Thank you.
So, area selection dialog can select only full folders, either everything in them, or nothing. I am sorry to hear that because it drastically reduces usability of the area selection dialog. Any attempt to be completely flexible and select only some of the folders, which is easily assumed to be the whole point of the unfolding tree-like dialog, will automatically exclude all files at that level, and all upper levels, and there is simply no way to test files at certain level without being forced to test every possible folder level below them. Upper level files cannot be included; lover level files cannot be excluded. I suggest at least an entry about that in manual.
If I use manual selection with Ctrl-A and scan from context menu, will that selection also include hidden and system files in that directory?