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What to do when Pacman is telling me there are conflicts in the file system?

This indicates that Pacman isn't sure it is safe to overwrite some files. This sometimes happens during regular package updates, but could also happen if you installed some software manually (make install, npm install npm -g etc.). To continue with the operation, pass --overwrite <conflicting_file_path> to the Pacman command line. For other options, see the Arch Linux FAQ entry about Pacman file conflicts.