Creating a new task of type 'Jar' will always jar-up the classes in 'classesDir' as well as those specified in the 'FileSet' directive:

(e.g.)
Running the following task with the '-d' flag:

task jarServiceFacade(type: Jar, dependsOn: compileServiceFacade) {
baseName = 'ias_ta_common_service_facade'
fileSet(dir: servicesFacadeClassesDir) {
include("ie/vhi/ias/ta/common/services/facade/**")
}

produces:

• Creating archive: jarServiceFacade
• fileset: Setup scanner in dir C:\workspace\Core\branches\TEMP_gradle\TA\ias_ta_common\build\classes with patternSet { includes: [] excludes: [] }
• fileset: Setup scanner in dir C:\workspace\Core\branches\TEMP_gradle\TA\ias_ta_common\build\facade-classes with patternSet { includes: [ie/vhi/ias/ta/common/services/facade/**] excludes: [] }

This can be worked around by setting 'resourceCollections = []'

See thread: http://article.gmane.org/gmane.comp.programming.tools.gradle.user/1908