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did you see these instructions about re-doctoring?
" NOTE ON "RE-DOCTORING": If this is not your first time through this process, you should do a "git pull" and a "make clobber" to ensure you have the latest scripts and a pristine build folder. From the command line, type "cd meta-doctor" without the quotes and press enter. Then type "git pull" without the quotes and press enter. Then type "make clobber" without the quotes and press enter. Voila! You now have the latest scripts and a clean folder to build your doctor in."
those instructions are found in the webOS 2 upgrade wiki
I would suggest running the stock vz 2.1 doctor again first, though
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