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This would allow me to check in the .classpath file into cvs, so that my development team would be able to maintain only one libraries configuration. Right now, the file contains the actual path to the libraries.
Which build are you using? If you are using PDE classpath containers then it should just work...the classpath can be shared in the repository and it is computed dynamically when you load it. (this is how we work) Moving to JDT/Core for comment/closure.
You did you construct your build path ? You should be then using "Add JARs" instead of "Add external JARs". Please reopen with accurate steps if you can reproduce it with 3.0M9 builds.