spencerp,
I don’t exactly have a real fix, since I doubt just replacing the trunk/branch code with 2.0.3 code would be a proper fix. Obviously the change was made for a reason, so it probably fixed something with the IIS cookie bug that wasn’t properly fixed in 2.0.3.
As it stands now, I’m not sure what to do to properly fix it. If I understood more about that IIS cookie bug (that is addressed by the code), maybe I’d have a good fix.
I’ll definitely keep track of the bug though, and see if anybody has any ideas to make sure the code works properly for all users.
One thing to note though is that the stripping code only runs upon clicking “Update File” on the Theme Editor page. Before this point, both $file and $files_allowed have matching values for the file being edited. I’m not sure if that helps at all, but figured I’d mention it. Maybe that stripping code can just not be called upon submission somehow?
If I think of anything else, I’ll be sure to post it to the bug ticket.