Latest update to the end to end workflow

[philouail]

In this PR i have added the code for the whole workflow, as well as simplified some parts.

Tell me if it is too over simplified.

Important update:

• Addition of annotation part : I used filterRanges() for matching with features. Tell me what you think of it ! I could also try to merge the resulting list of spectra instead of keeping it as a list. Or go the classic route of matchValues()
• I added the Abstract.md file for the conferences . It is too short, do you have an idea of what point i could develop a bit further ?

I won't change anything so you can merge my branch to yours to make changes so there won't be any clash when merging back to mine :)

[jorainer]

Thanks @philouail ! I will merge your branch into mine and locally check/update.

[philouail]

So everything was merged and the code run with no problems. @jorainer just need to be merged to the main now and we can share with co-authors !