As far as I know Fantastico doesnt do this as per what you have said.
It doesnt compare any difference in the files and make PATHCES accordingly.
Its actually a very complex procedure to do so and the RAM requirements would be intense.
Because it would be something like a SVN and could you imagine comparing 1000s of file in just seconds.
It impossible and it would crash the server.
Making a list of differences is very complex and sometimes even SVNs fail to do it.
Also as far as I know all software recommend making different files for langs and themes.
I guess only scripts like SMF have a efficient Mod management system but in case of major updates you simply have to REINSTALL all patches.
Regards,
Alons
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