What I don't understand is, when I created a new project with the latest installation, the general structure of files changed. In the previous version, I ran the processor expert and it created a skeleton main.c/main.h set, and an MCUinit.c/MCUinit.h set. In the MCUinit files were the configuration of every hardware device I had selected, along with ISRs for every interrupt, and a vector table. The ISR functions were all empty, but they were defined. The new version of codewarrior created ProcessorExpert.c, and Events.c/Events.h. Looking in the Events files, there was a declaration that I had to create all my own interrupt functions, they wouldn't do it.
Thinking I should move forward with the new installation, I migrated my application into ProcessorExpert.c, and constructed ISRs in Events.c, which I had to do in order to compile the code. Then the application barfed when trying to enter debug mode.
Why did this change so dramatically? When I initially opened my application in the new version, I got the warning at the end of the list in the original post:
Generator: Warning: Device Initialization is obsolette and might not be supported in next release
The misspelling of obsolete is the actual message, not a typo on my end.
Realizing this was not going anywhere, I uninstalled codewarrior, and any Segger software I could find. I then rebooted and reinstalled the previous version of CW. Enough already. I'm not in to being a beta tester for free, and I'm not able to ask my customer to pay for the time I spent jerking around with this. At least now I'm up and running, and will ignore the "updates are available" popup window from now on.
Lastly, to answer your question about the debug session being open: of course there was a debug session open! I'm developing an application and was in the middle of working on it. I was not only _not_ cautioned against having a debug session open, but clicked the "run in background" button on the update window so I could continue working. If this was going to break the installation, or if the installation would fail if I didn't restart Eclipse before running it and make sure I had closed the debug perspective prior to relaunching, and that there was no debug session started after relaunching, why was this even allowed to run? More importantly, why wasn't this tested prior to releasing the update?