When I run Sphinx on my machine it installs for example

developers/integration.rst into developers/integration.html

but on readthedocs it installs it in

developers/integration/index.html

This makes the use of relative links in any raw commands fail.

Is there a way to force my machine install to use the same directory structure as readthedocs? Or other solutions?

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That's basically the difference between the Standalone HTML Builder and the Directory HTML Builder. You can change the builder with the sphinx-builder option of the read-the-doc configuration file, or change your build option on the command line by specifying it with -b.