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Ignore this thread. I found my answer on the TMS9900 yahoo group.
Believe it or not, there are assembly programmers *here* too...
There is a lot of good information back-logged in this forum, and none of it is "out of date" just because no one has talked about it in a while. Here are two threads (among many) I recommend anyone getting in to 9900 assembly read:
http://www.atariage....nder-emulation/
http://www.atariage....ly-on-the-994a/
As for tools, there are a *lot* depending on what you are doing (see the sticky development thread in this forum.) Programming is more than just code, so at some point you will also have to consider graphics tools, sound tools, screen editors, etc., unless you are writing a DSR...
I think most people develop on a modern PC (personal computer) since the code/compile/test/debug cycle is a *lot* faster than on real hardware. Editing is also easier with a modern PC (IMO, since that statement can cause a *lot* of debate...)
For editing I use a programmer's text editor with syntax highlighting. Textpad and Notepad++ are two examples. It would be *really nice* to have a "context aware" editor like what Eclipse does for C/C++ or Java programming, but to my knowledge there is nothing like that for 9900 assembly.
For emulation I use Classic99 pretty much exclusively these days. The other emulators/simulators are usually lagging or no longer being supported. I have never used MESS so I can not speak on that community, but the author of Classic99 (Tursi) reads this forum and is right here to help out, fix bugs, etc. and that is hard to beat.
For compiling I currently use Asm994a (the assembler that comes with the Win994a simulator), but if you do use it, make sure you get the unreleased v10 (see the assembly-under-emulation thread I linked to above.) The version that comes with the latest release of Win994a has a bug. Asm994a is convenient since it works on the PC and can write files to the PC's file system, which works very nicely with Classic99.
Of course Fred's TIdir is an absolute requirement no matter what you are doing.
I also have a pile of real hardware which I use to test everything I write, once it is working under emulation. Getting data over to the real 99/4A is another issue (for which there are already many threads in this forum on the topic), and I also have an EPROM programmer for making real cartridges.