Make parameter language clearer

[nebfield]

• --target_build means the build of input genotypes, but people might think it means that we are targeting that build (i.e. lifting over genomes)
• be consistent with language around stuff like keep_ambiguous (change in pgscatalog_utils too). i.e. figure out to use exclude/keep, think about discussions with Niki

[smlmbrt]

I think skip_flips is missing from the documentation/CLI? We should probably go through each of our commands and see what options could be adjusted and add them to documentation/nextflow inputs as these might get out of sync