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.

Logs/File.hs

@@ -5,11 +5,12 @@
  - Licensed under the GNU AGPL version 3 or higher.
  -}
 
-module Logs.File (writeLogFile, appendLogFile, streamLogFile) where
+module Logs.File (writeLogFile, withLogHandle, appendLogFile, streamLogFile) where
 
 import Annex.Common
 import Annex.Perms
 import Annex.LockFile
+import Annex.ReplaceFile
 import qualified Git
 import Utility.Tmp
 
@@ -23,6 +24,19 @@ writeLogFile f c = createDirWhenNeeded f $ viaTmp writelog f c
 		liftIO $ writeFile f' c'
 		setAnnexFilePerm f'
 
+-- | Runs the action with a handle connected to a temp file.
+-- The temp file replaces the log file once the action succeeds.
+withLogHandle :: FilePath -> (Handle -> Annex a) -> Annex a
+withLogHandle f a = do
+	createAnnexDirectory (parentDir f)
+	replaceFile f $ \tmp ->
+		bracket (setup tmp) cleanup a
+  where
+	setup tmp = do
+		setAnnexFilePerm tmp
+		liftIO $ openFile tmp WriteMode
+	cleanup h = liftIO $ hClose h
+
 -- | Appends a line to a log file, first locking it to prevent
 -- concurrent writers.
 appendLogFile :: FilePath -> (Git.Repo -> FilePath) -> String -> Annex ()