Hello, I am using Ory Hydra in my application. Currently, the TLS certificate and key can be provided either as file paths or as base64-encoded content in the Ory Hydra configuration file. Is there a way to supply the TLS certificate and key via the command-line interface, either as file paths or base64 content?

You can set all config values as environment variables https://www.ory.sh/docs/ecosystem/configuring#loading-configuration-from-environment-variables

But I want to set the configuration temporarily, because from UI users can change the configuration

That's not possible in self hosted.

In our application, we initially generate a default TLS certificate and store it in memory to establish a secure TLS connection with Ory Hydra. Once the client uploads their own TLS certificate, we save it to the file system and use that certificate for all subsequent connections.

You should be able to just update the config file. Probably the better option though would be to do TLS termination in a dedicated component (potentially your WAF), as that would be more flexible especially when you scale Hydra.