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I'd installed the Beta El Capitan inline, which imported everything from my Yosemite system on my MBP, and everything, including Mail, worked fine. However, I wanted to do a clean install with the GM release. So I manually copied my User folder from my El Capitan Beta installation to an external HDD, and then did a clean install with El Capitan GM. Mail works fine with all IMAP folder configurations, (once I manually added the email accounts). However, there was one archive MBOX hierarchy, (called Work which has multiple sub-folders), which was stored "On My Mac", which I wanted to move over, and I mistakenly thought a simple copy process could move it.I first tried to copy this Work MBOX hierarchy, (18G, about 90k emails), from my backup ~/Library/Mail/V3/Mailboxes folder, to a manually created ~/Library/Mail/V3/Mailboxes folder, and after starting Mail, it doesn't show any folders as being "On My Mac". After reversing those changes, I tried copying the entire ~/Library/Mail/V3/Mailboxes folder from my backup to the new system, and still, Mail doesn't show any folders being "On My Mac". Finally, after reversing those changes, I tried copying the entire ~/Library/Mail and ~/Library/Containers/com.apple.mail from my backup to my new system, and again, Mail won't show any folders being "On My Mac".I even created some new mailboxes, which do show up as being "On My Mac" on my system, to try to find where these folders are created, and all I could determine is that Mail isn't creating a ~/Library/Mail/V3/Mailboxes folder for them. Lastly, I tried importing the mailbox from within Mail, and the exact same thing that happened to this user posting to the Apple Communities forum regarding Mail on OSX 10.10, happended to me. After selecting import mailbox, and then selecting Apple mail format, and the Work MBOX top level container, the import process comes back within a few seconds, and says that the new folder is in the folder called Imported, but nothing has been done, and there is no Imported folder.Is there no way to manually add an Apple Mail MBOX folder hierachy to an already running Apple Mail system? I know I've done it before with earlier versions.Worst case, I don't mind doing a complete Mail wipe and manual copy from backup, because I don't actually need anything Mail related on my new installation. So if there was some brute force way to copy over the entire Mail configuration from my prior El Capitan system, to this new clean install, it would at least get me my "On My Mac" folder archive back.Thanks for any guidance..