Use topic: channels for all the software details, clean and easy implementation

[keiran-rowell-unsw]

Nextflow 25.04 introduced the topic: channel construct to make generating a versions.yml less cumbersome and more multi-tool 🤩

This seems ideal for #579 in the modelCIF protocol details.

Since I'm implementing modelCIF spec anyway, and we'll be nextflow >25 complaint from v2.1 release onwards, I'm going to wire in those software details are topic: channels, not traditional versions.yml, in order to make this cleaner to populate and less subworkflow dependent.

[keiran-rowell-unsw]

topic: channels are going to be encouraged through the nextflow linter in 2026+, so now this future-proofs the pipeline and makes implementation easier

[keiran-rowell-unsw]

Marking as 'done' until #625 hits an appropriate merge window to be reviewed.