Fix 'Cannot nest <source folder>'

org.eclipse.m2e.apt.core/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: org.eclipse.m2e.apt.core;singleton:=true
-Bundle-Version: 2.3.100.qualifier
+Bundle-Version: 2.3.200.qualifier
 Bundle-Localization: plugin
 Require-Bundle: org.eclipse.core.runtime;bundle-version="[3.27.0,4.0.0)",
  org.eclipse.core.resources,

org.eclipse.m2e.apt.core/src/org/eclipse/m2e/apt/internal/AbstractAptConfiguratorDelegate.java

@@ -238,6 +238,7 @@
   @Override
   public void configureClasspath(IClasspathDescriptor classpath, IProgressMonitor monitor) throws CoreException {
 
+    removeStaled(classpath);
     AnnotationProcessorConfiguration configuration = getAnnotationProcessorConfiguration(monitor);
 
     if((configuration == null) || !configuration.isAnnotationProcessingEnabled()) {
@@ -259,6 +260,10 @@
       File outputFolder = new File(mavenProject.getBuild().getTestOutputDirectory());
       addToClassPath(eclipseProject, generatedTestSourcesDirectory, outputFolder, classpath, true);
     }
+    if (generatedSourcesDirectory != null || generatedTestSourcesDirectory != null) {
+      IJavaProject javaProject = JavaCore.create(eclipseProject);
+      javaProject.setRawClasspath(classpath.getEntries(), monitor);
+    }
   }
 
   protected abstract AnnotationProcessorConfiguration getAnnotationProcessorConfiguration(IProgressMonitor monitor)
@@ -283,11 +288,9 @@
     IPath[] includes = new IPath[] {};
     IPath[] excludes = new IPath[] {};
 
-    // If the source folder is non-nested, add it
+    // If the source folder doesn't exist, add it
     if((generatedSourcesFolder != null) && generatedSourcesFolder.getProject().equals(project)) {
-      IClasspathEntryDescriptor enclosing = getEnclosingEntryDescriptor(classpath,
-          generatedSourcesFolder.getFullPath());
-      if((enclosing == null) || (getEntryDescriptor(classpath, generatedSourcesFolder.getFullPath()) != null)) {
+      if(getEntryDescriptor(classpath, generatedSourcesFolder.getFullPath()) == null) {
         IClasspathEntryDescriptor entry = classpath.addSourceEntry(generatedSourcesFolder.getFullPath(), outputPath,
             includes, excludes, true);
         entry.setClasspathAttribute(IClasspathAttribute.IGNORE_OPTIONAL_PROBLEMS, "true"); //$NON-NLS-1$
@@ -322,7 +325,7 @@
    * @return the {@link IClasspathEntryDescriptor} in the specified {@link IClasspathDescriptor} that is a prefix of the
    *         specified {@link IPath}
    */
   private static IClasspathEntryDescriptor getEnclosingEntryDescriptor(IClasspathDescriptor classpath, IPath path) {
     for(IClasspathEntryDescriptor cped : classpath.getEntryDescriptors()) {
       if(cped.getPath().isPrefixOf(path)) {
         return cped;
@@ -331,20 +334,25 @@
     return null;
   }
 
-  private IClasspathEntryDescriptor getEntryDescriptor(IClasspathDescriptor classpath, IPath fullPath) {
+  private void removeStaled(IClasspathDescriptor classpath) {
     List<IPath> stalePaths = new ArrayList<>();
-    IClasspathEntryDescriptor matchingDescriptor = null;
     for(IClasspathEntryDescriptor cped : classpath.getEntryDescriptors()) {
-      if(cped.getPath().equals(fullPath)) {
-        matchingDescriptor = cped;
-      } else if(Boolean.parseBoolean(cped.getClasspathAttributes().get(M2E_APT_KEY))) {
+      if(Boolean.parseBoolean(cped.getClasspathAttributes().get(M2E_APT_KEY))) {
         stalePaths.add(cped.getPath());
       }
     }
     for(IPath stalePath : stalePaths) {
       classpath.removeEntry(stalePath);
     }
-    return matchingDescriptor;
+  }
+
+  private IClasspathEntryDescriptor getEntryDescriptor(IClasspathDescriptor classpath, IPath fullPath) {
+    for(IClasspathEntryDescriptor cped : classpath.getEntryDescriptors()) {
+      if(cped.getPath().equals(fullPath)) {
+        return cped;
+      }
+    }
+    return null;
   }
 
   protected <T> T getParameterValue(String parameter, Class<T> asType, MojoExecution mojoExecution)

org.eclipse.m2e.apt.tests/projects/nested/pom.xml

@@ -0,0 +1,77 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" 
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>org.sample</groupId>
+    <artifactId>nested-test</artifactId>
+    <version>1.0-SNAPSHOT</version>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    </properties>
+
+    <dependencies>
+        <dependency>
+	        <groupId>org.mapstruct</groupId>
+	        <artifactId>mapstruct</artifactId>
+	        <version>1.6.3</version>
+	    </dependency>
+        <dependency>
+            <groupId>org.mapstruct</groupId>
+            <artifactId>mapstruct-processor</artifactId>
+            <version>1.6.3</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+            <version>1.7.36</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.mapstruct</groupId>
+                    <artifactId>mapstruct-processor</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>build-helper-maven-plugin</artifactId>
+                <version>3.2.0</version>
+                <executions>
+                    <execution>
+                    	<?m2e execute onConfiguration,onIncremental?>
+                        <id>add-source</id>
+                        <phase>generate-sources</phase>
+                        <goals>
+                            <goal>add-source</goal>
+                        </goals>
+                        <configuration>
+                            <sources>
+                                <source>${basedir}/target/generated-sources/</source>
+                            </sources>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+             <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.8.1</version>
+                <configuration>
+                    <release>21</release>
+                    <compilerArgs>
+                        <arg>-parameters</arg>
+                        <arg>-Xlint:all</arg>
+                    </compilerArgs>
+
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+</project>

org.eclipse.m2e.apt.tests/projects/nested/src/main/java/org/mapper/Main.java

@@ -0,0 +1,9 @@
+package org.mapper;
+
+public class Main {
+	public static void main(String[] args) {
+		Person person = new Person(1l, "test");
+		PersonDto personDto = PersonMapper.INSTANCE.personToPersonDto(person);
+		System.out.println(personDto);
+	}
+}

org.eclipse.m2e.apt.tests/projects/nested/src/main/java/org/mapper/Person.java

@@ -0,0 +1,34 @@
+package org.mapper;
+
+public class Person {
+
+	private Long id;
+	private String name;
+
+	public Person(Long id, String name) {
+		this.id = id;
+		this.name = name;
+	}
+
+	public Long getId() {
+		return id;
+	}
+
+	public void setId(Long id) {
+		this.id = id;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	@Override
+	public String toString() {
+		return "Person [id=" + id + ", name=" + name + "]";
+	}
+
+}

org.eclipse.m2e.apt.tests/projects/nested/src/main/java/org/mapper/PersonDto.java

@@ -0,0 +1,29 @@
+package org.mapper;
+
+public class PersonDto {
+
+	private Long id;
+	private String name;
+
+	public Long getId() {
+		return id;
+	}
+
+	public void setId(Long id) {
+		this.id = id;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	@Override
+	public String toString() {
+		return "PersonDto [id=" + id + ", name=" + name + "]";
+	}
+
+}

org.eclipse.m2e.apt.tests/projects/nested/src/main/java/org/mapper/PersonMapper.java

@@ -0,0 +1,10 @@
+package org.mapper;
+
+import org.mapstruct.Mapper;
+import org.mapstruct.factory.Mappers;
+
+@Mapper
+public interface PersonMapper {
+	PersonMapper INSTANCE = Mappers.getMapper(PersonMapper.class);
+    PersonDto personToPersonDto(Person person);
+}

org.eclipse.m2e.apt.tests/src/org/eclipse/m2e/apt/tests/M2eAptProjectconfiguratorTest.java

@@ -444,4 +444,13 @@ public void testDependencyManagement() throws Exception {
 		assertNotNull(javaProject);
 		assertNoErrors(p);
 	}
+
+	@Test
+	public void testNestedSourceFolders() throws Exception {
+		IProject project = importProject("projects/nested/pom.xml");
+		waitForJobsToComplete();
+		IJavaProject javaProject = JavaCore.create(project);
+		assertNotNull(javaProject);
+		assertNoErrors(project);
+	}
 }

org.eclipse.m2e.jdt/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: org.eclipse.m2e.jdt;singleton:=true
-Bundle-Version: 2.5.100.qualifier
+Bundle-Version: 2.5.101.qualifier
 Bundle-Localization: plugin
 Export-Package: org.eclipse.m2e.jdt,
  org.eclipse.m2e.jdt.internal;x-friends:="org.eclipse.m2e.jdt.ui",

org.eclipse.m2e.jdt/src/org/eclipse/m2e/jdt/internal/ClasspathDescriptor.java

@@ -25,7 +25,10 @@
 import org.eclipse.jdt.core.IClasspathAttribute;
 import org.eclipse.jdt.core.IClasspathEntry;
 import org.eclipse.jdt.core.IJavaProject;
+import org.eclipse.jdt.core.JavaCore;
 import org.eclipse.jdt.core.JavaModelException;
+import org.eclipse.jdt.internal.core.ClasspathEntry;
+import org.eclipse.jdt.internal.core.util.Util;
 
 import org.eclipse.m2e.jdt.IClasspathDescriptor;
 import org.eclipse.m2e.jdt.IClasspathEntryDescriptor;
@@ -148,6 +151,59 @@
       }
     }
 
+    // check nested source entries
+    List<IClasspathEntry> toRemove = null;
+    List<IClasspathEntry> toAdd = null;
+    for(IClasspathEntry entry : result) {
+      int kind = entry.getEntryKind();
+      IPath entryPath = entry.getPath();
+      if(kind == IClasspathEntry.CPE_SOURCE) {
+        for(IClasspathEntry otherEntry : result) {
+          int otherKind = otherEntry.getEntryKind();
+          if(otherKind != IClasspathEntry.CPE_SOURCE)
+            continue;
+          if(entry != otherEntry) {
+            IPath otherPath = otherEntry.getPath();
+            char[][] inclusionPatterns, exclusionPatterns;
+            if(otherPath.isPrefixOf(entryPath) && !otherPath.equals(entryPath)
+                && !Util.isExcluded(entryPath.append("*"), //$NON-NLS-1$
+                    inclusionPatterns = ((ClasspathEntry) otherEntry).fullInclusionPatternChars(),
+                    exclusionPatterns = ((ClasspathEntry) otherEntry).fullExclusionPatternChars(), false)) {
+              String exclusionPattern = entryPath.removeFirstSegments(otherPath.segmentCount()).segment(0);
+              if(!Util.isExcluded(entryPath, inclusionPatterns, exclusionPatterns, false)) {
+                IPath[] newExclusions;
+                IPath[] oldExclusions = otherEntry.getExclusionPatterns();
+                if(otherEntry.getExclusionPatterns() == null)
+                  newExclusions = new IPath[2];
+                else {
+                  newExclusions = new IPath[oldExclusions.length + 2];
+                  System.arraycopy(oldExclusions, 0, newExclusions, 0, oldExclusions.length);
+                }
+                IPath path = entryPath.removeFirstSegments(otherPath.segmentCount()).addTrailingSeparator();
+                IPath projectRelativePath = entryPath.removeFirstSegments(1).addTrailingSeparator();
+                newExclusions[newExclusions.length - 1] = projectRelativePath;
+                newExclusions[newExclusions.length - 2] = path;
+                if(toRemove == null || toAdd == null) {
+                  toRemove = new ArrayList<>();
+                  toAdd = new ArrayList<>();
+                }
+                IClasspathEntry newOtherEntry = JavaCore.newSourceEntry(otherEntry.getPath(),
+                    otherEntry.getInclusionPatterns(), newExclusions, otherEntry.getOutputLocation(),
+                    otherEntry.getExtraAttributes());
+                toRemove.add(otherEntry);
+                toAdd.add(newOtherEntry);
+              }
+            }
+          }
+        }
+      }
+    }
+    if(toRemove != null) {
+      toRemove.stream().forEach(e -> result.remove(e));
+    }
+    if(toAdd != null) {
+      toAdd.stream().forEach(e -> result.add(e));
+    }
     return result.toArray(new IClasspathEntry[result.size()]);
   }