refix bug in a better way

Always run Git.Config.store, so when the git config gets reloaded,
the override gets re-added to it, and changeGitRepo then calls extractGitConfig
on it and sees the annex.* settings from the override.

Remove any prior occurance of -c v and add it to the end. This way,
-c foo=1 -c foo=2 -c foo=1 will pass -c foo=1 to git, rather than -c foo=2

Note that, if git had some multiline config that got built up by
multiple -c's, this would not work still. But it never worked because
before the bug got fixed in the first place, the -c value was repeated
many times, so the multivalue thing would have been wrong. I don't think
-c can be used with multiline configs anyway, though git-config does
talk about them?

CmdLine/GitAnnex/Options.hs

@@ -94,9 +94,7 @@ gitAnnexGlobalOptions = commonGlobalOptions ++
   where
 	setnumcopies n = Annex.changeState $ \s -> s { Annex.forcenumcopies = Just $ NumCopies n }
 	setuseragent v = Annex.changeState $ \s -> s { Annex.useragent = Just v }
-	setgitconfig v = Annex.adjustGitRepo $ \r ->
-		Git.Config.store (encodeBS' v) Git.Config.ConfigList $ 
-			r { gitGlobalOpts = gitGlobalOpts r ++ [Param "-c", Param v] }
+	setgitconfig v = Annex.addGitConfigOverride v
 	setdesktopnotify v = Annex.changeState $ \s -> s { Annex.desktopnotify = Annex.desktopnotify s <> v }
 
 {- Parser that accepts all non-option params. -}