Here is an example to reproduce - paste these snippets into a `build.gradle` file in empty directory and run gradle.

This works:

file('src/main/groovy').mkdirs()
file('src/main/groovy/Test.groovy').text = 'class Foo {}'

apply plugin: 'groovy'
dependencies {
compile "org.codehaus.groovy:groovy-all:2.3.3" // WORKS
}
defaultTasks 'build', 'groovydoc'

This doesn't:

file('src/main/groovy').mkdirs()
file('src/main/groovy/Test.groovy').text = 'class Foo {}'

apply plugin: 'groovy'
dependencies {
compile "org.codehaus.groovy:groovy:2.3.3" // NoClassDefFoundError: groovy/util/AntBuilder
}
defaultTasks 'build', 'groovydoc'

I shouldn't have to add tool dependencies to my application classpath, but even this doesn't work:

file('src/main/groovy').mkdirs()
file('src/main/groovy/Test.groovy').text = 'class Foo {}'

apply plugin: 'groovy'
dependencies {
compile "org.codehaus.groovy:groovy:2.3.3", // NoClassDefFoundError: groovy/util/AntBuilder
"org.codehaus.groovy:groovy-ant:2.3.3" // groovy.util.AntBuilder is here, groovydoc is dragged in transitively
}
defaultTasks 'build', 'groovydoc'

While this is being investigated, the following seems to work as a workaround

configurations {
  groovyall
}
dependencies {
   groovyall "org.codehaus.groovy:groovy-all:2.3.3"
}
groovydoc.groovyClasspath = configurations.groovyall