Currently, the warnings-ng-plugin saves a copy of all files with any warnings in a directory files-with-issues in the run directory. While those are mostly small text files, in some cases those might get a little bigger

I'd suggest to save them in an archive instead. ZIP should probably be enough, but if there is an easy way to use a format with solid compression (maybe 7z?), that would probably save quite a bit more space on projects with many issues.