composer.json is just a configuration file stating the dependencies for you application. The application does not have any connection with the composer.json directly. when you run composer install, composer will read the composer.json and install all the dependencies and the dependencies of the dependencies. The installed package details will be saved to the composer.lock file. Your application should work with or without composer.json file on project root.
Did you migrate from L4 to L5? the possible cause would be that.
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