fix duplicated classes in bootstrap jar (#2347)

* fix duplicated classes in bootstrap jar

* update binary resources

Author: SylvainJuge

apm-agent-bootstrap/pom.xml

@@ -60,6 +60,18 @@
                     </execution>
                 </executions>
             </plugin>
+            <plugin>
+                <artifactId>maven-jar-plugin</artifactId>
+                <executions>
+                    <!-- '.esclazz' resources have to be excluded as they are re-generated after shading from '.class' -->
+                    <execution>
+                        <id>default-jar</id>
+                        <configuration>
+                            <includes>**/*.class</includes>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
             <plugin>
                 <artifactId>maven-shade-plugin</artifactId>
                 <executions>
@@ -103,13 +115,19 @@
                                 with regular classloading. Their content will be injected as resources into the bootstrap
                                 classloader -->
 
+                                <delete dir="${tmpdir}"/>
                                 <mkdir dir="${tmpdir}"/>
+
                                 <unzip dest="${tmpdir}" src="${project.basedir}/target/${project.build.finalName}.jar"/>
+
+                                <delete dir="${tmpdir}/bootstrap"/>
                                 <mkdir dir="${tmpdir}/bootstrap"/>
+
                                 <move todir="${tmpdir}/bootstrap">
                                     <fileset dir="${tmpdir}" includes="**/*.class"/>
                                     <mapper type="regexp" from="^(.*)\.class$$" to="\1\.esclazz"/>
                                 </move>
+
                                 <delete dir="${tmpdir}/java"/>
                                 <delete dir="${tmpdir}/co"/>
                                 <delete dir="${tmpdir}/META-INF"/>

apm-agent-bootstrap/src/main/resources/bootstrap/co/elastic/apm/agent/modulesetter/ModuleSetter.esclazz

@@ -362,7 +362,6 @@
             <plugin>
                 <groupId>org.jacoco</groupId>
                 <artifactId>jacoco-maven-plugin</artifactId>
-                <version>0.8.7</version>
                 <configuration>
                     <excludes>**/*.esclazz</excludes>
                 </configuration>
@@ -477,7 +476,7 @@
                 <plugin>
                     <groupId>org.jacoco</groupId>
                     <artifactId>jacoco-maven-plugin</artifactId>
-                    <version>0.8.5</version>
+                    <version>0.8.7</version>
                 </plugin>
                 <plugin>
                     <groupId>org.codehaus.mojo</groupId>