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While testingI was running a test where I was getting a config export of the standard installation profile, setting up a new drupal install on minimal, and then trying to do a config import of the standard profile YAML files.
Because we have
standard: '1000' inside the system.module.yml when we come to do a config import it tries to enable the module 'standard'.
We can get around the module enable issue by filtering out any install profiles in the function that enables all the modules that need to be enabled, but that doesn't feel quite right.
Additionally, after running the config import, it still shows system.module as having config changes that need to be imported, and doing a diff between the staging and active directories, shows that is because it still thinks 'standard' needs to be imported.
Maybe it would be a better idea to have a system.profile.yml file, which included just the installation profile. This would perhaps get around the config import issues, and it may make more sense, given that standard is a profile, and not a module?