regarding conflicting extensions, its like targetting the lowest common denominator, but first you have to figure out what exactly that is.
renamed builtins are not a problem with fte or dp. the engine really doesn't care what the builtin is called. rename it if you want. only the # and the number of arguments is important.
renamed arguments is not something the engine is aware of. its safe. prototypes can have different argument names from your actual function body too!
additional arguments in entry points (qc functions) may have undefined values in the engine which does not define them. the qcc may care, but the engine sure as heck does not.
additional arguments in builtins may generate some annoying error in DP. FTE will ignore additional arguments, while missing arguments will be undefined - as in vanilla... so pay attention to warnings about missing arguments!
pr_dumpplatform will give you a dump that is meant to exactly match the binary you use the command from.
http://triptohell.info/moodles/fteqcc/fteextensions.qc is a link to one that is generated from the latest nightly build.
regarding your console inputs issue, I tried to add support for XIM for proper unicode text entry, and it worked in debian, however, I later noticed that it didn't work in cygwin which should now also be fixed.
If you still have issues, you can use -noxim to use the old code.
actually, the skeletal object is not an entity, but rather both are 'objects' in the programming sense, so you're mostly correct. model indexes refer to a model object too, which contain their own framegroup objects, which in turn contain pose objects, if that helps... a skeletal object is just some generic pose object that can be used independantly of the model that it came from, and can be dynamically changed.
by 'independantly', you can actually build a skeletal object from one model and use it with a different one instead. this is useful when you have all-animation models and mesh-only models like with doom3's md5mesh/md5anim formats, or whatever.
but yeah, the skeletal objects are referenced by index, much like entities are (except with floats instead of an entity/hidden-int type).
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