At one point they were grouped by top-level project the same as the main repo. Perhaps it might be enough to collate them back into that structure and update the readme? As you say there are a lot of wildfly and tomcat ones that could certainly be grouped. Perhaps that might be a useful first step to see if then further moving of the existing quickstarts is required?
After that I agree that updated the readme would be useful.
Regarding tags, is there some provision for that in github/markdown we can use such that when someone clicks on a tag it can return a list of matching files I wonder?