Add ability to add source/resource folder outside of the project basedir

using linked folder

org.eclipse.m2e.jdt.tests/projects/add-source-resource/parent/src/main/java/A.java

@@ -0,0 +1,5 @@
+import java.io.Serializable;
+
+class A implements Serializable {
+
+}

org.eclipse.m2e.jdt.tests/projects/add-source-resource/parent/src/test/java/ATest.java

@@ -0,0 +1,5 @@
+import java.io.Serializable;
+
+class ATest implements Serializable {
+
+}

org.eclipse.m2e.jdt.tests/projects/add-source-resource/pom.xml

@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>foo.bar</groupId>
+  <artifactId>add-source-resource</artifactId>
+  <version>0.0.1-SNAPSHOT</version>
+  <packaging>pom</packaging>
+  <modules>
+  	<module>submoduleA</module>
+  </modules>
+</project>

org.eclipse.m2e.jdt.tests/projects/add-source-resource/submoduleA/pom.xml

@@ -0,0 +1,80 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>foo.bar</groupId>
+  <artifactId>submoduleA</artifactId>
+  <version>0.0.1-SNAPSHOT</version>
+  <build>
+    <pluginManagement>
+      <plugins>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-compiler-plugin</artifactId>
+          <version>3.10.1</version>
+        </plugin>
+      </plugins>
+    </pluginManagement>
+    <plugins>
+      <plugin>
+      <groupId>org.codehaus.mojo</groupId>
+      <artifactId>build-helper-maven-plugin</artifactId>
+      <executions>
+        <execution>
+        <id>java</id>
+        <phase>generate-sources</phase>
+        <goals>
+          <goal>add-source</goal>
+        </goals>
+        <configuration>
+          <sources>
+          <source>../parent/src/main/java</source>
+          </sources>
+        </configuration>
+        </execution>
+        <execution>
+          <id>test</id>
+          <phase>generate-sources</phase>
+          <goals>
+            <goal>add-test-source</goal>
+          </goals>
+          <configuration>
+            <sources>
+              <source>../parent/src/test/java</source>
+            </sources>
+          </configuration>
+        </execution>
+        <execution>
+          <id>resources</id>
+          <phase>generate-resources</phase>
+          <goals>
+            <goal>add-resource</goal>
+          </goals>
+          <configuration>
+            <resources>
+              <resource>
+                <directory>../parent/src/main/resources</directory>
+              </resource>
+            </resources>
+          </configuration>
+        </execution>
+        <execution>
+          <id>test-resources</id>
+          <phase>generate-resources</phase>
+          <goals>
+            <goal>add-test-resource</goal>
+          </goals>
+          <configuration>
+            <resources>
+              <resource>
+                <directory>../parent/src/test/resources</directory>
+              </resource>
+            </resources>
+          </configuration>
+        </execution>
+      </executions>
+      </plugin>
+    </plugins>
+  </build>
+</project>

org.eclipse.m2e.jdt.tests/src/org/eclipse/m2e/jdt/tests/JavaConfigurationTest.java

@@ -20,6 +20,7 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Arrays;
+import java.util.List;
 import java.util.function.Predicate;
 
 import org.eclipse.core.resources.IFile;
@@ -29,12 +30,14 @@
 import org.eclipse.core.resources.IncrementalProjectBuilder;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.FileLocator;
+import org.eclipse.core.runtime.IPath;
 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.m2e.core.MavenPlugin;
 import org.eclipse.m2e.core.internal.preferences.MavenConfigurationImpl;
+import org.eclipse.m2e.core.project.ResolverConfiguration;
 import org.eclipse.m2e.tests.common.AbstractMavenProjectTestCase;
 import org.junit.Before;
 import org.junit.Test;
@@ -132,6 +135,26 @@ public void testComplianceVsEnablePreviewSettings() throws CoreException, IOExce
 		assertEquals(JavaCore.ENABLED, project.getOption(JavaCore.COMPILER_PB_ENABLE_PREVIEW_FEATURES, false));
 		assertEquals(JavaCore.IGNORE, project.getOption(JavaCore.COMPILER_PB_REPORT_PREVIEW_FEATURES, false));
 	}
+
+	@Test
+	public void testAddSourceResource() throws CoreException, IOException, InterruptedException {
+		File baseDir = new File(FileLocator
+				.toFileURL(JavaConfigurationTest.class.getResource("/projects/add-source-resource/submoduleA/pom.xml"))
+				.getFile()).getParentFile().getParentFile();
+		waitForJobsToComplete();
+		IProject project = importProjects(baseDir.getAbsolutePath(), new String[] { "submoduleA/pom.xml" },
+				new ResolverConfiguration())[0];
+		waitForJobsToComplete();
+		IJavaProject javaProject = JavaCore.create(project);
+
+		// FIXME: compare entries explcitly
+		List<String> paths = Arrays.stream(javaProject.getRawClasspath())
+				.filter(cp -> IClasspathEntry.CPE_SOURCE == cp.getEntryKind())
+				.map(IClasspathEntry::getPath).map(IPath::toString).toList();
+		System.out.println(paths);
+		assertEquals(8, Arrays.stream(javaProject.getRawClasspath())
+				.filter(cp -> IClasspathEntry.CPE_SOURCE == cp.getEntryKind()).count());
+	}
 	// --- utility methods ---
 
 	private static final Predicate<IClasspathEntry> TEST_SOURCES = cp -> cp.isTest()

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: 2.3.3.qualifier
+Bundle-Version: 2.3.400.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/AbstractJavaProjectConfigurator.java

@@ -14,6 +14,9 @@
 package org.eclipse.m2e.jdt.internal;
 
 import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -30,9 +33,11 @@
 import org.eclipse.core.resources.IFolder;
 import org.eclipse.core.resources.IProject;
 import org.eclipse.core.resources.IResource;
+import org.eclipse.core.resources.ResourcesPlugin;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IPath;
 import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.core.runtime.QualifiedName;
 import org.eclipse.core.runtime.SubMonitor;
 import org.eclipse.jdt.core.IAccessRule;
 import org.eclipse.jdt.core.IClasspathAttribute;
@@ -134,6 +139,9 @@ public abstract class AbstractJavaProjectConfigurator extends AbstractProjectCon
 
   protected static final String DEFAULT_COMPILER_LEVEL = "1.5"; //$NON-NLS-1$
 
+  private static final QualifiedName LINKED_MAVEN_RESOURCE = new QualifiedName(MavenJdtPlugin.PLUGIN_ID,
+      "linkedSource");
+
   @Override
   public void configure(ProjectConfigurationRequest request, IProgressMonitor monitor) throws CoreException {
     IProject project = request.mavenProjectFacade().getProject();
@@ -361,6 +369,9 @@ protected void addProjectSourceFolders(IClasspathDescriptor classpath, Map<Strin
           isTestResourcesSkipped.add(Boolean.FALSE);
         }
       }
+
+      cleanLinkedSourceDirs(project, monitor);
+
       addSourceDirs(classpath, project, mavenProject.getCompileSourceRoots(), classes.getFullPath(), inclusion,
           exclusion, mainSourceEncoding, mon.newChild(1), false);
       addResourceDirs(classpath, project, mavenProject, mavenProject.getBuild().getResources(), classes.getFullPath(),
@@ -468,6 +479,14 @@ protected void addSourceDirs(IClasspathDescriptor classpath, IProject project, L
 
   }
 
+  private void cleanLinkedSourceDirs(IProject project, IProgressMonitor monitor) throws CoreException {
+    for(IResource resource : project.members()) {
+      if(resource instanceof IFolder && "true".equals(resource.getPersistentProperty(LINKED_MAVEN_RESOURCE))) {
+        resource.delete(false, monitor);
+      }
+    }
+  }
+
   private IClasspathEntryDescriptor getEnclosingEntryDescriptor(IClasspathDescriptor classpath, IPath fullPath) {
     for(IClasspathEntryDescriptor cped : classpath.getEntryDescriptors()) {
       if(cped.getPath().isPrefixOf(fullPath)) {
@@ -495,10 +514,14 @@ private void addResourceDirs(IClasspathDescriptor classpath, IProject project, M
       if(directory == null) {
         continue;
       }
-      File resourceDirectory = new File(directory);
-      IPath relativePath = getProjectRelativePath(project, directory);
-      IResource r = project.findMember(relativePath);
-      if(r == project) {
+      File resourceDirectory = null;
+      try {
+        resourceDirectory = new File(directory).getCanonicalFile();
+      } catch(IOException ex) {
+        resourceDirectory = new File(directory).getAbsoluteFile();
+      }
+      IFolder r = getFolder(project, resourceDirectory.getPath());
+      if(resourceDirectory.equals(project.getLocation().toFile())) {
         /*
          * Workaround for the Java Model Exception:
          *   Cannot nest output folder 'xxx/src/main/resources' inside output folder 'xxx'
@@ -517,10 +540,6 @@ private void addResourceDirs(IClasspathDescriptor classpath, IProject project, M
         log.error("Skipping resource folder " + r.getFullPath());
         return;
       }
-      if(r == null) {
-        //this means the resources does not exits (yet) but might be created later on!
-        r = project.getFolder(relativePath);
-      }
       if(project.equals(r.getProject())) {
         IPath path = r.getFullPath();
         IClasspathEntryDescriptor enclosing = getEnclosingEntryDescriptor(classpath, path);
@@ -533,12 +552,11 @@ private void addResourceDirs(IClasspathDescriptor classpath, IProject project, M
           addResourceFolder(classpath, path, outputPath, addTestFlag);
         }
         // Set folder encoding (null = platform default)
-        IFolder resourceFolder = project.getFolder(relativePath);
-        if(resourceFolder.exists()) {
-          resourceFolder.setDefaultCharset(resourceEncoding, monitor);
+        if(r.exists()) {
+          r.setDefaultCharset(resourceEncoding, monitor);
         }
       } else {
-        log.info("Not adding resources folder " + resourceDirectory.getAbsolutePath());
+        log.info("Not adding resources folder " + resourceDirectory);
       }
     }
   }
@@ -864,11 +882,22 @@ private void removeMavenClasspathContainer(IProject project) throws JavaModelExc
     }
   }
 
-  protected IFolder getFolder(IProject project, String absolutePath) {
-    if(project.getLocation().makeAbsolute().equals(IPath.fromOSString(absolutePath))) {
-      return project.getFolder(project.getLocation());
+  protected IFolder getFolder(IProject project, String absolutePath) throws CoreException {
+    Path projectLocation = project.getLocation().toPath();
+    Path folderPath = Path.of(absolutePath);
+    if(projectLocation.toAbsolutePath().equals(folderPath)) {
+      return project.getFolder("/");
+    }
+    IPath relativePath = getProjectRelativePath(project, absolutePath);
+    if(!project.exists(relativePath) && Files.exists(folderPath)
+        && !ResourcesPlugin.getWorkspace().getRoot().getLocation().toPath().equals(folderPath)) {
+      String linkName = projectLocation.relativize(folderPath).toString().replace("/", "_");
+      IFolder folder = project.getFolder(linkName);
+      folder.createLink(folderPath.toUri(), IResource.REPLACE, null);
+      folder.setPersistentProperty(LINKED_MAVEN_RESOURCE, "true");
+      return folder;
     }
-    return project.getFolder(getProjectRelativePath(project, absolutePath));
+    return project.getFolder(relativePath);
   }
 
   protected IPath getProjectRelativePath(IProject project, String absolutePath) {