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The .project file for plugin org.eclipse.datatools.sqltools.ddlgen.ui has the project name as org.eclipse.datatools.sqltools.ddlgen.internal.ui. This causes a problem when the project is loaded from the Git repository. It's been like this for a long time, but apparently the CVS import ignored the name in the .project file.
Here's the change log entry: http://git.eclipse.org/c/datatools/org.eclipse.datatools.sqltools.git/commit/?id=7aeea44a5af38c6677f88c04aac6567513d8adaf