[WIP] New ebi submit [WIP]

Almost there, but I thought I'd get this in now so that people can begin reviewing, it's kind of big.

Needs:
- [ ] Logging
- [ ] Test code
- [ ] Script file (this is the library code)
- [ ] Final step that calls ASCP on the XML files generated
it looks like some of this logic for writing could be decomposed based on overlap on the following methods