Hi all, just posting what worked for me, it might help anyone else.
TL;DR: run the commands in the box below, then "Rebuild macOS Metadata".
I'm also using Alfred (4.2.1 [1187]) and I installed Big Sur (11.0.1) recently.
I was not seeing applications nor folders in Alfred.
The "File Search Troubleshooting" showed similar responses as in the posts above: "Direct metadata is missing, this file is likely not indexed by macOS".
I tried these solutions from posts above with no luck:
Alfred Preferences / Advanced / Clear Application Cache
Alfred Preferences / Advanced / Rebuild macOS Metadata
Remove and add back folders in System Preferences / Spotlight / Privacy
These commands worked for me:
sudo mdutil -a -i off
sudo launchctl unload -w /System/Library/LaunchDaemons/com.apple.metadata.mds.plist
sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.metadata.mds.plist
sudo mdutil -a -i on
I found the solution in this article: How to fix Spotlight search not working on macOS.
This was the output:
$ sudo mdutil -a -i off
/:
2020-11-24 21:16:03.161 mdutil[65865:26582587] mdutil disabling Spotlight: / -> kMDConfigSearchLevelFSSearchOnly
Indexing disabled.
/System/Volumes/Data:
Error: invalid operation.
Error: unknown indexing state.
✘-1 ~
$ sudo launchctl unload -w /System/Library/LaunchDaemons/com.apple.metadata.mds.plist
✔ ~
$ sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.metadata.mds.plist
✔ ~
$ sudo mdutil -a -i on
/:
Indexing enabled.
/System/Volumes/Data:
Indexing enabled.
Just to be sure, I ran: Alfred Preferences / Advanced / Rebuild macOS Metadata.
Now everything works.
I don't know if it's related, but I have Apple's System Integrity Protection turned off.
I didn't want to format and reinstall Big Sur to solve the problem.
I refuse to format and reinstall fresh unless it's the very last resort.
Thank you all!