use TopFilePath for associated files

Fixes several bugs with updates of pointer files. When eg, running
git annex drop --from localremote
it was updating the pointer file in the local repository, not the remote.
Also, fixes drop ../foo when run in a subdir, and probably lots of other
problems. Test suite drops from ~30 to 11 failures now.

TopFilePath is used to force thinking about what the filepath is relative
to.

The data stored in the sqlite db is still just a plain string, and
TopFilePath is a newtype, so there's no overhead involved in using it in
DataBase.Keys.

Command/Smudge.hs

@@ -15,6 +15,7 @@ import Annex.FileMatcher
 import Annex.Ingest
 import Logs.Location
 import qualified Database.Keys
+import Git.FilePath
 
 import qualified Data.ByteString.Lazy as B
 
@@ -58,7 +59,7 @@ smudge file = do
 						=<< catchMaybeIO (B.readFile content)
 				, liftIO $ B.putStr b
 				)
-			Database.Keys.addAssociatedFile k file
+			Database.Keys.addAssociatedFile k =<< inRepo (toTopFilePath file)
 	stop
 
 -- Clean filter is fed file content on stdin, decides if a file