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diff --git a/nbbuild.xml b/nbbuild.xml
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+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+<!-- You may freely edit this file. See commented blocks below for -->
+<!-- some examples of how to customize the build. -->
+<!-- (If you delete it and reopen the project it will be recreated.) -->
+<!-- By default, only the Clean and Build commands use this build script. -->
+<!-- Commands such as Run, Debug, and Test only use this build script if -->
+<!-- the Compile on Save feature is turned off for the project. -->
+<!-- You can turn off the Compile on Save (or Deploy on Save) setting -->
+<!-- in the project's Project Properties dialog box.-->
+<project name="jalview" default="default" basedir=".">
+    <description>Builds, tests, and runs the project jalview.</description>
+    <import file="nbproject/build-impl.xml"/>
+    <target name="-pre-compile">
+        <ant antfile="build.xml" target="buildindices">
+        <property name="outputDir" value="build/classes"/>    
+        <property name="packageDir" value="build/dist"/>    
+        </ant>
+        
+    </target>
+    <!--
+
+    There exist several targets which are by default empty and which can be 
+    used for execution of your tasks. These targets are usually executed 
+    before and after some main targets. They are: 
+
+      -pre-init:                 called before initialization of project properties
+      -post-init:                called after initialization of project properties
+      -pre-compile:              called before javac compilation
+      -post-compile:             called after javac compilation
+      -pre-compile-single:       called before javac compilation of single file
+      -post-compile-single:      called after javac compilation of single file
+      -pre-compile-test:         called before javac compilation of JUnit tests
+      -post-compile-test:        called after javac compilation of JUnit tests
+      -pre-compile-test-single:  called before javac compilation of single JUnit test
+      -post-compile-test-single: called after javac compilation of single JUunit test
+      -pre-jar:                  called before JAR building
+      -post-jar:                 called after JAR building
+      -post-clean:               called after cleaning build products
+
+    (Targets beginning with '-' are not intended to be called on their own.)
+
+    Example of inserting an obfuscator after compilation could look like this:
+
+        <target name="-post-compile">
+            <obfuscate>
+                <fileset dir="${build.classes.dir}"/>
+            </obfuscate>
+        </target>
+
+    For list of available properties check the imported 
+    nbproject/build-impl.xml file. 
+
+
+    Another way to customize the build is by overriding existing main targets.
+    The targets of interest are: 
+
+      -init-macrodef-javac:     defines macro for javac compilation
+      -init-macrodef-junit:     defines macro for junit execution
+      -init-macrodef-debug:     defines macro for class debugging
+      -init-macrodef-java:      defines macro for class execution
+      -do-jar-with-manifest:    JAR building (if you are using a manifest)
+      -do-jar-without-manifest: JAR building (if you are not using a manifest)
+      run:                      execution of project 
+      -javadoc-build:           Javadoc generation
+      test-report:              JUnit report generation
+
+    An example of overriding the target for project execution could look like this:
+
+        <target name="run" depends="jalview-impl.jar">
+            <exec dir="bin" executable="launcher.exe">
+                <arg file="${dist.jar}"/>
+            </exec>
+        </target>
+
+    Notice that the overridden target depends on the jar target and not only on 
+    the compile target as the regular run target does. Again, for a list of available 
+    properties which you can use, check the target you are overriding in the
+    nbproject/build-impl.xml file. 
+
+    -->
+</project>