review clean and squeaky-clean targets in this repo and others

[turbomam]

My original intent for squeaky-clean was that I wanted to add more cleaning steps wihtout changing teh clean target provided by LinkML templates, cookiecutter etc.

• unify them into one target?
• just provide better documentation of their differences?

there may be places in which they are being used inconsistently or without enough intentionality in microbiomedata repos.