I haven't read your exact setup but some things that might help:
Add this to your pom.xml
<build>
<outputDirectory>${project.build.directory}/${project.build.finalName}/WEB-INF/classes</outputDirectory>
I use the Eclipse plugin FileSync to keep src/main/webapp synchronised with
/target/myapp-1.0/
In Eclipse preferences, under Google > Web Application I have ticked "This
project has a war directory" and set it to "src/main/webapp"
I do not include any of the App Engine jars in my pom because the Eclipse
plugin seems to depend on the location of some of them to find other bits
and pieces in the SDK - at least it did a number of releases back.
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