You might find it easiest to have three master document files (index.rst, 
index-intermediate.rst, index-advanced.rst) and three separate conf.py 
files (conf.py, conf-intermediate.py, conf-advanced.py). This should let 
you have each configuration encompass a wider set of all the available 
documentation topics/chapters with a minimum of fuss.

The downside to this method: whenever you want to make a content addition 
to your documentation, you'll need to add the reference to three different 
master documents (potentially) and whenever you want to make a 
configuration change to the way you're building your documents, you'll need 
to change (potentially) three different configuration files.

There are ways around that, but all of them might require complex setup 
that you could find not worth the cost of this duplication of work. At the 
very least, the "three different master/conf file" method might get you up 
off the ground and working, giving you time to get more used to the system 
so you can improve it later.

--
Viktor Haag

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