Heh, that brings back memories ;) I spent a considerable amount of my time while working on my thesis, tinkering with the LaTeX bundle instead. TM is just too addictive in that respect (in a good way of course). ;)
Well I'm glad to hear that it's possible to tinker with TM, and finish your thesis off ;-) Thing is, there's so much to learn, and to do one thing requires a whole load of other knowledge. Plus the fact that learning things like ruby feels like such a 'good' thing :-) regexps on the other hand are the root of all evil!!!
I do however think that knowing if things have been saved in the bundle editor is something I'm struggling with. I don't always close the editor after I've made a change, and do things like toggle between two different commands before I try the command again, which feels like a bit of a fudge. Again even in non-language files, an 'Activate' button would be very handy.
Oh, and if you're interested do know why I wanted to know if it was possible to persist commands, I was thinking about the possibility of embedding an irb console within TM. I think it woudl be wonderful to have a syntax highlighted irb console, and it would a cool place to try out new commands etc - as it would have access to all the TM variables. I'm sure it's possible (why managed to achieve something similar with his Try Ruby site), but that's definitely a post-PhD project ;-) irbmate!
Take care, Sam