fix: remove_application_command missing case

[Dorukyum]

Summary

The current implementation of CogMixin.remove_application_command ignores the fact that commands with IDs (synchronised commands) stay in the list of pending commands. The new implementation takes this into account.

This intends to fix #1383, requires testing.

Information

• [x] This PR fixes an issue.
• [ ] This PR adds something new (e.g. new method or parameters).
• [ ] This PR is a breaking change (e.g. methods or parameters removed/renamed).
• [ ] This PR is not a code change (e.g. documentation, README, typehinting, examples, ...).

Checklist

• [x] I have searched the open pull requests for duplicates.
• [x] If code changes were made then they have been tested.
  • [x] I have updated the documentation to reflect the changes.
• [ ] If type: ignore comments were used, a comment is also left explaining why.
• [x] I have updated the changelog to include these changes.

[Dorukyum]

Tested and added a changelog entry.