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extras: tools: Only patch libtool's ltmain.in

Instead of ltmain.sh, in order to ensure all changes will used. If ltmain.sh gets modified as well, there is no way to garanty that all changes to the .in file will trigger a regenetation since both file will likely have the same modification timestamp

Refs !182 (merged)

An updated version of our current libtool patchset has been pushed to https://github.com/chouquette/libtool/tree/vlc_patches

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