@magdalena @tom I recently also ran into this issue and was able to resolve it, and I think I have some insights on the problem. The main additional thing I had to do that hasn’t been mentioned in other discussion was that I explicitly disabled the default path fixing.
The repo and PR in which I dealt with this is here. Describing my observations in a little more detail:
Firstly, similar to the cases described in #825 Missing files in codecov (but not in report), it was happening where the missing files shared names with other files in other subdirectories. It does seem like the automatic path resolution has some problem where it confuses files with the same name.
Secondly, adding the missing directory was needed. In my case, that was applying "::erdantic/".
Thirdly, even when I had the correct manual fix applied, I still wasn’t seeing the missing files. My hypothesis is that the default path fixing was still happening and caused the filename aliasing issue. This was resolved when I added
codecov:
disable_default_path_fixes: yes
As a note, I think the code snippet at the bottom of this doc page mistakenly says false instead of true or `yes.