Consider revamping to a command-oriented folder structure

Right now commands live in a folder structure like this:

client/src/python_modules/CMDNAME
server/src/python_modules/CMDNAME

When you write a new command you put things in two places. But increasingly we want more things about each command: tests, documentation, AI skill definitions, etc.

Perhaps we should think about:

commands/CMDNAME/client/...
commands/CMDNAME/server/...
commands/CMDNAME/test
commands/CMDNAME/README.md
commands/CMDNAME/SKILL.md

Then "installation" of a new command is just putting a new folder in the right place.

The bootstrap logic would have to make the right zip based on a wildcard commands/*/server/* but that's doable.

Maybe also have a shared system where things like the rate limiter would go, divided into server-side deployed or client-side executed?

shared/client/rate-limiter/...
shared/server/rate-limiter/...

We are where we are because we wrote the server side. Then realized we wanted a client-side piece as well. And now I'm wondering where to put command-specific docs and unit tests. I've always envisioned each command as its own pluggable playground. Perhaps the folder structure should match this.

Start by mapping the existing client/src/python_modules and server/src/python_modules command locations, then inspect the bootstrap logic that creates the server zip. Compare that structure with the proposed commands/* and shared/* layout. Done means the project has an agreed folder design and a defined migration or implementation plan.

Written by the indexing model from the issue text.