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You can use the SDL library (joystick stuff) or GLFW. If you don't want to use SDL, you might need to do some googling how to do it. Of course you can always read the raw joystick data (doable). :D I use xboxdrv userspace driver to play with my xbox controller and SDL-based games usually work quite nicely.
Pulse is fine. There's no way I'm going back to pure alsa anymore. Alsa just doesn't work flexible enough when you have multiple outputs like usb-headsets and hdmi. With pulseaudio, you can have a total control over all alsa/oss/whatever input/output/whatever and redirect it anywhere easily without breaking everything like a modern system should do. When pulseaudio doesn't work it's mostly because of the crappy linux audio drivers or/and bad configuration in general (yes, I have also suffered from this). Luckily, the situation with the drivers and Pulseaudio has improved. :)
Nevertheless, using the pulse library for audio in game is a pretty bold move as there are many "cross-audio" libraries for linux too. Oh, well. I guess the developers know what they're doing. The game looks cool btw. :)