Which files should I tell my VCS to ignore when using Sphinx for documentation?

If you create a new project on GitHub, it will offer to create a Python-flavored .gitignore file for you. This file includes one reference to Sphinx-generated files:

# Sphinx documentation
docs/_build/

Note: This assumes that you accept the defaults when you run sphinx-quickstart. You may need to adjust it depending on how you answered these questions:

1. Root path:

   Enter the root path for documentation.
   > Root path for the documentation [.]:
   

   This determines the path where documentation is stored. If you made it something other than docs, then you'll need to update .gitignore accordingly.

2. Build directory:

   You have two options for placing the build directory for Sphinx output.
   Either, you use a directory "_build" within the root path, or you separate
   "source" and "build" directories within the root path.
   > Separate source and build directories (y/n) [n]:
   

   If you answered n (default), then Sphinx will create the build directory at <root>/_build (your source files will be stored directly under <root>/).

   If you answered y, then Sphinx will create the build directory at <root>/build (your source files will be stored in <root>/source).

   Note the presence/absence of the leading underscore; make sure the corresponding pattern in your .gitignore matches.

If you take a look at the contents of Makefile you'll see something as follows:

BUILDDIR      = build

...

clean:
    -rm -rf $(BUILDDIR)/*

This means that make clean just removes the build directory so, with regard to version control, ignoring the contents of the build directory should be enough as you already suspected.