[eluser]kilishan[/eluser]
Sorry about the confusion. Though some of that is probably because I haven't fully thought through or provided solutions to that yet.
For those that upgrade Bonfire often, it's probably a pain. If you start with a point release (0.2 when it's final, for example) and continue that site on from there, you will be fine and will not run into collisions.
However, one of the things just added to the ToDo list was to modify migrations to work with modules, also. When this gets done, it will support ordering of files (001, 002, etc) within each module to keep the abilities separate.