Add apt output dir as source directly in sourcesJar task

Code generation and subsequent compilation is performed within a single
java compiler call. Gradle, on the other hand, checks whether
the inputs of a task have changed before starting the task.
So if we call compileJava for the first time after cleaning build dir
before starting the task, Gradle sees that generatedSrcDir is empty
and remembers that. When we call compileJava again, Gradle sees that
new files have been added to generatedSrcDir and restarts compilation.
On the third compileJava call in a row, nothing has changed for Gradle
and it marks the task as up to date.
As far as I understand, adding generatedSrcDir as sourceSet is only
needed to include generated sources in sourcesJar. So instead of adding
generatedSrcDir as sourceSet, we can add it directly to sourcesJar.

Signed-off-by: Denis Buzmakov <me@bacecek.dev>

buildSrc/src/main/groovy/ShadowsPlugin.groovy

@@ -19,8 +19,6 @@ class ShadowsPlugin implements Plugin<Project> {
         // write generated Java into its own dir... see https://github.com/gradle/gradle/issues/4956
         def generatedSrcDir = project.file("build/generated/src/apt/main")
 
-        project.sourceSets.main.java { srcDir generatedSrcDir }
-
         project.tasks.named("compileJava").configure { task ->
             task.options.annotationProcessorGeneratedSourcesDirectory = generatedSrcDir
 
@@ -47,6 +45,7 @@ class ShadowsPlugin implements Plugin<Project> {
         }
 
         project.tasks.named("sourcesJar").configure { task ->
+            task.from(generatedSrcDir)
             task.doLast {
                 def shadowPackageNameDir = project.shadows.packageName.replaceAll(/\./, '/')
                 checkForFile(task.archivePath, "${shadowPackageNameDir}/Shadows.java")