Improving guide handling

[mmatera]

Changes needed to work together with https://github.com/Mathics3/mathics-core/pull/1025#issue-2194876664

[mmatera]

This is how the documentation associated with a package looks:

And this is how it looks for a flat module:

Still, some aesthetic improvements must be done, like removing the blank lines in the index of a guide section.

[rocky]

LGTM - Many good improvements and simplification of code. Thanks! Merge when you are ready. See also the various comments should you want to address.