Using Docker in a dev environment: ongoing maintenance? Question

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I followed the instructions to set up Docker on my developer machine and it works great. Sometimes, though, I run into problems after I've pulled updates or switched branches. I don't really understand Docker; I just followed some instructions to get an environment that has fewer challenges than running an oft-changing platform on bare metal. I don't feel like I really know what I'm doing.

Can we compile a guide to common QPixel-specific pitfalls and their remedies? I'm not asking for a full Docker tutorial (a job for their doc), but rather a guide to how it applies to us. Here are some issues I've run into:

git frequently reports that Gemfile.lock is modified, which is often innocuous but can cause pulls to abort. It turns out that a running Docker container was (modifying? locking?) the file in a way that git couldn't handle. It appears that sometimes I should shut down Docker containers before pulling, but I don't have a good mental model of when.
After dependency changes, the qpixel-uwsgi-1 container sometimes needs to be rebuilt. When should I do this and what is the correct way to do so? I've made note of the command docker compose --progress=plain up --build --detach --force-recreate uwsgi but am not sure if it is sometimes overkill?
Sometimes, upon starting the qpixel-uwsgi-1 container, the server will hit a bunch of errors and exit. What should my next step be -- just try to rebuild, or is there something more diagnostic that I can try first?
The qpixel-uwsgi-1 container is configured, by default, to stop trying after three failures. Where is that configured, if I want to change it? (Should I want to change it?)
Is there any harm in leaving Docker Desktop and the containers running continuously for days to weeks, through changes in branches?

(I started to draft a Wiki post instead of this question, but didn't feel I have a solid-enough foundation for how to lay it out. If a Wiki post would be better long-term than answers to this question, it is completely fine with me if we create that Wiki post and just point to it from an answer here. I also considered asking several questions instead of one, but I don't have a good sense of granularity. If some part of this is big, I'm happy to spin it off.)