Clean the api directory and bind javadoc and copy to different phases

Currently the api directory is not cleaned so it can potentially contain
stale data. Beside that javadoc and copy goal where bound to the same
phases what can have odering side effects in maven.

Additional to this, ignore uninteresting javadoc changes

Jenkinsfile

@@ -22,7 +22,8 @@ pipeline {
 						-Papi-check \
 						-Pjavadoc \
 						-Dmaven.test.error.ignore=true -Dmaven.test.failure.ignore=true \
-						-Dtycho.debug.artifactcomparator
+						-Dtycho.debug.artifactcomparator \
+						-Dpde.docs.baselinemode=fail
 					'''
 				}
 			}

org.eclipse.pde.doc.user/pom.xml

@@ -21,11 +21,31 @@
   <packaging>eclipse-plugin</packaging>
 
   <properties>
-    <eclipse.pde.ui.apitools>../apitools</eclipse.pde.ui.apitools>
-    <eclipse.pde.ui.ui>../ui</eclipse.pde.ui.ui>
-    <eclipse.pde.build>../build</eclipse.pde.build>
+    <eclipse.pde.ui.apitools>${basedir}/../apitools</eclipse.pde.ui.apitools>
+    <eclipse.pde.ui.ui>${basedir}/../ui</eclipse.pde.ui.ui>
+    <eclipse.pde.build>${basedir}/../build</eclipse.pde.build>
   </properties>
 
+  <profiles>
+		<profile>
+			<!-- Only enable this for individual bundles builds as otherhwise the ibuild repository is not aviable and we might run into problems -->
+			<id>build-individual-bundles</id>
+			<properties>
+				<pde.docs.baselinemode>warn</pde.docs.baselinemode>
+			</properties>
+			<build>
+				<plugins>
+					<plugin>
+						 <groupId>org.eclipse.tycho</groupId>
+				        <artifactId>tycho-p2-plugin</artifactId>
+				        <configuration>
+							<baselineMode>${pde.docs.baselinemode}</baselineMode>
+						</configuration>
+					</plugin>
+				</plugins>
+  			</build>
+		</profile>
+  </profiles>
   <build>
     <pluginManagement>
       <plugins>
@@ -37,6 +57,29 @@
       </plugins>
     </pluginManagement>
     <plugins>
+		<plugin>
+		    <artifactId>maven-clean-plugin</artifactId>
+		    <configuration>
+		      <filesets>
+		        <fileset>
+		          <directory>reference/api</directory>
+		        </fileset>
+		      </filesets>
+		    </configuration>
+		  </plugin>
+         <plugin>
+            <groupId>org.eclipse.tycho</groupId>
+            <artifactId>tycho-p2-plugin</artifactId>
+            <configuration>
+                <ignoredPatterns combine.children="append">
+                    <!-- Uninteresting Javadoc changes  -->
+                    <pattern>reference/api/*.css</pattern>
+                    <pattern>reference/api/*.js</pattern>
+                    <pattern>reference/api/legal/**/*</pattern>
+                    <pattern>reference/api/script-dir/**/*</pattern>
+                </ignoredPatterns>
+            </configuration>
+          </plugin>
           <plugin>
             <groupId>org.eclipse.tycho</groupId>
             <artifactId>target-platform-configuration</artifactId>
@@ -109,11 +152,11 @@
                     </goals>
                     <configuration>
                         <manifests>
-                            <manifest>${basedir}/${eclipse.pde.ui.ui}/org.eclipse.ui.trace/plugin.xml</manifest>
-                            <manifest>${basedir}/${eclipse.pde.ui.ui}/org.eclipse.pde.core/plugin.xml</manifest>
-                            <manifest>${basedir}/${eclipse.pde.build}/org.eclipse.pde.build/plugin.xml</manifest>
-                            <manifest>${basedir}/${eclipse.pde.ui.ui}/org.eclipse.pde.ui/plugin.xml</manifest>
-                            <manifest>${basedir}/${eclipse.pde.ui.ui}/org.eclipse.pde.launching/plugin.xml</manifest>
+                            <manifest>${eclipse.pde.ui.ui}/org.eclipse.ui.trace/plugin.xml</manifest>
+                            <manifest>${eclipse.pde.ui.ui}/org.eclipse.pde.core/plugin.xml</manifest>
+                            <manifest>${eclipse.pde.build}/org.eclipse.pde.build/plugin.xml</manifest>
+                            <manifest>${eclipse.pde.ui.ui}/org.eclipse.pde.ui/plugin.xml</manifest>
+                            <manifest>${eclipse.pde.ui.ui}/org.eclipse.pde.launching/plugin.xml</manifest>
                         </manifests>
                         <destination>${basedir}/reference/extension-points</destination>
                     </configuration>
@@ -154,7 +197,7 @@
             <executions>
                 <execution>
                     <id>attach-javadocs</id>
-                    <phase>prepare-package</phase>
+                    <phase>process-classes</phase>
                     <goals>
                         <goal>javadoc</goal>
                     </goals>
@@ -190,7 +233,6 @@
             <executions>
               <execution>
                 <id>copy-resources</id>
-                <!-- here the phase you need -->
                 <phase>prepare-package</phase>
                 <goals>
                   <goal>copy-resources</goal>