include locked files in the keys database associated files

Before only unlocked files were included.

The initial scan now scans for locked as well as unlocked files. This
does mean it gets a little bit slower, although I optimised it as well
as I think it can be.

reconcileStaged changed to diff from the current index to the tree of
the previous index. This lets it handle deletions as well, removing
associated files for both locked and unlocked files, which did not
always happen before.

On upgrade, there will be no recorded previous tree, so it will diff
from the empty tree to current index, and so will fully populate the
associated files, as well as removing any stale associated files
that were present due to them not being removed before.

reconcileStaged now does a bit more work. Most of the time, this will
just be due to running more often, after some change is made to the
index, and since there will be few changes since the last time, it will
not be a noticable overhead. What may turn out to be a noticable
slowdown is after changing to a branch, it has to go through the diff
from the previous index to the new one, and if there are lots of
changes, that could take a long time. Also, after adding a lot of files,
or deleting a lot of files, or moving a large subdirectory, etc.

Command.Lock used removeAssociatedFile, but now that's wrong because a
newly locked file still needs to have its associated file tracked.

Command.Rekey used removeAssociatedFile when the file was unlocked.
It could remove it also when it's locked, but it is not really
necessary, because it changes the index, and so the next time git-annex
run and accesses the keys db, reconcileStaged will run and update it.

There are probably several other places that use addAssociatedFile and
don't need to any more for similar reasons. But there's no harm in
keeping them, and it probably is a good idea to, if only to support
mixing this with older versions of git-annex.

However, mixing this and older versions does risk reconcileStaged not
running, if the older version already ran it on a given index state. So
it's not a good idea to mix versions. This problem could be dealt with
by changing the name of the gitAnnexKeysDbIndexCache, but that would
leave the old file dangling, or it would need to keep trying to remove
it.

Command/ReKey.hs

@@ -15,8 +15,6 @@ import Annex.Link
 import Annex.Perms
 import Annex.ReplaceFile
 import Logs.Location
-import Git.FilePath
-import qualified Database.Keys
 import Annex.InodeSentinal
 import Utility.InodeCache
 import qualified Utility.RawFilePath as R
@@ -79,7 +77,7 @@ perform file oldkey newkey = do
 		, unlessM (Annex.getState Annex.force) $
 			giveup $ fromRawFilePath file ++ " is not available (use --force to override)"
 		)
-	next $ cleanup file oldkey newkey
+	next $ cleanup file newkey
 
 {- Make a hard link to the old key content (when supported),
  - to avoid wasting disk space. -}
@@ -119,8 +117,8 @@ linkKey file oldkey newkey = ifM (isJust <$> isAnnexLink file)
 					LinkAnnexNoop -> True
 	)
 
-cleanup :: RawFilePath -> Key -> Key -> CommandCleanup
-cleanup file oldkey newkey = do
+cleanup :: RawFilePath -> Key -> CommandCleanup
+cleanup file newkey = do
 	ifM (isJust <$> isAnnexLink file)
 		( do
 			-- Update symlink to use the new key.
@@ -131,8 +129,6 @@ cleanup file oldkey newkey = do
 			liftIO $ whenM (isJust <$> isPointerFile file) $
 				writePointerFile file newkey mode
 			stagePointerFile file mode =<< hashPointerFile newkey
-			Database.Keys.removeAssociatedFile oldkey 
-				=<< inRepo (toTopFilePath file)
 		)
 	whenM (inAnnex newkey) $
 		logStatus newkey InfoPresent