Merge branch 'Tcoffee_JAL-1065' of https://source.jalview.org/git/jalview into test_p...

diff --combined .classpath
index 01cf242,0c39740..cbb8f6b
--- 1/.classpath
--- 2/.classpath
+++ b/.classpath
@@@ -1,7 -1,9 +1,9 @@@
  <?xml version="1.0" encoding="UTF-8"?>
  <classpath>
        <classpathentry kind="src" path="src"/>
+       <classpathentry kind="src" path="test"/>
        <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+       <classpathentry kind="lib" path="/Library/Java/JavaVirtualMachines/1.6.0_29-b11-402.jdk/Contents/Home/lib/plugin.jar"/>
        <classpathentry kind="lib" path="lib/activation.jar"/>
        <classpathentry kind="lib" path="lib/axis.jar" sourcepath="D:/axis-1_2RC2-src/axis-1_2RC2"/>
        <classpathentry kind="lib" path="lib/commons-discovery.jar"/>
@@@ -39,7 -41,8 +41,9 @@@
        <classpathentry kind="lib" path="lib/min-jaba-client.jar"/>
        <classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
        <classpathentry kind="lib" path="lib/Jmol-12.2.4.jar"/>
 +      <classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
+       <classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
+       <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
        <classpathentry kind="output" path="classes"/>
  </classpath>