[SyncFS] Clean up MetadataDatabase update methods

 * Drop unneeded change_id parameter
 * Fix deletion behavior of UpdateBy{ChangeList,FileResource}
 * Add UpdateByDeletedFile

BUG=240165
R=kinuko@chromium.org, nhiroki@chromium.org

Review URL: https://codereview.chromium.org/95143002

git-svn-id: svn://svn.chromium.org/chrome/trunk/src@237872 0039d316-1c4b-4281-b951-d872f2087c98
SVN changes up to revision 237872