rdj

Hmm, that's certainly unfortunate. I'll see if I can list all the steps at some level of detail in case there's anything in there that could matter.
System Preferences > Users and Groups > Click the lock to make changes + button > New Account: Administrator Apple Menu > Lock Screen Login Screen > Switch User Login as the new user Skip all of the OOBE stuff: no iTunes account, no siri, no TouchID, etc. Run Alfred 4 under the new account Add /Users/ryan (my original account) to the search path Test a "find" command in Alfred, which discovered things under my home directory (though due to file permissions, it could find e.g. stuff in my Downloads but not my Dropbox) Apple Menu > Log out Login as my original user Test a "find" command in Alfred, seems to be working now System Preferences > Users and Groups — delete the temporary user The only thing that's popping out at me as a possible important variable is that I created a new Administrator account, not a Standard Account. Not sure which you tried.

Ok, yeah, this is super weird.
 
1. Create a new user account
2. Add /Users/original to the Alfred search path
3. Search for and successfully find the exact same files in Alfred that you couldn't when logged in as original.
 
Switching to an entirely different user account would be quite a hassle, though. Especially given my understanding that the original admin account on an Apple Silicon mac is a special super admin account that ties into some of the hardware locking and activation.
 
BTW, `ls -le` isn't showing extended ACLs for any of the home directory folders other than the usual everyone deny delete on the built-in default user folders like Desktop and Music.
 
EDIT: WOW. Step 4: Switch back to your original account. Alfred can now find the files it couldn't find before. So this isn't even just a diagnostic thing; creating a new user profile actually fixed my existing user. The only thing I see that's different is that my original user account got added to a new group called com.apple.sharepoint.group.#.