When using the eclipse plugin (gradle cleanEclipse eclipse) the generated files aren't correct at least the Deployment Assembly is broken.
It appears that in the shared projects the files 'org.eclipse.wst.common.component' and 'rg.eclipse.wst.common.project.facet.core.xml' are either missing or incorrectly generated.
Next to that in the .classpath file of the web project it appears to be creating a wrong classpathentry
<classpathentry exported="true" kind="src" path="/bookstore-shared"/>
instead of the following.
<classpathentry exported="true" kind="src" path="/bookstore-shared">
<attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
We used Gradle for the sample project for our book (Pro Spring MVC) but although it works flawlessly from the command line using the IDE integration is a bit of a pain (at least the Eclipse integration).