Adding 'Built-in' code

You'll be able to do E.setBootupCode(E.dumpStr()) which will have pretty much the same effect.

Actually avoiding the problem by just not totally resetting is a really interesting thought though - it solves a whole lot of problems.

would it be possible to add a step in compilation that writes a .js file into the binary as an initial program?

Yep - that's kind of the idea with E.setBootupCode - what is does could also be done in the compilation process... or, like you can do right now you can actually just save() your code, and can then go into bootloader mode and read the whole binary out (including your saved code).