Ok, I think I found the problems:
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The Debian package installed old historical files (from arduino 0017) that existed before I got there. I cleaned them out.
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Debian package is 1.0, and WProgram.h has been renamed to Arduino.h. So line 9 of the *.h needs to be updated in the Eclipse plug-in. Those are the new errors now that Makefile clobbering is fixed.
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pins_arduino.h doesn't exist in the same place in 1.0 as it did in 0022, which you already brought up at Arduino Forum
In conclusion: I've fixed the Debian Arduino package so there are no more Makefile clobbering. However, version Arduino 1.0 seems to be incompatible with the Eclipse plug-in. Debian uses 1.0, so the Eclipse plugin won't work with the debian package for that reason.