This is a little awkward but since it only needs to be performed once for each email address, it is the only solution to date.
Let's assume your login user name on your machine is maxx, your email address is
maxx@somedomain.net. Lets also assume the folder name you want to store your mail in is /home/maxx/987654321/somedomain.
1. CLOSE Claws mail application.
2. Open the file /home/maxx/.claws-mail/folderlist.xml in your favorite text editor.
3. Locate the first line that reads something like this:
<folder type="mh" path="maxx@somedomain.net" sort="10" collapsed="1" name="maxx@somedomain.net">
4. Modify it to look like this:
<folder type="mh" path="/home/maxx/987654321/somedomain/maxx" sort="10" collapsed="1" name="maxx@somedomain.net">
5. Save the folderlist.xml file.
6. Close your text editor.
7. Disconnect from the Internet. Open Claws mail application.
8. Close Claws mail application.
9. Look in your files for the folder "/home/maxx/987654321/somedomain/maxx".
10. If it is not there, check your spelling and step through these instructions again.
11. If it is there, Hurray, go to step 12.
12. I am going to assume that you did the default adding of your email address when you first setup Claws mail. If you did, then you should have a folder /home/maxx/maxx@somedomain.net. Go to that folder and copy everything in that fold EXCEPT the "queue" folder. Paste the contents into /home/maxx/987654321/somedomain/maxx.
13. Reconnect to the Internet. Open Claws mail application.
14. Your done! Unless you have more than one email address.
15. Repeat.