Remove do-apply pattern from Definition and Instance

[adkian-sifive]

Contributor Checklist

• Did you add Scaladoc to every public function/method?
• Did you add at least one test demonstrating the PR?
• Did you delete any extraneous printlns/debugging code?
• Did you specify the type of improvement?
• Did you add appropriate documentation in docs/src?
• Did you request a desired merge strategy?
• Did you add text to be included in the Release Notes for this change?

Type of Improvement

• API modification
• API deprecation

Desired Merge Strategy

• Squash: The PR will be squashed and merged (choose this if you have no preference).

Release Notes

Do-apply pattern for Definition/Instance apply methods was removed

Reviewer Checklist (only modified by reviewer)

• Did you add the appropriate labels? (Select the most appropriate one based on the "Type of Improvement")
• Did you mark the proper milestone (Bug fix: 3.6.x, 5.x, or 6.x depending on impact, API modification or big change: 7.0)?
• Did you review?
• Did you check whether all relevant Contributor checkboxes have been checked?
• Did you do one of the following when ready to merge:
  • Squash: You/ the contributor Enable auto-merge (squash), clean up the commit message, and label with Please Merge.
  • Merge: Ensure that contributor has cleaned up their commit history, then merge with Create a merge commit.