I'm running Kmail 4.8rc. I was driven to try it because the 4.7.3 version kept giving me "waiting" messages when I was reading my mail. Now my inbox seems to be in a state of chaos. Often the message shown in the lower pane is different than the one that is highlighted in the index. Deleting messages seems to make matters even worse. I also tried deleting the .inbox index, hoping that it would be reconstructed correctly, but that didn't help either. It didn't make matters even worse, though.

In addition, kmail now always crashes on exit.

Is there any way I can get kmail to index my inbox correctly?

It sounds like there is a severe corruption in your installation. Can you try under a different user account?

Ok, at this point I think we should go for the slash and burn approach to repairing it. This will remove the configuration and databases used by Nepomuk and Akonadi. Fresh copies of their configuration will hopefully cure this.

First, note the locations where your local mail, calendars and contacts are stored as well as settings for other relevant accounts (IMAP, POP, etc). You can use Akonadi Console to do this.
This is especially relevant if your data is not stored in default locations used by Akonadi.

Next take complete backups of ~/.local, ~/.config and ~/.kde* outside KDE. This is essential in case this procedure fails.

Then remove the following files/folders in their entirety:
~/.config/akonadi/
~/.local/share/akonadi
~/.kde4/share/apps/nepomuk
~/.kde4/share/config/akonadi*
~/.kde4/share/config/email*

Then log back into KDE. You will now need to setup your KDE PIM applications again. This is where you will need the information you noted previously. If you use the default locations then your mail should become visible and accessible immediately.

I tried clearing out the directories and files you suggested, saving them to another location. And indeed, kmail opens cleanly and closes cleanly. I've even managed to send a test message and then read it. No problem with that.

However, none of my old mail is visible now. In the Folders pane under Local Folders, I have the usual inbox, outbox, sent-mail, trash, drafts, and templates, All those folders are empty except for sent-mail, which contains the test message as it should.

But here's what I really don't understand. If I go into Settings / Configure Kmail / Accounts / Receiving, I see a bar with Local Folders. If I then select Modify, the indicated location is /home/pwa/.local/share/local-mail. Now if I go to that very same location via konsole, I see all my old mail from before I attempted this cleanup. It's as though kmail isn't looking in the folder that it says it's looking in.

Do you have any idea what might be going on here?

Can you try right click on "Local Folders" in the main KMail window, and select "Update folder and it's subfolders", and see if that has any effect?