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Integrity check misses files from removed CustomVariables and Provider plugins

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Missing file: /var/www/matomo/plugins/CustomVariables/.github/workflows/translations.yml
Missing file: /var/www/matomo/plugins/CustomVariables/plugin.json
Missing file: /var/www/matomo/plugins/CustomVariables/README.md
Missing file: /var/www/matomo/plugins/Provider/.github/workflows/translations.yml
Missing file: /var/www/matomo/plugins/Provider/plugin.json
Missing file: /var/www/matomo/plugins/Provider/README.md
Missing file: /var/www/matomo/plugins/Provider/screenshots/Report.png

From what I found, both plugins have been removed from core and as well the Provider plugin seems to not work anymore (I cannot the Provider info in the UI anymore). Strangely, after I uninstalled those plugins, the integrity check misses the above files.

This PR seems to be somehow related? https://github.com/matomo-org/matomo/pull/16415

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