Clean-up after testbeam

[Skelpdar]

Making an issue to keep track of these two vague projects:

1. There are a lot of references to testbeam-specific details, e.g. config versioning, DMA, triggering setups and so on, that are not relevant while using this at a teststand (a bit irritating). We should clean up the tools to hide such technical details.

2. While we are at it, let's take a second look at the code that was hastily written during the testbeam. Some tools have very messy code.