Show all files in a folder, whether in catalogue or not

New User to Elements 9 but heavy user of other photo editing software. 
Have significant investment of time in a structured folder/file organization with thousands of photos.  Now having experimented  with the organizer, moving stuff in the organizer, moving files with Windows explorer, adding new files external to the organizer, moving files elsewhere as any user should be able to do,  I've got a total mess.
Why can't I see ALL the photos that are in my folder (or subfolder).  Instead the organizer gives (in folders view) what it thinks SHOULD be in my subfolder, but when I go to Windows explorer there are many files in the subfolder that are NOT SHOWING UP in the organizer folder view.
How do I get organizer back to showing what is actually in each subfolder?
Is Photoshop telling me that I can't move photos around using other software?
Do I have any option in Organizer to actually see all my files as they exist in each folder?

Now having experimented  with the organizer, moving stuff in the organizer, moving files with Windows explorer, adding new files external to the organizer, moving files elsewhere as any user should be able to do,  I've got a total mess.
Organizer is not a file browser, and wasn't intended to be a file manipulation software similar to Windows Explorer (although it has some of the same features as Windows explorer).
Why can't I see ALL the photos that are in my folder (or subfolder). Instead the organizer gives (in folders view) what it thinks SHOULD be in my subfolder, but when I go to Windows explorer there are many files in the subfolder that are NOT SHOWING UP in the organizer folder view.
Because Organizer is not a file browser. It only knows about the photos you have imported. It does not know about any other photos.
How do I get organizer back to showing what is actually in each subfolder?
Import all the photos in the folder into Organizer.
Is Photoshop telling me that I can't move photos around using other software?
No, its not telling you that. You can move your photos using any other software you want, but it will screw up the links in Organizer, essentially making Organizer unusable for those photos until you fix the links (File->Reconnect). So while it is probably not a good idea to move photos using other software, you can if you want to, as long as you are willing to do the work in Organizer to reconnect.
Do I have any option in Organizer to actually see all my files as they exist in each folder?
I think I answered that one already
Bottom line: if you want to use Organizer as a "replacement" for Windows Explorer, and to continue to do your organization via folders, don't bother, Organizer is a waste of your time in this case. It isn't as capable as Windows Explorer. Organizer was designed to give you better tools (and different tools) than Windows Explorer to organize photos. If you want to use Organizer for the purpose it was intended for, you will begin adding tags and captions and notes to your photos and stop moving photos/folders from here to there. Organizer allows you to assign multiple keywords to your photos, but Windows Explorer allows each photo to be "organized" into one and only one folder. Organizer allows you to search in almost unlimited ways, once you assign tags and captions and notes, while Windows Explorer has very limited searching.

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