You will have to change the location of your imap folders from ~/imap to nothing. You should only do this after the e-mail migration, not before. If you use the KCC WebMail you will not have to do anyhting

Here are instructions on how to change this setting for several poplular mail clients.

For ThunderBird:
Goto Tools->Account Settings
Select Server Settings under the KCC Mail Account
Click on Advanced Settings
Delete the "~/imap/" under IMAP server Directoy:

Deleting IMAP folder location
For Outlook:
Goto Tools->E-Mail Accounts
Select "View or Change esiting e-mail acounts" and push the Next button
Select ehe KCC/mail.jci.tju.edu mail account and push the Change button
Click on More Settings
Click onthe Advanced Tab
Delete the "~/imap/" in the Root Folder Path Field:

Deleting IMAP folder location
For Eudora:
Goto Tools->Options
Select "Incoming Mail" in the option listingh at the left
Delete the "~/imap/" in the IMAP Mailbox Location Prefix Field:

Deleting IMAP folder location
For MacMail:
Goto Mail->Preferences
Click on the Advanced tab.
Delete the "~/imap/" from the IMAP Path Prefix box

(NOTE: It may take several minutes to "save" your preferences. MacMail will be re-creating your folders on your Mac during this time. LET IT FINISH.)

Deleting IMAP folder location