Implement a mechanism for deprecation of features

[Gedochao]

Describe what needs to be done and why
We need a mechanism to deprecate individual features of the runner/CLI, similar to the one we have for features which are experimental.
It should become easy to tag or annotate individual features as deprecated, label them as such in our docs and log warnings.

Features which should be deprecatable:

• command line options
  • individual command line option aliases
• using directives
  • individual using directive aliases
• sub-commands
  • individual sub-command aliases
• global config keys

Additionally, we need:

• a warning suppression command line option, which will silence deprecation warnings altogether
• a corresponding global config key for suppression of deprecation warnings
• all deprecation warnings should be gathered into a single log (like is the case for experimental features), rather than each being logged separately

Is your feature request related to a past ticket or discussion?

• Deprecate the --source command line option for the package sub-command #3257
• Add deprecation reporting mechanism for using directives #2622

Describe alternatives you've considered
What we have in place are rough and/or partial hacks, we need a proper solution.