New matUtils Features

[jmcbroome]

This PR includes a couple new options, an expansion of the translate output, and some reorganization without functional change to make developing an API wrapper more straightforward.

1. matUtils mask has gained the -M option, which can be used to forcibly move nodes within the tree between two locations with identical sets of final mutations/alleles associated with the original and new parents. This was a recent request from Angie to help secure the stability of some Omicron lineage assignments in the face of long series of backmutation/remutation branches. It's under mask since it doesn't fit very well in any other tool; mask is gradually developing into a cautious tree editing command.
2. I've added an option to select ALL samples under the MRCA of the current sample set to matUtils extract, -U. This was because I needed to do this operation at one point and I realized that there was no explicit way to perform it, and it feels like it'll come up enough to be worth it. We are running out of letters for this command, though- it may be worth considering some reorganization or splitting up extract somehow to make the package more navigable in the future.
3. I've added an additional output column to matUtils summary translation output. It now includes a codon change string as the fourth column in the output table, formatted as original-codon>new-codon (e.g. "AAC>AAG"). It's delimited in the same way as amino acid and nucleotide changes. This was very useful while I was doing some surveys of selective pressures on amino acid changes, and I think our users may appreciate the additional detail as well. It does not in any way affect taxonium output.
4. I've reorganized and split some functions into smaller pieces. This is not a functional change for the user, just a useful change that allows the API I'm testing to wrap specific parts of the function.

[yatisht]

Thank you for such a quick turnaround on an important new feature.