mark missing packages instead of failing them in the first pass

WIP - do not merge

Following down the path of marking missing packages instead of failing them up front. So far (unsurprisingly) it resolves the specific issue in question, but unsurprisingly does break error resolution and culprit finder  when a package is not available.


Also borrowed the test from @oferrigni 's branch as I was not confident that my own hand-rolled test scenario was the same.