I wrote:
> In the case of the warning popups when saving, why show them
> at all? Of course it needs to flatten layers when saving to JPEG;
> why not just do it without asking me every time? It's not like
> I have an option to save without flattening; all I can do is
> press OK.

I posted hastily: this dialog does have more than one option. And
the other dialog, that I said no longer existed in CVS HEAD, is
still there (I don't know why it didn't come up for me earlier).
Here's the sequence if a layer mask is selected:

First, a dialog that says "You are about to save a layer mask as
JPEG. This will not save the visible layers." So what WILL it save?
There's no way of telling from the text in the dialog.
Options are:  [Cancel]  [Confirm], so Confirming is really
the only choice.

If you Confirm this, then at least for jpeg, you get the
flatten dialog: JPEG can't handle transparency, Flatten?
The choices here are:  [Ignore] [Cancel] [Export]
Export is almost always the right answer, since that saves the
image as you're looking at it in the image window -- even if you
just dismissed that scary layer mask dialog that said it wouldn't
save the visible layers.

It turns out that what [Ignore] means here is "Save the current
layer instead of the whole flattened image". And in that case,
if you went through the layer mask dialog earlier, what will be
saved is the layer mask, otherwise you'll get the layer (with no
layer mask applied).

If you wanted to save a layer or layer mask in a format that
doesn't call up the Flatten dialog (say, as XCF), you're out of luck.
The only option is to paste it as a new image and save that.

This would all be so much clearer if Save As just saved the current
image (the whole thing, flattening as necessary without pestering
the user about it). For people who want to save just one layer
(or mask), offer a separate menu item for that, perhaps in the
context menu of the layers dialog, as well as in either the File
or Layers main menubar.

Right now Save As is overloaded to do two fairly different
operations -- but only if you're saving to a format that doesn't
allow layers. Why not separate those two operations as separate
menu items, and have it work the same regardless of format?

Bug http://bugzilla.gnome.org/show_bug.cgi?id=75328 seems to
be the best discussion of these export dialogs, but it doesn't
really address the issues I mentioned (I should probably add
a comment).

As long as we're talking about Save issues, bug 75459 is another
one worth looking at (both referenced from the bug 119545 that
GSR mentioned).

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