This is indeed a mess and could cause some serious problems. You have moved your catalog and your media files from their default locations to another (external??) hard drive. That would be OK. But it also looks like you have copied your media files to inside of the catalog folder. That folder should NOT contain your media files. Here is my suggestion for what you should do:
In Windows File Explorer, move the folder marked in my screenshot to another location, preferably on another drive to avoid confusion:
If I am interpreting your diagram correctly, you should now have two main folders on your X:\ drive - the PSE X Catalog folder (with the catalog sub-folder) and the Users folder (with the Pictures sub-folder).
Open the catalog and see how many media files are present
Select Find>All Missing Files. The number of missing files should be approximately half of the total. This may not be an exact number since there may be differences in how many files you have edited and saved in stacks.
If you are confident that the missing files are merely duplicates, press Ctrl+A to select them all, and then press Delete to remove them from the catalog.
If the catalog is now complete and has all of your tags, you can delete the media files that you moved in the first step or keep them as a backup.
... View more