After having a nice chat with blargg on IRC, we both agreed that the current core architecture is like "spaghetti" with all the callbacks and global variables.
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Additionally, blargg informed me, that "...maintaing GB emulation seems like a real waste, since Gambatte exists and is probably the most accurate GB emulator."
IMO, there are enough GB emulators out there, but VBA is the ONLY open source GBA emulator.
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Having written most of the Qt GUI part until now, I feel like it is useless to rewrite the GUI but leave the core in this state. The current architecture prevents or makes it much harder to run multiple instances of it in different threads, and of course it is anything else than self-explaining how to use the cores.
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So guys, what do you think about rewriting the GBA core additionally to the Qt GUI? I know it will be a lot of work, but I think the result would be much more pleasant than the current mess.