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AppConfig may not be the best fit for this use case as described: it doesn't deliver configuration files to disk, but instead requires the application to call its API to refresh the configuration. (So you would then update your configuration in AppConfig, deploy it, and your application would, on next refresh*, receive the updated configuration.) Your application would need to be modified to call the AppConfig API instead of loading the configuration off disk. If you're happy reading Python, there's a sample library which you can dig in to to see how you might do it.
However, if you can arrange for a script to run inside your container, you could use the AWS CLI (or another language with an SDK, e.g. Python/boto3) to fetch the configuration from the API and store it in the file for your application, and then notify the application it should reload. An alternative for the last step would be to have the application monitor the modification time of the file, and reload when it is updated. AppConfig itself does not provide any native tooling to do this, I'm afraid, but the documentation has sample AWS CLI commands to get you started.
If neither of those options suit you, then the option you suggest in your third point may be the most straightforward to get you unblocked, although of course you lose some of AppConfig's benefits like validation and automatic rollbacks.
(* subject to your deployment rate)
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Thank you for the quick reply. I will try to modify my setup to work with the suggested "pull"-workflow as I really like the functionality provided by AppConfig. At least I am on the right track now!