Of all the (graphics) programs I use, PDN is the only one that shows this behavior. Not sure if other software acts in different ways...
I open a JPG (or PNG, or whatever) file.
I make edits, adding some layers, your general graphics program usage.
I hit CTRL-S (or File/Save, if I feel particularly mousy).
I'm asked what file type I want to save the file as, with the PDN extension preselected. Uh, what?
It gets quite frustrating when I hit CTRL-S, upload what I think is an adjusted file to my web server, refresh the web page to see the result... and see no changes, because PDN is waiting for me to indicate in what format I want to save my file, which already had a format, because I opened an existing file.
I understand that PDN is a simple, free application. So I understand that code is kept simple, so layers are permanently flattened when saving. However, certain shortcut key-combinations have a pretty well-defined resulting action in Windows, CTRL-S being a quick save without dialog. That is, of course, unless certain changes have a big enough effect on a file that a confirmation is needed - the keyword being "confirmation".
In the case of a graphics program, if I edit a non-layer-supporting file to have layers, a quick-save should simply ask if I want to flatten (Y/N), do it, save, and be done. Push come to shove, it shouldn't be too hard to do a quick save, and then automate the "undo" history to go back to the state my edits were in before I hit Save.
If I want to make copies in another file format, I know where to find the Save As function, really, I do.
Please make CTRL-S behave like CTRL-S. Thanks!