I want to begin Firefox OS development, but I'm a bit lost. I've tried 
researching in the past, but there were never direct answers to my questions 
and I'm assuming some of the problems I've run into are just because some 
things aren't ready yet (for example I saw remote debugging is disabled until 
it's changed to be reimplemented).

Remote debugging is available in the simulator and can also be done on the devices though it requires some hacks to work; see here for more information on the topic:

https://developer.mozilla.org/en-US/docs/Mozilla/Firefox_OS/Debugging/Setting_up

Anyways the point is I want to test my web app so I can bring it to my Firefox 
Phone and hopefully continue to develop for Firefox OS. The big problem I ran 
into in the past is that I haven't been able to test a local app on the Firefox 
OS Simulator. I don't have a website of my own and it seems that by uploading 
it to my school's site, it forces one of a set of MIME types that makes Firefox 
OS not recognize the manifest.webapp file. Either that, or I set up my 
manifest.webapp file wrong, which I'm fairly certain I didn't. If I need to, I 
can set up a server on my own computer so that it's ideal for testing, but I'm 
pretty new to that (I've only truly immersed myself into server-sided 
development over the past few months).

The next problem is testing the app on my phone. Is there a way to get it on 
there without have it uploaded somewhere? From what I've seen, there's no way 
to access the OS's files at all, except by a MicroSD card (which doesn't really 
help). I'm using the GP Peak, if that helps figure out the answer. And is there 
currently any way to debug the app while it's running live? I saw remote 
debugging is disabled, but I'm not so sure how necessary that is given that I 
have a USB cable to plug into my computer (unless that'd be considered remote 
debugging too).

The best environment for getting started is the Firefox OS simulator. It allows for very easy testing and debugging and the last version allows you to push your app directly to your device:

https://developer.mozilla.org/en-US/docs/Tools/Firefox_OS_Simulator

And last (which kinda ties into the question I just asked), how can I modify 
the OS? If I could somehow get access to the actual file system on the phone, 
that'd be a great start and I could probably go from there on my own.

The OS itself is split in three parts, the low-level platform called Gonk, the Gecko rendering engine and finally Gaia which includes the user interface, standard application and all related code. I assume you would be interested in modifying the latter. You can read about it here:

https://developer.mozilla.org/en-US/docs/Mozilla/Firefox_OS/Platform/Gaia

I also encourage you to subscribe to the dev-gaia mailing list ([email protected]).

 Gabriele
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