build.xml | 30 0 + 30 - 0 !
1 file changed, 30 deletions(-)

 do not build targets figtree-pdf.jar and figtree.war

src/figtree/application/FigTreeApplication.java | 33 1 + 32 - 0 !
src/figtree/application/FigTreeFrame.java | 8 1 + 7 - 0 !
src/figtree/treeviewer/ControllerOptionsPanel.java | 1 0 + 1 - 0 !
src/figtree/treeviewer/TreeViewerController.java | 3 0 + 3 - 0 !
4 files changed, 2 insertions(+), 43 deletions(-)

 quaqua (http://www.randelshofer.ch/quaqua/)
   is a Java class which provides OSX look and feel but only
   works on Mac.  So this is simply not used on Linux and I
   simply deleted all lines containing the string [qQ]aqua
   which seems to lead to a usable application.

src/figtree/webui/FigTreeWebApplication.java | 298 0 + 298 - 0 !
src/figtree/webui/FileUploadWidget.java | 56 0 + 56 - 0 !
src/figtree/webui/Main.java | 18 0 + 18 - 0 !
src/figtree/webui/TreeWidget.java | 128 0 + 128 - 0 !
4 files changed, 500 deletions(-)

 the web gui (servlet) is not used nor shipped in the
    binary packages.  If the files that are belonging to this gui
    are removed there is no need for shipping lib/jwt/*.jar which
    is one further step in the direction to remove binary only code
    from the tarball

build.xml | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 fix classpath to use debian packaged classes