FYI, if this helps anyone, I found the following thread useful in the final repairs:
http://www.hackint0sh.org/forum/show...23&postcount=2
Here where my steps (tweaked from those contained in above thread) (PROCEED AT YOUR OWN RISK!!) Assumes a jailbroken 1.1.3 phone:
1. SSH into phone
2. "cd /"
3. "ls -le"
Should get something like this:
lrwxr-xr-x 1 root admin 25 Feb 8 03:57 Applications -> /private/var/Applications
drwxrwxr-x 8 root admin 408 Feb 8 09:31 Library
drwxr-xr-x 3 root wheel 102 Dec 14 23:22 System
drwxr-xr-x 2 root wheel 1394 Feb 8 01:21 bin
drwxrwxr-t 2 root admin 68 Dec 12 02:39 cores
dr-xr-xr-x 3 root wheel 740 Feb 8 11:40 dev
lrwxr-xr-x 1 root admin 11 Feb 8 00:52 etc -> private/etc
lrwxr-xr-x 1 root admin 11 Feb 8 00:52 mach -> mach_kernel
drwxr-xr-x 4 root wheel 136 Dec 14 23:51 private
drwxr-xr-x 2 root wheel 646 Feb 8 01:21 sbin
lrwxr-xr-x 1 root admin 15 Feb 8 00:52 tmp -> private/var/tmp
drwxr-xr-x 7 root wheel 238 Dec 14 23:49 usr
lrwxr-xr-x 1 root admin 11 Feb 8 00:53 var -> private/var
Likely, you should see the Applications folder without the -> private/var/Applications - that's where we start fixing... The remainder of my steps taken presume it does not have that sym link.
4. Now comes the fun part - reconcile the folders. Issue a "cd /private/var" followed by "ls -le". What has bosstool done yet? Here are some scenarious:
4a) Applications folder does not exist : Well, this one is simple - issue a "cp -
pr /Applications /private/var/Applications"
4b) Applications folder exists : Issue a "cd ./Applications" followed by "ls -le". If there is an embedded Applications folder, again in this folder - issue a "mv ./Applications ./Applications.old". Now, reconcile the file lists from the /Applications to this folder. In my case, the /Applications folder was a subset of the /private/var/Applications folder.
5. "cd /"
6. "mv Applications Applications.old"
7. "ln -s /private/var/Applications Applications"
8. Reboot phone
9. Test EVERY application. Any failures will require going back to the backups and moving where appropriate..
10. If everything tested fine, you can than run a, b, and c below:
10a) "rm -r /Applications.old"
10b) "rm -r /private/var/Applications.old"
10c) "rm -r /private/var/Applications/Applications.old"
This is how I went about this. It now works just fine. For those wanting to use my outline above, please use it as a general guideline - not as a concrete step by step since 1) i've drafted this in short time with competing priorities (work) and 2) there might be better ways, this happened to work for me and 3) my steps can't possibly contemplate the variations which might exist...
Cheers