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If you have an update site project that is under source control, and you do an update site build, the build will fail unless the jar files for the feature and plugin packages are themselves already checked out. Our Team Provider's validateEdit/validateSave methods are never called, although the site.xml file does automatically get checked out.
PDE Build does not support this use case as it is not being workspace aware.
Under 3.2, this problem gets compounded by the fact that if the jar files are not writable, there is a modal error message telling you that the update site can't be built due to the read-only status of the jar files. Then, the temporary files and folders created inside the plugins and features folders do NOT get deleted like they should... also again like with 114030, they are not marked derived and notification for adding to source control occurs which you definately do NOT want because on a successful build, they are deleted.
Currently we are not actively enhancing PDE build anymore. Therefore, I close this bug as WONTFIX. Please reopen, if you plan to provide a fix.