"Could not reset project classpath" with duplicate source folders

[mikera]

I ran into an issue getting "Could not reset project classpath" error with latest CCW on Neon.

The underlying excpetion in the Eclipse .log file was:

!ENTRY ccw.core 4 0 2016-08-25 09:54:45.030
!MESSAGE Unexpected exception while executing Job Configuring Leiningen classpath dependencies for project unilever-clj
!STACK 1
org.eclipse.core.runtime.CoreException: Could not reset project classpath
    at ccw.leiningen.nature$reset_project_build_path.invoke(nature.clj:147)
    at ccw.leiningen.nature$factory$reify__6746$fn__6750.invoke(nature.clj:167)
    at ccw.eclipse$workspace_job$fn__2956.invoke(eclipse.clj:774)
    at ccw.eclipse.proxy$org.eclipse.core.resources.WorkspaceJob$ff19274a.runInWorkspace(Unknown Source)
    at org.eclipse.core.internal.resources.InternalWorkspaceJob.run(InternalWorkspaceJob.java:39)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
Caused by: Java Model Exception: Java Model Status [Build path contains duplicate entry: 'src/main/clojure' for project 'unilever-clj']
    at org.eclipse.jdt.internal.core.JavaModelOperation.runOperation(JavaModelOperation.java:786)
    at org.eclipse.jdt.internal.core.JavaProject.setRawClasspath(JavaProject.java:3097)
    at org.eclipse.jdt.internal.core.JavaProject.setRawClasspath(JavaProject.java:3059)
    at org.eclipse.jdt.internal.core.JavaProject.setRawClasspath(JavaProject.java:3112)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:93)
    at clojure.lang.Reflector.invokeInstanceMethod(Reflector.java:28)
    at ccw.leiningen.nature$reset_project_build_path.invoke(nature.clj:141)
    ... 5 more
!SUBENTRY 1 ccw.core 4 0 2016-08-25 09:54:45.031
!MESSAGE Could not reset project classpath
!STACK 1
Java Model Exception: Java Model Status [Build path contains duplicate entry: 'src/main/clojure' for project 'unilever-clj']
    at org.eclipse.jdt.internal.core.JavaModelOperation.runOperation(JavaModelOperation.java:786)
    at org.eclipse.jdt.internal.core.JavaProject.setRawClasspath(JavaProject.java:3097)
    at org.eclipse.jdt.internal.core.JavaProject.setRawClasspath(JavaProject.java:3059)
    at org.eclipse.jdt.internal.core.JavaProject.setRawClasspath(JavaProject.java:3112)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:93)
    at clojure.lang.Reflector.invokeInstanceMethod(Reflector.java:28)
    at ccw.leiningen.nature$reset_project_build_path.invoke(nature.clj:141)
    at ccw.leiningen.nature$factory$reify__6746$fn__6750.invoke(nature.clj:167)
    at ccw.eclipse$workspace_job$fn__2956.invoke(eclipse.clj:774)
    at ccw.eclipse.proxy$org.eclipse.core.resources.WorkspaceJob$ff19274a.runInWorkspace(Unknown Source)
    at org.eclipse.core.internal.resources.InternalWorkspaceJob.run(InternalWorkspaceJob.java:39)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
!SUBENTRY 2 org.eclipse.jdt.core 4 977 2016-08-25 09:54:45.032
!MESSAGE Build path contains duplicate entry: 'src/main/clojure' for project 'unilever-clj'

I traced it down to the following two lines in the project.clj

  :source-paths ["src/main/clojure"]
  :test-paths ["src/main/clojure" "src/test/clojure"]

Removing the duplicate entry fixed the issue, however Leiningen doesn't complain with the same project.clj so it may be a sign of an underlying issue that needs fixing.