checkout: Always replace existing content in overlay mode

The combination of the "honor whiteout" and "union" flags
are intended to basically be "merge trees like overlayfs does".
But we were missing this case in order to support e.g. replacing
a symlink with a directory.

src/libostree/ostree-repo-checkout.c

@@ -1062,6 +1062,21 @@ checkout_tree_at_recurse (OstreeRepo *self, OstreeRepoCheckoutAtOptions *options
         if (!glnx_shutil_rm_rf_at (destination_parent_fd, destination_name, cancellable, error))
           return FALSE;
       }
+    else if (options->process_whiteouts
+             && options->overwrite_mode == OSTREE_REPO_CHECKOUT_OVERWRITE_UNION_FILES)
+      {
+        /* In this mode, we're flattening in a manner similar to overlayfs, so ensure
+         * any non-directory content there is gone. /
+         */
+        struct stat stbuf;
+        if (!glnx_fstatat_allow_noent (destination_parent_fd, destination_name, &stbuf, AT_SYMLINK_NOFOLLOW, error))
+          return FALSE;
+        if (errno == 0 && !S_ISDIR (stbuf.st_mode))
+          {
+            if (!glnx_shutil_rm_rf_at (destination_parent_fd, destination_name, cancellable, error))
+              return FALSE;
+          }
+      }
 
     /* Create initially with mode 0700, then chown/chmod only when we're
      * done.  This avoids anyone else being able to operate on partially

tests/basic-test.sh

@@ -1159,6 +1159,18 @@ if touch overlay/baz/.wh.cow && touch overlay/.wh.deeper && touch overlay/baz/an
     assert_has_file overlay-co/baz
     test -L overlay-co/anewdir
 
+    rm overlay-co overlay -rf
+    mkdir -p overlay/somelink overlay/yet/ovlnewdir
+    echo ovlnewf > overlay/yet/ovlnewdir/ovlnewf
+    $OSTREE --repo=repo commit ${COMMIT_ARGS} -b overlay-symlink-convert --tree=dir=overlay
+    for branch in test2 overlay-symlink-convert; do
+        $OSTREE --repo=repo checkout --union --whiteouts ${branch} overlay-co
+    done
+    test -d overlay-co/somelink || fatal "should replace symlink with dir"
+    assert_has_dir overlay-co/yet/another
+    assert_has_dir overlay-co/yet/ovlnewdir
+    assert_file_has_content overlay-co/yet/ovlnewdir/ovlnewf ovlnewf
+    rm overlay-co overlay -rf
     echo "ok whiteouts enabled"
 
     # Now double check whiteouts are not processed without --whiteouts