localrepo: prevent executable-bit only changes from being lost on amend
If you have just executable-bit change and amend it twice it will vanish:
* After the first amend the commit will have the proper executable bit set
in manifest but it won't have the the file on the list of files in
changelog.
* The second amend will read the wrong list of files from changelog and it
will copy the manifest entry from parent for this file.
* Voila! The change is lost.
This change repairs the bug in localrepo causing this and adds a test for it.