Use the standard Maven directory layout, rename "lib" to "core". Mavenize submodules.

tools/pom.xml

@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  ~ Copyright 2012 Google Inc.
+  ~
+  ~ Licensed 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.
+  -->
+
+<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">
+    <parent>
+        <artifactId>bitcoinj</artifactId>
+        <groupId>com.google</groupId>
+        <version>0.5-SNAPSHOT</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>bitcoinj-tools</artifactId>
+
+    <dependencies>
+        <dependency>
+            <groupId>com.google</groupId>
+            <artifactId>bitcoinj-core</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>net.sf.jopt-simple</groupId>
+            <artifactId>jopt-simple</artifactId>
+            <version>4.3</version>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-jdk14</artifactId>
+            <version>1.6.4</version>
+        </dependency>
+    </dependencies>
+</project>

tools/tools.iml

@@ -1,17 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<module type="JAVA_MODULE" version="4">
-  <component name="NewModuleRootManager" inherit-compiler-output="true">
-    <exclude-output />
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="false">
+    <output url="file://$MODULE_DIR$/target/classes" />
+    <output-test url="file://$MODULE_DIR$/target/test-classes" />
     <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
+      <excludeFolder url="file://$MODULE_DIR$/target" />
     </content>
     <orderEntry type="inheritedJdk" />
     <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module" module-name="lib" />
-    <orderEntry type="library" name="Maven: net.sf.jopt-simple:jopt-simple:4.3" level="project" />
-    <orderEntry type="library" name="Maven: org.bouncycastle:bcprov-jdk15:1.46" level="project" />
+    <orderEntry type="module" module-name="core" />
     <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.2" level="project" />
-    <orderEntry type="library" name="Maven: org.slf4j:slf4j-jdk14:1.6.2" level="project" />
+    <orderEntry type="library" name="Maven: org.bouncycastle:bcprov-jdk15:1.46" level="project" />
+    <orderEntry type="library" name="Maven: com.google.protobuf:protobuf-java:2.4.1" level="project" />
+    <orderEntry type="library" name="Maven: net.sf.jopt-simple:jopt-simple:4.3" level="project" />
+    <orderEntry type="library" name="Maven: org.slf4j:slf4j-jdk14:1.6.4" level="project" />
   </component>
   <component name="org.twodividedbyzero.idea.findbugs">
     <option name="_basePreferences">

tools/wallet-tool

@@ -0,0 +1,2 @@
+#!/bin/sh
+mvn -q exec:java -Dexec.mainClass=WalletTool -Dexec.args="$*"