Troubleshoot Old files conflicting

[cscs]

Well, it explains not having mhwd as those are manjaro packages.

Your general question might be similar to this thread:

Manjaro System repair / integrity check?

-Dkk will perform on the repos, what is available, not what you have. Something more like what OP is asking for might be pacman -Qkk | grep -v '0 altered files' Though I fear what this will mean for people looking at the output. Its likely there willl be ‘modified’ files or ‘mismatched time’ etc that is ignorable. Well, the single Dk pacman -Dk will report big goofs like missing dependencies… though that will likely only happen if someone did -Rdd manually.