Switch to src layout

[alchemyst]

Using a src directory makes certain kinds of packaging-related errors less likely to occur. The issues are discussed in this article. Now that we are using uv which defaults to installing the local package into the .venv I think we should switch to the src layout.

This would basically involve mkdir src; mv shgo src followed by whatever packaging cleanup we need to do to get it all to work properly.

[alchemyst]

@Stefan-Endres I'm happy to do this if you approve of the idea.

[Stefan-Endres]

This could be mildly- to moderately painful for us due to our group's reliance on vendoring in many experimental libraries on our clusters (which in turn have issues with GPU access venv builds) to make use of the latest pre-release features of shgo.

Can we do one of:

1. Try this on a test branch first (I think simply adding src to all directories in the scripts "should work" without issues).
2. Do this after the 2025 neurips deadline.