Environment files are confused for users that run Stork manually.

I noticed many questions about properly setting the parameters for Stork Agent/Server. Some users specify the parameters in the /etc/stork/agent.env and /etc/stork/server.env files and run the Stork manually from the executable. It's unclear that these files are used only by the SystemD services.

We should:

1. Improve the documentation
2. Add a warning message that the files aren't used if they exist
3. Add a flag that enables reading these files