The latter changed the site-project-archetype resources exclusions for setting up the archetype, including the templated autoexport (modules) config from the main project-archetype.
Which already resulted in an incorrect autoexport modules config where then both the main and child site modules were setup.
The changes for
ARCHE-604 however now has it broken seriously because it separated the configuration for application and development, moving the application configuration (back) in the, now excluded ( REPO-2142) autoexport-module.yaml config file.
As as consequence, all projects generated with the site-project-archetype since 13.0.1/13.1.0 will have their autoexport modules config setup broken, causing export for the HST site config to be lost (not exported).
The fix is trivial (I've a local fix, will push once I have a bugfix branch number), but will not repair broken configurations 'out there': those will need to be fixed manually (with proper instructions).