Only build submodule docs which are included in toctrees

[eharkins]

It seems like the build tries to also build the augur and cli api docs, which are not included in any of the toctree statements and so are not reachable by any links in the main documentation (intentionally - since they are in their respective subprojects). Because of this, we could optimize the build by not building these docs in the main documentation build since we don't need them, and to get rid of warnings like this:

/Users/eharkins/nextstrain/docs.nextstrain.org/src/augur/docs/usage/cli/version.rst:5: WARNING: Failed to import "make_parser" from "augur".                  
No module named 'augur'                                                                                                                                       
/Users/eharkins/nextstrain/docs.nextstrain.org/src/cli/doc/commands/build.rst:5: WARNING: Failed to import "make_parser" from "nextstrain.cli".               
No module named 'nextstrain.cli' 

[eharkins]

#36 removed submodules. In general, to exclude docs from the build, we use https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-exclude_patterns