I accidentally removed some necessary packages, messing up apt's dependency checking, with a bad pip3 command. I think I have things almost back to normal except for some packages that apt claims are safe to remove. I need to see if they really are safe to remove or if some things that depend on said packages need to be reinstalled. These are the packages in question:

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The following packages were automatically installed and are no longer required:
  avahi-utils cups-pk-helper gir1.2-notify-0.7 gir1.2-polkit-1.0 libextutils-depends-perl liblur3 lur-command
  python-pip-whl python3-bs4 python3-evdev python3-html5lib python3-lxml python3-webencodings python3-wheel python3-xdg

Or is there a way to automatically detect and install anything that is missing from the original base install?

What is broken, or rather what dependency problems are you seeing, specifically - ie specific error messages.

Packages marked for removal with autoremove are usually safe, as they are stray packages that used to be dependencies of something else that had been removed. I would just leave them for the moment as they are not harming anything.

I don't think pip has anything to do with apt in any way, let alone Debian packages and dependencies, so it should not really have an effect with anything, iirc. But good error messages will help us see what is going on.

Maybe:

$ sudo pkcon refresh
$ sudo pkon --allow-reinstall install neon-all

Thanks for the replies. I failed to mention that this is a brand new installation, so I'm concerned about things I may use in the near future being broken. It had gotten to the point of listing 50-60 packages that were safe to remove, so I restored a couple of apt's files that I had backed up before trying one method I googled. Since it's a new install I may just tar /home, backup some config files I edited and reinstall.