I would really love to be able to create sub folders under the main categories for example something like.
Internet
--Web Browsers
----Firefox
--Communication
----Thunderbird
--Downloading
----Qbittorrent
etc.
I think that it would really help people in organizing all of their apps.
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It's a possibility. But it's not a definite as there are much better ways to organize your apps. Currently, you can type to find, so you can easily get to Firefox, Thunderbird, etc. And if you're looking for email clients, you'll be able to just type email and have them show up in an upcoming release. Those two plus favorites up top and most recently used below mean you shouldn't really need to click to browse into categories often as it is.
Most people never browser their apps this way anymore, which is why the major OSes have switched to some combination of favorites, most used, and find as you type.
That said, we'll may explore it at some point in the future and it is in the list: https://portableapps.com/node/28593
Sometimes, the impossible can become possible, if you're awesome!
I agree with the OP. I've been using portableapps for a few months now and love it. However, not being able to create subfolders/categories makes things a little cluttered. fyi, I do love the platform.