Fix #3461 by removing file from issues after removing last issue

[still-dreaming-1]

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[still-dreaming-1]

You can ignore the branch name being a little strange. This ended up going in a different direction than I imagined. I was originally thinking I would just change the $issues type as used in AfterAnalysisInterface. I tried changing it to @param array<string, non-empty-list<IssueData>> $issues, hoping that would cause Psalm to reveal where that is not honored in the code. But there is a Psalm suppression preventing it from surfacing, and it says it is because of a bug. I tried deleting that comment, but then there was other technical debt that got revealed that I didn't know how to deal with. So I abandoned that approach and just fixed the bug directly in IssueBuffer::remove() as suggested by @muglug.

I tested this in my plugin, and it does fix #3461.

[muglug]

Awesome, thanks!