add back non-preferred files to imported tree

Prevents merging the import from deleting the non-preferred files from
the branch it's merged into.

adjustTree previously appended the new list of items to the old, which
could result in it generating a tree with multiple files with the same
name. That is not good and confuses some parts of git. Gave it a
function to resolve such conflicts.

That allowed dealing with the problem of what happens when the import
contains some files (or subtrees) with the same name as files that were
filtered out of the export. The files from the import win.

Command/Export.hs

@@ -442,19 +442,29 @@ removeEmptyDirectories r db loc ks
 -- expression.
 newtype PreferredFiltered t = PreferredFiltered t
 
+-- | Filters the tree to files that are preferred content of the remote.
+--
+-- A log is written with files that were filtered out, so they can be added
+-- back in when importing from the remote.
 filterPreferredContent :: Remote -> Git.Ref -> Annex (PreferredFiltered Git.Ref)
-filterPreferredContent r tree = do
+filterPreferredContent r tree = logExportExcluded (uuid r) $ \logwriter -> do
 	m <- preferredContentMap
 	case M.lookup (uuid r) m of
-		Just matcher | not (isEmpty matcher) -> 
-			PreferredFiltered <$> go matcher
+		Just matcher | not (isEmpty matcher) -> do
+			PreferredFiltered <$> go matcher logwriter
 		_ -> return (PreferredFiltered tree)
   where
-	go matcher = do
+	go matcher logwriter = do
 		g <- Annex.gitRepo
-		Git.Tree.adjustTree (checkmatcher matcher) [] [] tree g
+		Git.Tree.adjustTree
+			(checkmatcher matcher logwriter)
+			[]
+			(\_old new -> new)
+			[]
+			tree
+			g
 	
-	checkmatcher matcher ti@(Git.Tree.TreeItem topf _ sha) =
+	checkmatcher matcher logwriter ti@(Git.Tree.TreeItem topf _ sha) =
 		catKey sha >>= \case
 			Just k -> do
 				-- Match filename relative to the
@@ -464,7 +474,9 @@ filterPreferredContent r tree = do
 				let mi = MatchingKey k af
 				ifM (checkMatcher' matcher mi mempty)
 					( return (Just ti)
-					, return Nothing
+					, do
+						() <- liftIO $ logwriter ti
+						return Nothing
 					)
 			-- Always export non-annexed files.
 			Nothing -> return (Just ti)