A dedicated scope for `.md` inputs

[Gedochao]

Is your feature request related to a problem? Please describe. .md inputs are currently treated as main / test scopes, just like other kinds of inputs. As a result, logic included in them could accidentally be included on the classpath when a whole directory is passed from the command line.

Describe the solution you'd like Markdown files should fall under a dedicated markdown scope, separate from main and test. However, we should still have an option to include certain (or all) Markdown inputs in main or test, when the user desires it.

Describe alternatives you've considered We could theoretically exclude .md inputs when an app is packaged or published, but it's not ideal, as a user might want them included in some circumstances (i.e. if a user actually decides to write business logic or tests inside of .md sources).

Additional context This ticket is the minimal requirement for treating Markdown as a stable feature and removing the --enable-markdown flag.