We made the warning progressively more red, and more scary, and made you click a checkbox to confirm you understood, etc -- unfortunately, people continued to blow past all the warnings and use the feature to cause irreversible problems for themselves.. Which points to something fundamentally wrong with the design of the feature.
There were really two issues here: first off, the underlying logic of the file organization needed a good deal of work, just to function as expected. In particular, it had difficulty with complex situations where you have multiple versions of the same album that were all named similarly.
In these cases, Roon needs to split the albums into folders, label them in a sensible way, etc. Organized folders never worked properly in these cases, and the results were often unacceptable, with multiple versions of an album merged into a single folder.
The second issue is more fundamental -- a folder that automatically moves files around without warning or confirmation needs to be perfect, but basing those actions on metadata (which can never really be perfect) is always going to yield some unpredictable results.
So, we decided to address the first issue by designing some very smart logic to ensure that albums are sorted into folders as expected, even when multiple editions exist. And we deployed that new logic in the newly rewritten Export feature, since the 2nd issue is really insoluble -- unpredictable automatic file moves are always going to catch people by surprise, and simply don't make for a good, predictable feature.
I also used organized folders, and my personal use case was for podcasts and DJ mixes -- files I could download from wherever, tag, and drop into my organized folder so they end up neatly organized someplace. What I've realized testing 1.3 over the last few months is that when I tagged these files correctly, they tend to show up correctly in Roon -- the folder structure on my hard drive didn't actually matter very much. And, when I actually want to organize files into folders, export is absolutely sufficient.
So, from that perspective no functionality has been removed here; Roon can still organize your files, but it does it in a safe, deliberate way. Only the automatic nature of the file moves -- the cause of so much confusion and frustration -- has been removed.