Move `env2yaml` tool logics to the core.

### 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 https://github.com/elastic/logstash/issues/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).