I rebased on the master with #2500 included and then added two commits for a typo and to use the parameter instead of a constant column name

Looks good to me.
One challenge is how to select only the "MS1" samples for chromatogram builder.

Could add an option "skip files without ms1 scans" in the chromatogram builder

I find the new grouping parameter very promising, but I was wondering: has it been tested in setups where the reference file (used for quantification and alignment) contains only MS1 scans, and the MS2 scans come from separate files which also contain MS1 scans?
I'm currently working with iterative DDA data acquired on both Thermo and Agilent platforms, with plenty of data. In our workflow, the first injection(s) are MS1-only (used for robust quantification), while the subsequent injections are DDA-MS2 runs with dynamic exclusion (but also include MS1 scans). I'd be happy to help test this or contribute feedback.