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When creating a new JPA project, persistence.xml and orm.xml files are not created in the primary source folder, and many problems ensue. This is most likely due to the *.wst.common.component metadata file not being created, which is most likely due to problems created in the wtp-sdk-S-3.0RC1-20080519195353 build.
Please note that the missing metadata file is due to an EMF change: https://bugs.eclipse.org/bugs/show_bug.cgi?id=231430 We are working with the EMF team to find a proper solution.
With the respin of RC1 (including EMF RC1a), this no longer occurs