The fix isn't exactly hard but before I did that, I decided to give my Freerunner's wifi configuration another try. It turns out the reason I couldn't get wifi to work before was due to a really silly thing. In the new keyboard app in Om2008, it shows what word it thinks you're typing, but it doesn't actually enter it unless you tap on the word. Whenever I tried to enter my WPA password, I would see the word suggestion from the keyboard app right below the blank password textbox, and I thought I was typing in the password box. Actually I hadn't entered anything yet because I didn't click on the word. Once I figured that out, I was able to connect to my wifi network.
But how to be sure that I was connected? I hit upon the idea of going into my router configuration to see if it had assigned a DHCP address to my Freerunner. Sure enough, there it was, and now I knew what IP to type in to ssh to it. Having wifi working solves some of my problems I had with USB networking. Even though my ssh session still freezes when the Freerunner goes into standby, the ssh session also unfreezes when I wake the phone back up, so I can continue where I left off while working. Still trying to figure out how to fix the shutdown problem.
Once you have wifi connected, you should be able to ping internet IP addresses, but DNS doesn't work yet because the Freerunner doesn't know your DNS server. I followed the instructions from the USB networking page to set up DNS, using the address of my router, as that part of the instructions works equally well for wifi networking as it does for USB networking.
Once DNS works, then the package manager works.
Update: I must have missed that in the known issues for Om2008, they said that the builds from the last days of August (which I'm using) have to have the X screensaver disabled. The fix is to run the command "xset s off". What they didn't mention (and since it's a wiki, I was able to fix it for them :) ) is that you can't run xset from the ssh session, you have to install the terminal app (after getting DNS working) and run the command on the phone itself.