fpe is not the best way to go since it usually is managed/customized by the user, I means GG has not control over them, I myself almost never care about correct material id, never state my sounds on the fpe file, and so on.
And about customized scripts, most likely could need some check system before include them on standalone.
About sounds, scripts I most relies on entity properties, after all user has to set all via that properties panel, even changing fpe values there, like static value, script, sounds, another reason not to trust the data in the fpe file.
When user save level, GG has to make some sort of entities inventory over the map, those entities has their own properties such textures, x file, fpe file, scripst attached, a buch of data that should go to that inventory, being maybe some sort of database or json file, and them GG can rely on that level inventory data.
The fact than user can do or has to do many things via LUA is good and bad thing. Is good because thus GG don`t has to provide those features, bad is bad because GG can't control them, as instance the sprites going via lua nor generate and controled by GG, but for the user itself.
if GG had a sprite system then GG would not have this problem, if GG had a controlled system of generating the fpe file, and so on.
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