Hello,
Starting a few days ago, my Alfred setup completely broke. Alfred no longer shows results from any folders other than /System/Applications, ~/Applications, my home (~) directory, and for some reason, a lone result from /usr/local/Cellar. I figured this out by manually searching for every a-z letter (i.e. find a, find b, ...). Interestingly enough, most of what I'm trying to search on is within my home directory, but Alfred only shows the top level folders (and no results appear when I search on a known file outright).
I have uninstalled and reinstalled Alfred, deleted the Alfred files by following this guide, restarted (not factory reset) my Mac, forced spotlight to reindex, and added all files to "Prevent spotlight from searching..." and removed them (this was another suggestion to get spotlight to reindex).
Of considerable note here, Alfred cannot find applications in Macintosh HD/Applications but it CAN find apps in Macintosh HD/System/Applications, and in ~/Applications. Also of importance, Spotlight CAN find these files, so that makes me think Alfred is the problem here.
Some things that I recently did with my Mac include:
Within the past month
Installed a Windows 10 and Ubuntu 18.04 instance in Parallels (Alfred STILL worked after/during this)
Installed MacOS 10.15.2 security update
Within the past week (around the time problems started)
Installed RStudio which required the installation of Xcode command line tools ( I was surprised to find I didn't have this installed, but alas, I upgraded my Mac a few months ago and haven't had the need for in until now)
My Parallels Ubuntu had this weird issue where Shared Network didn't want to work. I had to run it in bridged mode, then it just went back to normal on its own.
Any ideas here?
Edit: Forgot to mention, I also ran the "Clean Drive" utility in parallels toolbox. It cleared out a bunch of crap, mostly old backups that I didn't want on the native drive anyway.