I just noticed the same thing. I'm hoping there is a way to *NOT* update 
nested folders. Please let me know if there is.

On Sunday, November 24, 2013 10:48:44 PM UTC-5, Neil Faiman wrote:
>
> I'm running BBEdit 10.5. I have a web site that I hadn't worked on 
> recently. Tonight I tried to update a folder. 
>
> Instead of the dialog box that I've always gotten for Update Folder..., 
> and that the BBEdit User Manual describes (A box containing the folder 
> path, with an up/down arrow control next to it; A "Skip (...) Folders" 
> checkbox; and a "Check Nested Folders" checkbox), I now get a dialog box 
> with a single label, "Folder to update:", and a chained series of folder 
> icons representing the path, with a clock-icon popdown menu next to it for 
> selecting the folder. But the two checkboxes are gone! 
>
> What happened? How do I check just the 30 files in a folder and ignore the 
> 300 files subfolders? 
>
> Oh, no! I just looked, and the Check Folder Syntax dialog box has suffered 
> the same transformation. 
>
> Regards, 
>
>         Neil Faiman 
>
>

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