qualified Utility.Gpg
 #endif
+import qualified Messages
 
 main :: [String] -> IO ()
 main ps = do
+	Messages.enableDebugOutput
 	let tests = testGroup "Tests"
 		-- Test both direct and indirect mode.
 		-- Windows is only going to use direct mode,