[Fixed] Documents, PortableApps folders and sub-folders invisible to PocketSearch and other apps

I could disable it by default and make it an advanced option, letting folks who want it turn it on. The issue is that it requires setting the system flag to true on the folders. Turning this off normally requires the command line for an end-user (which is non-trivial). It breaks the ability for many non-standard file open windows to find it (since they ignore system files) as well as things like the app referenced in this thread. It also apparently makes the folders invisible by default on some Linux OSes, which is an even bigger issue. Thus, I'm inclined to disable it entirely so folks don't encounter random problems later. If we do have it available as an option, we'd likely need a warning explaining this.

Setting a directory as read-only via flags (not via Windows Explorer) only sets the flag on the actual directory. You can still create, edit, delete files and folders within that directory without issue. And it does seem to accomplish the goal of maintaining the special folder icons. Maybe I'll try it in the next beta and see if it works for folks.

Now that I've taken the time to look, Changing the Icon of a folder via the "Customize" tab of the "Properties" window sets the ReadOnly flag, not the System flag, and I've got tons of folders that I now see are set to be ReadOnly, but since their contents is not, it still works normally, and I've never even noticed.

I think it'd work fine.
(Though you'll have to remove the System flag as well as add the ReadOnly flag to achieve the desired result on upgrade. ☺)