In this case it seems like we want to remove the command rather than to increase the version number. I also thought about a mechanism that prevents us missing the removal of deprecated commands in future releases. We could add a version argument to the deprecated command that throws an error when the current version is above the given version of removal, so a new release PR that bumps the version would throw errors until the deprecated commands are really removed.
Some deprecation messages are not up to date. For example https://github.com/aiidateam/aiida-core/blob/23d2aa5ee3c08438cfc4b4734e9670e19c090150/src/aiida/cmdline/commands/cmd_database.py#L27-L30
In this case it seems like we want to remove the command rather than to increase the version number. I also thought about a mechanism that prevents us missing the removal of deprecated commands in future releases. We could add a version argument to the deprecated command that throws an error when the current version is above the given version of removal, so a new release PR that bumps the version would throw errors until the deprecated commands are really removed.