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My plugin projects all have their main source directory set to "src/main". If I use PDE Tools > Update Classpath to update the dependencies on other plugins, the source directory is reset to "src"
Make sure your build.properties references src/main, not src. The mapping of the jar to the source folder supercedes any nesting of folders. is that the case here?
Ah, yes it is =). Is it possible to have PDE automatically update the build.properties with the list of source directories from the project? We could avoid this duplication of effort in the future...
the thing is that your plugin can have more than one library and multiple source folders (some of which may not map to any library). So we can never guess what you want to do. What we could do is flag a warning on your build.properties file if it references a non-existing source folder, since that is the big problem.
This extra build.properties validation will be addressed as part of bug 34165 *** This bug has been marked as a duplicate of 34165 ***