Justman10000 by design it seems like you are replacing the current composer.json file with the one you curated in the git repository. This is a perfectly fine approach to use with a new forum. But on an existing forum this would replace the user's current list of extensions, and composer install would then uninstall anything that is no longer in the composer.json file.
If you are only adding extensions, you could use a long composer require vendor1/package1:* vendor2/package2:* command with all extensions, letting Composer modify the existing composer.json file. Or you could create a Composer package that only requires other Composer packages (like https://github.com/extiverse/flarum-most-downloaded-extensions did, but I'm not sure if it's still maintained)
