I'll have to look it back up in the mailinglist logs, although I didn't mention every missing file; I'll see what I can hand you.
Thanks.
Well, from memory, please add it to *all* binary files (graphics mostly), and all files which have CR/LF endings because they were created or intended for DOS/Windows.
I see now that I've forgotten to give the script a --mime-types file. That would mean it can't guess filetypes correctly for graphics etc. That's probably the root of the problem. Without any content-type information, it appears to set eol-style "native". This means that it will convert LF to CR/LF if you check out on a DOS/Windows machine.