Clean up metadata issues

[mjpost]

Once this is merged, a good task will be go to through the hundreds off issues matching this query and process them using the new framework. Many of them seem to have been addressed but perhaps not correctly marked as closed.

Originally posted by @mjpost in #4147 (comment)

[mjpost]

One suggestion here that would be easiest on our end:

• go through every old-style issue
• add a link to the paper page for convenience
• ask authors to use the new version
• close the issue