Reader Judy Agid asks very reasonably:
I would like the Finder windows to allow me to always have folders on top and all files within the folders to be in alphabetical order. Is there any way to do that, especially now that both TotalFinder and XtraFinder do not work with El Capitan?
Unfortunately, there is no current solution. It may be impossible for a developer working within the constraints of System Integrity Protection (SIP), a feature added in El Capitan that offers better protection against malware by blocking changes to a lot of system files, but also disabled the tools Judy mentions. (The developers of those apps opted to cease development, not having a clear path forward.)
Default Folder was notably rewritten from the ground up to work alongside SIP. However, it only offers limited folder/file segregation and ordering, and only within submenus it displays. It can’t change the display of Finder windows.
Judy noted in her email that she’s aware of using Sort By or Arrange By coupled with Kind, which puts folders into their own category. But it doesn’t put folders first.
It’s unclear to me if SIP would allow a developer to re-order Finder windows’ file lists. If it could, I’d think someone might develop such a utility; since it hasn’t happened after several months, I’m inclined to believe it can’t be done neatly or at all.
Update: Readers offered two useful suggestions, if you’re willing to work outside of automatic Finder organization. In the Finder, you can precede all folder names with a space. While invisible, it will shift folders alphabetically to the top. You can use a renaming utility to rename all your folders if you want to avoid the manual tedium. Several readers also recommeded Path Finder 7 ($40), which is a file-management app you can use in place of OS X’s Finder, as it lets you sort folders first.
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