Move env2yaml tool logics to the core.

[mashhurs]

Description

We faced a discrepancy when running Logstash on docker env and non-docker env (ex: with tarball) that, if same ${VAR} exists in both keystore and ENV, keystore lost its power. We fixed it with #15766 issue but the main deep reason for this env2yaml tool writes into logstash.yml. Although we fixed a bug we had, we would like to re-address env2yaml tool and move its logics to core without writing to the logstash.yml (maybe directly interact with Settings in the core?! as it has all allowed config definitions and default values).