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Comparing a couple of directory trees with some ignores (in my case: Thumbs.db), if a tree has one branch with some leaf directories with only ignored files (i.e. Thumbs.db) and the other tree doesn't have those directories, then those directories simply doesn't appear at all in any pane.

I'm intrigued: is this behaviour purposedly introduced or is it a bug?

Now that I think of it: if I remember well, removing the ignores makes the subdirs appear as empty!
But usually Thumbs.db is "hidden" and "system".

Uhm, I should try better to be more precise.
As soon as I'll find some time to investigate I'll tell you more details.

Well, ok.
To begin with: it's not the "ignores" but the "Excludes".
"Directory compare->Filters->Exclude"

If I exclude the Thumbs.db from the comparison and the subdirectory doesn't contain anything else, if in the other pane directory that subdir isn't present at all, then that subdir doesn't appear in any way.

If I remove the exclude then everything is as expected.

I'd like to know that that subdir actually exists but, since, after all, it's NOT really empty, it can not appear as emplty, but I told EDP to ignore that (those) file(s), so no file appears to show that subdir presence...

Maybe a different qualification, like "virtually empty"?

Sorry for the messy explication.

There is an option for this: Options | Dir Compare | Other | Show empty directories in recursive comparison.

Yes, I know, and indeed that option is set.
That's exactly why I say it could be incorrect.
Those subdir aren't empty, but at the same time they officially contain nothing useful so they simply disappear.

I see. Could you zip a pair of small sample directories along with your options and the screenshot?

Well, it is more a matter of philosophy than a bug or a glitch.

I often compare two disks: the main one (C:) and the backup one (D:).
I started wondering because I discovered I had many subdirs in D: that don't exist on C: (anymore) but I don't see them in EDP.

The fix is easy: change the "exclude" filters.

Maybe a quick way to change filters (Shorter than Options->Directory compare->Filters->Manage->(combo))?

Oh, I think I can survive.

To answer you original question: after taking a look at this and giving it some thought, I believe that EPD works correctly. If the directory with all it files being excluded was shown as empty, it would in fact be a lie, since it's not. Moreover, some further operation in EDP (copy, delete) would be confused, since EDP would thing it's dealing with an empty directory while in fact it has files. So, to conclude, nothing needs to be changed.

Maybe a quick way to change filters (Shorter than Options->Directory compare->Filters->Manage->(combo))

There's actually a shortcut to Options->Directory compare->Filters: double-click on the red filter icon in either of the comparison panes' status bars.

Wow, I never clicked it!
Not even thought to click it.
I completely missed that shortcut.
Thank you.