The tools have been incredibly slow at several operations, mostly install, update, and patch. I think the root cause is just how many times it checks out its cached clone of nf-core/modules because it (or git) falsely detects it as dirty. What's the best way to troubleshoot this?

Can you run these commands with

nf-core --verbose modules install

etc

When I do that I see that it sits for a minute at a time checking out whichever branch it needs in nf-core/modules, there's also a phase where it schizophrenically cleans and force checks out its local clone of nf-core/modules.

try with

nf-core modules  --no-pull

then

--no-pull

does not change anything other than it doesn't do the initial pull anymore. It still needs to switch branches several times, which is where the slowdown happens.