Sample to reproduce multi module problem, plus a fix for it

org.maven.ide.eclipse.scala/.settings/org.eclipse.jdt.core.prefs

@@ -1,4 +1,3 @@
-#Wed Nov 24 10:29:41 CET 2010
 eclipse.preferences.version=1
 org.eclipse.jdt.core.builder.cleanOutputFolder=clean
 org.eclipse.jdt.core.builder.duplicateResourceTask=warning
@@ -160,9 +159,12 @@ org.eclipse.jdt.core.formatter.indent_statements_compare_to_body=true
 org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases=true
 org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch=true
 org.eclipse.jdt.core.formatter.indentation.size=2
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field=insert
 org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable=insert
-org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_member=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_method=insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_package=insert
 org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_parameter=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_type=insert
 org.eclipse.jdt.core.formatter.insert_new_line_after_opening_brace_in_array_initializer=do not insert
 org.eclipse.jdt.core.formatter.insert_new_line_at_end_of_file_if_missing=insert
 org.eclipse.jdt.core.formatter.insert_new_line_before_catch_in_try_statement=do not insert

org.maven.ide.eclipse.scala/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Maven Integration for Scala IDE
 Bundle-SymbolicName: org.maven.ide.eclipse.scala;singleton:=true
-Bundle-Version: 0.4.0
+Bundle-Version: 0.4.1
 Bundle-RequiredExecutionEnvironment: J2SE-1.5
 Require-Bundle: 
  org.eclipse.jdt.core,

org.maven.ide.eclipse.scala/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>org.maven.ide.eclipse.scala</groupId>
     <artifactId>m2eclipse-scala</artifactId>
-    <version>0.4.0</version>
+    <version>0.4.1</version>
   </parent>
   <artifactId>org.maven.ide.eclipse.scala</artifactId>
   <packaging>eclipse-plugin</packaging>

org.maven.ide.eclipse.scala/src/org/maven/ide/eclipse/scala/ScalaProjectConfigurator.java

@@ -115,6 +115,9 @@ public void configure(ProjectConfigurationRequest request, IProgressMonitor moni
       if (request != null)  {
         IProject project = request.getProject();
         if(!project.hasNature(scalaNature) && isScalaProject(request.getMavenProjectFacade(), monitor)) {
+          if(!project.hasNature("org.eclipse.jdt.core.javanature")) {
+            addNature(project, "org.eclipse.jdt.core.javanature", monitor);
+          }
           addNature(project, scalaNature, monitor);
         }
       }

org.maven.ide.eclipse.scala_feature/feature.xml

@@ -2,7 +2,7 @@
 <feature
       id="org.maven.ide.eclipse.scala_feature"
       label="Maven Integration for Scala IDE"
-      version="0.4.0"
+      version="0.4.1"
       provider-name="Sonatype, Inc.">
 
    <description url="github.com/sonatype/m2eclipse-scala/">

org.maven.ide.eclipse.scala_feature/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>org.maven.ide.eclipse.scala</groupId>
     <artifactId>m2eclipse-scala</artifactId>
-    <version>0.4.0</version>
+    <version>0.4.1</version>
   </parent>
 
   <artifactId>org.maven.ide.eclipse.scala_feature</artifactId>

org.maven.ide.eclipse.scala_site/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>org.maven.ide.eclipse.scala</groupId>
     <artifactId>m2eclipse-scala</artifactId>
-    <version>0.4.0</version>
+    <version>0.4.1</version>
     <relativePath>../pom.xml</relativePath>    
   </parent>
 

pom.xml

@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.maven.ide.eclipse.scala</groupId>
   <artifactId>m2eclipse-scala</artifactId>
-  <version>0.4.0</version>
+  <version>0.4.1</version>
   <packaging>pom</packaging>
 
   <properties>

samples/prj-parent-with-plugin/child/pom.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<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/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>example</groupId>
+		<artifactId>parent</artifactId>
+		<version>0.0.1-SNAPSHOT</version>
+		<relativePath>..</relativePath>
+	</parent>
+
+	<artifactId>child</artifactId>
+</project>

samples/prj-parent-with-plugin/pom.xml

@@ -0,0 +1,46 @@
+<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>example</groupId>
+	<artifactId>parent</artifactId>
+	<version>0.0.1-SNAPSHOT</version>
+	<packaging>pom</packaging>
+
+	<build>
+		<pluginManagement>
+			<plugins>
+				<plugin>
+					<groupId>net.alchim31.maven</groupId>
+					<artifactId>scala-maven-plugin</artifactId>
+					<version>3.0.1</version>
+					<executions>
+						<execution>
+							<id>scala-compile-first</id>
+							<phase>process-resources</phase>
+							<goals>
+								<goal>add-source</goal>
+								<goal>compile</goal>
+							</goals>
+						</execution>
+						<execution>
+							<id>scala-test-compile</id>
+							<phase>process-test-resources</phase>
+							<goals>
+								<goal>testCompile</goal>
+							</goals>
+						</execution>
+					</executions>
+				</plugin>
+			</plugins>
+		</pluginManagement>
+
+		<plugins>
+			<plugin>
+				<groupId>net.alchim31.maven</groupId>
+				<artifactId>scala-maven-plugin</artifactId>
+			</plugin>
+		</plugins>
+	</build>
+</project>