Annotate deprecated methods

[MarkEWaite]

Annotate deprecated methods

Reduce compiler warnings about deprecations and declare them consistently.

Testing done

Opened the generated javadoc in a web browser and navigated briefly. Deprecated items are shown correctly.

Submitter checklist

• Make sure you are opening from a topic/feature/bugfix branch (right side) and not your main branch!
• Ensure that the pull request title represents the desired changelog entry
• Please describe what you did
• Link to relevant issues in GitHub or Jira
• Link to relevant pull requests, esp. upstream and downstream changes
• Ensure you have provided tests - that demonstrates feature works or fixes the issue