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 guarantee that
all changes to the .in file will trigger a regenetation since both file
will likely have the same modification timestamps

Refs !182

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