Proper fix for #44

pom.xml

@@ -451,22 +451,46 @@
                         <version>3.2.0</version>
                         <configuration>
                             <debug>true</debug>
-                            <cloneProjectsTo>${project.build.directory}/it</cloneProjectsTo>
                             <postBuildHookScript>verify</postBuildHookScript>
                             <localRepositoryPath>${project.build.directory}/local-repo</localRepositoryPath>
                             <settingsFile>src/it/settings.xml</settingsFile>
-                            <goals>
-                                <goal>clean</goal>
-                                <goal>test-compile</goal>
-                            </goals>
                         </configuration>
                         <executions>
                             <execution>
-                                <id>integration-test</id>
+                                <id>install</id>
                                 <goals>
                                     <goal>install</goal>
+                                </goals>
+                            </execution>
+                            <execution>
+                                <id>run-clean-test-compile</id>
+                                <goals>
+                                    <goal>run</goal>
+                                </goals>
+                                <configuration>
+                                    <cloneProjectsTo>${project.build.directory}/it</cloneProjectsTo>
+                                    <goals>
+                                        <goal>clean</goal>
+                                        <goal>test-compile</goal>
+                                    </goals>
+                                </configuration>
+                            </execution>
+                            <execution>
+                                <!-- Execute selected projects a second time without clean to catch problems like #44 -->
+                                <id>run-test-compile</id>
+                                <goals>
                                     <goal>run</goal>
                                 </goals>
+                                <configuration>
+                                    <!-- Reuse the cloned directories produced by the previous execution -->
+                                    <projectsDirectory>${project.build.directory}/it</projectsDirectory>
+                                    <pomIncludes>
+                                        <pomInclude>xjc-test/pom.xml</pomInclude>
+                                    </pomIncludes>
+                                    <goals>
+                                        <goal>test-compile</goal>
+                                    </goals>
+                                </configuration>
                             </execution>
                         </executions>
                         <dependencies>

src/it/xjc-test/pom.xml

@@ -46,7 +46,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-compiler-plugin</artifactId>
-          <version>2.5.1</version>
+          <version>3.5.1</version>
           <configuration>
             <source>1.6</source>
             <target>1.6</target>

src/it/xjc-test/src/test/java/Test.java

@@ -0,0 +1,25 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+import com.example.myschema.AddressType;
+
+public class Test {
+    public AddressType createAddress() {
+        return new AddressType();
+    }
+}

src/main/java/org/codehaus/mojo/jaxb2/AbstractJaxbMojo.java

@@ -350,19 +350,8 @@ public final void execute() throws MojoExecutionException, MojoFailureException
             log.info("No changes detected in schema or binding files - skipping JAXB generation.");
         }
 
-        // 4) If the output directories exist, add them to the MavenProject's source directories
-        if (getOutputDirectory().exists() && getOutputDirectory().isDirectory()) {
-
-            final String canonicalPathToOutputDirectory = FileSystemUtilities.getCanonicalPath(getOutputDirectory());
-
-            if (log.isDebugEnabled()) {
-                log.debug("Adding existing JAXB outputDirectory [" + canonicalPathToOutputDirectory
-                        + "] to Maven's sources.");
-            }
-
-            // Add the output Directory.
-            getProject().addCompileSourceRoot(canonicalPathToOutputDirectory);
-        }
+        // 4) Update the project always.
+        updateProject();
     }
 
     /**
@@ -390,6 +379,13 @@ public final void execute() throws MojoExecutionException, MojoFailureException
      */
     protected abstract boolean performExecution() throws MojoExecutionException, MojoFailureException;
 
+    /**
+     * Update the Maven project if necessary. This method will be called if {@code !shouldExecutionBeSkipped()}
+     * (even if {@link #performExecution()} is skipped).
+     */
+    protected void updateProject() {
+    }
+
     /**
      * Override this method to acquire a List holding all URLs to the sources which this
      * AbstractJaxbMojo should use to produce its output (XSDs files for AbstractXsdGeneratorMojos and

src/main/java/org/codehaus/mojo/jaxb2/javageneration/AbstractJavaGeneratorMojo.java

@@ -501,9 +501,6 @@ protected boolean performExecution() throws MojoExecutionException, MojoFailureE
                 }
             }
 
-            // Add the generated source root to the project, enabling tooling and other plugins to see them.
-            addGeneratedSourcesToProjectSourceRoot();
-
             // Copy all source XSDs to the resulting artifact?
             if (xsdPathWithinArtifact != null) {
 
@@ -578,13 +575,6 @@ protected boolean performExecution() throws MojoExecutionException, MojoFailureE
      */
     protected abstract List<File> getSourceXJBs();
 
-    /**
-     * Adds any directories containing the generated XJC classes to the appropriate Project compilation sources;
-     * either {@code TestCompileSourceRoot} or {@code CompileSourceRoot} depending on the exact Mojo implementation
-     * of this AbstractJavaGeneratorMojo.
-     */
-    protected abstract void addGeneratedSourcesToProjectSourceRoot();
-
     //
     // Private helpers
     //

src/main/java/org/codehaus/mojo/jaxb2/javageneration/TestXjcMojo.java

@@ -328,7 +328,7 @@ protected List<String> getClasspath() throws MojoExecutionException {
      * {@inheritDoc}
      */
     @Override
-    protected void addGeneratedSourcesToProjectSourceRoot() {
+    protected void updateProject() {
         getProject().addTestCompileSourceRoot(getOutputDirectory().getAbsolutePath());
     }
 

src/main/java/org/codehaus/mojo/jaxb2/javageneration/XjcMojo.java

@@ -339,8 +339,8 @@ protected List<String> getClasspath() throws MojoExecutionException {
      * {@inheritDoc}
      */
     @Override
-    protected void addGeneratedSourcesToProjectSourceRoot() {
-        getProject().addCompileSourceRoot(FileSystemUtilities.getCanonicalPath(getOutputDirectory()));
+    protected void updateProject() {
+        getProject().addCompileSourceRoot(getOutputDirectory().getAbsolutePath());
     }
 
     /**