Spring-boot gradle project creating empty webapp folder after building war - gradle

Question

I have a spring boot gradle project with a server module and I am using the gradle war plugin in my build.gradle file.
https://docs.gradle.org/current/userguide/web_project_tutorial.html
Per this link: https://docs.spring.io/spring-boot/docs/current/reference/html/howto-traditional-deployment.html (80.1)
I am overriding the configure method and I can see that a war file is being built and placed in the server/build/tmp directory.
When the project builds it also creates a empty webapp directory at server/src/main/webapp (this is the default webAppDirName).
http://www.petrikainulainen.net/programming/gradle/getting-started-with-gradle-creating-a-web-application-project/
The war is needed so that our ops guys can run it on an external Tomcat container. However, for convenience, us devs are just building and running with the gradle wrapper > ./gradlew :server:bootRun using the embedded Tomcat container.
My problem is that when we do a bootRun it is looking at the empty webapp folder that gets created during the build process and throwing this error:
2016-02-23 10:51:32.632 INFO 83043 --- [ main] s.b.c.e.t.TomcatEmbeddedServletContainer : Tomcat initialized with port(s): 22443 (https)
2016-02-23 10:51:32.641 INFO 83043 --- [ main] o.apache.catalina.core.StandardService : Starting service Tomcat
2016-02-23 10:51:32.642 INFO 83043 --- [ main] org.apache.catalina.core.StandardEngine : Starting Servlet Engine: Apache Tomcat/8.0.30
2016-02-23 10:51:32.673 ERROR 83043 --- [cat-startStop-1] org.apache.catalina.core.ContainerBase : A child container failed during start
java.util.concurrent.ExecutionException: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Tomcat].StandardHost[localhost].StandardContext[/imageretriever]]
at java.util.concurrent.FutureTask.report(FutureTask.java:122) [na:1.8.0_60]
at java.util.concurrent.FutureTask.get(FutureTask.java:192) [na:1.8.0_60]
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:916) ~[tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:871) [tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) [tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1408) [tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1398) [tomcat-embed-core-8.0.30.jar:8.0.30]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_60]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_60]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_60]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_60]
Caused by: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Tomcat].StandardHost[localhost].StandardContext[/imageretriever]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:154) [tomcat-embed-core-8.0.30.jar:8.0.30]
... 6 common frames omitted
Caused by: org.apache.catalina.LifecycleException: Failed to start component [org.apache.catalina.webresources.StandardRoot#7f31763e]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:154) [tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.c.core.StandardContext.resourcesStart(StandardContext.java:4928) ~[tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5058) ~[tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) [tomcat-embed-core-8.0.30.jar:8.0.30]
... 6 common frames omitted
Caused by: java.lang.IllegalArgumentException: The main resource set specified [/Users/carlc/intellij_workspace/image-retriever/src/main/webapp] is not valid
at org.apache.catalina.webresources.StandardRoot.createMainResourceSet(StandardRoot.java:723) ~[tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.webresources.StandardRoot.startInternal(StandardRoot.java:684) ~[tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) [tomcat-embed-core-8.0.30.jar:8.0.30]
... 9 common frames omitted
I thought the issue might be tangentially related to this: https://github.com/spring-projects/spring-boot/issues/1313
But I wasn't able to glean any helpful information out of it.
I can think of two solutions: 1) remove the offending webapp folder during the build process 2) Configure bootRun to ignore the webapp folder all together 3) Your suggestions go here _____________ :)
I can post the build.gradle or other code you think relevant upon request. Thanks for any help.