After thinking carefully about the new system search feature, I have decided to change it significantly in the name of safety. I was a little uneasy about releasing the feature considering it employed a search of the entire system looking for new installed tools that could be used in what-cmd. I have decided that this was an overreach. Having the tool do this posed quite a few security risks and although I attempted to mitigate those by hamstringing the search substantially, it still did not sit right with me.
When the solution to the problem occurred to me, it seemed so obvious I don't know how I didn't think of it initially. Changing the implementation to only search paths specified by the user in the config file is a much safer choice. Of course, this reduces the useability of the tool a bit. Now you'll have to find out where your tools and custom commands are stored and add the paths to their directories in your config files (although the most common paths are in the default config). However the improvements to security are so significant that it had to be done. You should now be able to use the tool and not be afraid that it goes poking around where it shouldn't.
Oh and there was a bug with the implementation of the caching of search results. This has now been fixed so you don't have to wait the precious seconds the search takes every time you want to use the tool.
As usual, thank you for using the tool and I hope it is of use as well. Please don't hesitate to open an issue or otherwise contact me if there are any questions or concerns regarding what-cmd.