Remove "muted" states of external tools

Currently, some external tools are marked as "muted" to prevent them from notifying user about validation errors. It was implemented because full package doesn't contain R with modules, so these tools write errors to the log on the first launch. To not confuse users some NGS tools were muted in the full package.

The NGS package will be removed soon, so the mechanism should be removed too. All tools should write error messages whenever they want.