repo-commit: preserve existing object inode when staging to objects/

When ostree commit --consume is used and an object with the same
checksum already exists in objects/, rename_pending_loose_objects() was
unconditionally renaming the staging copy over it.  On Linux, renameat(2)
atomically replaces the destination for two regular files, silently
changing the inode of the existing repo object.

Fix this by checking whether the object already exists in objects/
before renaming.  If it does, the content is identical by definition
(the object store is content-addressed by SHA256), so we can simply
unlink the staging copy and keep the existing object with its original
inode.

Exception: .commitmeta objects are keyed by commit checksum rather than
their own content, so they can be updated in place (e.g. when GPG
signatures are added or deleted via ostree gpg-sign).  These are always
renamed unconditionally.

Author: electricface

src/libostree/ostree-repo-commit.c

@@ -1801,8 +1801,33 @@ rename_pending_loose_objects (OstreeRepo *self, GCancellable *cancellable, GErro
                                                     cancellable, error))
             return FALSE;
 
-          if (!glnx_renameat (child_dfd_iter.fd, loose_objpath + 3, self->objects_dir_fd,
-                              loose_objpath, error))
+          /* If the object already exists in objects/, preserve it (and its
+           * inode) rather than replacing it with the staging copy.  The store
+           * is content-addressed, so an existing file at this path has the
+           * same content by definition.
+           *
+           * Exception: .commitmeta objects are keyed by commit checksum, not
+           * by their own content, so they can be updated in place (e.g. when
+           * GPG signatures are added or deleted).  Always rename those.
+           */
+          gboolean obj_exists = FALSE;
+          if (!g_str_has_suffix (child_dent->d_name, ".commitmeta"))
+            {
+              struct stat obj_stbuf;
+              errno = 0;
+              if (!glnx_fstatat_allow_noent (self->objects_dir_fd, loose_objpath, &obj_stbuf,
+                                             AT_SYMLINK_NOFOLLOW, error))
+                return FALSE;
+              obj_exists = (errno != ENOENT);
+            }
+          if (obj_exists)
+            {
+              /* Object already present with same content; drop staging copy */
+              if (!glnx_unlinkat (child_dfd_iter.fd, loose_objpath + 3, 0, error))
+                return FALSE;
+            }
+          else if (!glnx_renameat (child_dfd_iter.fd, loose_objpath + 3, self->objects_dir_fd,
+                                   loose_objpath, error))
             return FALSE;
         }
     }