diff --git a/resolve-trivial-conflicts.cabal b/resolve-trivial-conflicts.cabal
--- a/resolve-trivial-conflicts.cabal
+++ b/resolve-trivial-conflicts.cabal
@@ -2,7 +2,7 @@
 -- further documentation, see http://haskell.org/cabal/users-guide/
 
 name:                resolve-trivial-conflicts
-version:             0.3.2
+version:             0.3.2.1
 synopsis:            Remove trivial conflict markers in a git repository
 description:         Remove trivial conflict markers in a git repository
 homepage:            https://github.com/ElastiLotem/resolve-trivial-conflicts
diff --git a/resolve_trivial_conflicts.hs b/resolve_trivial_conflicts.hs
--- a/resolve_trivial_conflicts.hs
+++ b/resolve_trivial_conflicts.hs
@@ -297,13 +297,17 @@
     FilePath -> (FilePath -> Maybe FilePath -> Maybe FilePath -> IO b) -> IO b
 withAllStageFiles path action =
     do  let stdin = ""
-        [baseTmp, localTmp, remoteTmp] <-
+        [baseTmpRaw, localTmpRaw, remoteTmpRaw] <-
             take 3 . words <$>
             readProcess "git" ["checkout-index", "--stage=all", "--", path] stdin
+        cdup <-
+            takeWhile (/= '\0') . stripNewline <$>
+            readProcess "git" ["rev-parse", "--show-cdup"] stdin
         let maybePath "." = Nothing
-            maybePath p = Just p
-        let mLocalTmp = maybePath localTmp
-            mRemoteTmp = maybePath remoteTmp
+            maybePath p = Just (cdup </> p)
+        let mLocalTmp = maybePath localTmpRaw
+            mRemoteTmp = maybePath remoteTmpRaw
+            baseTmp = cdup </> baseTmpRaw
         action baseTmp mLocalTmp mRemoteTmp
             `E.finally`
             do  removeFile baseTmp