Suddenly, on January 14th, for reasons unknown to me, a new folder has appeared inside my Applications folder, and this folder is called… “Applications”. It seems to be a nearly identical copy of my regular Applications folder. The size of the new folder is almost exactly half the size of the containing folder, which suggests to me that it is simply a duplicate. Also, I notice that a new version of an app I installed yesterday only appears in “main” applications folder, not in this newcomer, which only contains the older version of the app. I assume I can probably just delete this new folder, but it seems scary. What would you do?
First, let me congratulate you on having a problem that is not somehow connected to iCloud. 
The first thing I would do is open a single program in the “main” application folder then try to delete the same named program in the duplicate. And see if it tells you that file is open too. If it doesn’t protest you are probably safe deleting the dup.
But I would wait until a couple more MPUs offer their opinions before doing anything.
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This is pretty strange. Not sure what could have caused it (perhaps a semi broken install or update script?) but this is easy to test: remove one application copy, empty trash, reboot (to be safe) and see if the original application is still working.
Yes, I have seen many similar complaints to mine on various forums, but they all have to do with iCloud!
I tried your approach with a single app that I don’t need anyway, and so far so good. I deleted the copy app, and got no complaints from the original. However, a new wrinkle has appeared - I think that in some cases, the duplicate apps have updated, so if I delete them, I will be regressing to an older version. Not that much older, it has only been a month or so, but still. So long as there is no data loss, then it doesn’t really matter, but I may need to check the “important” apps to make sure I keep the newer version.
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It’s really very mysterious. If it a cloud-synced folder I would be less surprised, but this is just my local drive. I followed your advice and tried deleting a duplicate app, emptying trash, and rebooting, and the original still works, so that is reassuring.
The way MacOS works these days is that there is an Applications folder in the read-only partition that has the OS supplied applications (/System/Applications) and a separate Application folder in a writable partition that has the user installed applications (/System/Volumes/Data/Applications). Also, /Applications seems to be the same as /System/Volumes/Data/Applications. I guess it is just an alias. Finder makes these look like one folder. As a side note, MacOS performs shenanigans with the Desktop and Documents folders for sharing over iCloud.
Interesting. I did notice that the OS supplied applications are not duplicated in the new Applications folder; it is only user installed applications that have been duplicated, which makes sense given what you say.