The eagle has landed.

Merge branch 'next'

Conflicts:
	org.eclipse.ice.caebat.batml/pom.xml
	org.eclipse.ice.client.widgets.rcp.test/META-INF/MANIFEST.MF
	org.eclipse.ice.client.widgets.rcp.test/pom.xml
	org.eclipse.ice.client.widgets.rcp/META-INF/MANIFEST.MF
	org.eclipse.ice.client.widgets.rcp/pom.xml
	org.eclipse.ice.core.test/pom.xml
	org.eclipse.ice.datastructures/pom.xml
	org.eclipse.ice.developer.moose/pom.xml
	org.eclipse.ice.developer/pom.xml
	org.eclipse.ice.feature/feature.xml
	org.eclipse.ice.feature/pom.xml
	org.eclipse.ice.filesimulation/pom.xml
	org.eclipse.ice.materials/pom.xml
	org.eclipse.ice.persistence.xml.test/pom.xml
	org.eclipse.ice.persistence.xml/pom.xml
	org.eclipse.ice.reflectivity.ui/pom.xml
	org.eclipse.ice.repository/category.xml
	org.eclipse.ice.repository/ice.product
	org.eclipse.ice.repository/pom.xml
	org.eclipse.ice.servicetester/pom.xml
	org.eclipse.ice.tablecomponenttester/pom.xml
	org.eclipse.ice.viz.service.geometry.test/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service.geometry.test/pom.xml
	org.eclipse.ice.viz.service.geometry/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service.geometry/pom.xml
	org.eclipse.ice.viz.service.jme3.test/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service.jme3.test/pom.xml
	org.eclipse.ice.viz.service.jme3/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service.jme3/pom.xml
	org.eclipse.ice.viz.service.mesh.test/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service.mesh.test/pom.xml
	org.eclipse.ice.viz.service.mesh/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service.mesh/pom.xml
	org.eclipse.ice.viz.service.paraview.test/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service.paraview.test/pom.xml
	org.eclipse.ice.viz.service.paraview.web/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service.paraview.web/pom.xml
	org.eclipse.ice.viz.service.paraview/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service.paraview/pom.xml
	org.eclipse.ice.viz.service.test/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service.test/pom.xml
	org.eclipse.ice.viz.service.visit.test/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service.visit.test/pom.xml
	org.eclipse.ice.viz.service.visit/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service.visit/pom.xml
	org.eclipse.ice.viz.service/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.service/pom.xml
	org.eclipse.ice.viz.service/src/org/eclipse/ice/viz/service/connections/VizConnection.java
	org.eclipse.ice.viz.test/META-INF/MANIFEST.MF
	org.eclipse.ice.viz.test/pom.xml
	org.eclipse.ice.viz/META-INF/MANIFEST.MF
	org.eclipse.ice.viz/pom.xml

Signed-off-by: Jay Jay Billings <billingsjj@ornl.gov>

docs/developerMenu/.gitignore

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+/bin/
+/tmp/
+/developerMen.synctex.gz

docs/developerMenu/.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>developerMenu</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>net.sourceforge.texlipse.builder.TexlipseBuilder</name>
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+	</buildSpec>
+	<natures>
+		<nature>net.sourceforge.texlipse.builder.TexlipseNature</nature>
+	</natures>
+</projectDescription>

docs/developerMenu/.texlipse

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+#TeXlipse project settings
+#Mon Jan 18 18:15:25 EST 2016
+markTmpDer=true
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docs/developerMenu/src/.gitignore

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+/main.aux
+/main.log
+/main.out
+/main.pdf

docs/developerMenu/src/main.tex

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+\documentclass{article}
+%\documentclass[11pt,letterpaper,twoside,english,final]{article}
+\usepackage{graphicx}
+\usepackage{caption}
+\usepackage{subcaption}
+\usepackage{hyperref}
+
+\begin{document}
+
+\section*{The Eclipse ICE Developer Menu}
+
+\subsection*{Overview}
+The Eclipse Integrated Computational Environment (ICE) has had a great track
+record of providing a comprehensive environment for general scientific
+computing. Tasks such as model input generation, local and remote simulation
+execution, and post-simulation data analysis and visualization are all very well
+supported in the application. These tasks take care of the majority of needs
+for \emph{using} general scientific computing codes, but what about
+\emph{developing} those applications to begin with? Is there any way ICE can be
+extended to provide support for the development of science codes?
+
+\begin{figure}[h]
+\includegraphics[width=\textwidth]{figures/icemenu.png}
+\centering
+\caption{The ICE Developer Menu}
+\label{fig:devmenu}
+\end{figure}
+
+The answer is yes! In 2015 ICE was extended to provide support for scientific
+application \emph{development} through a custom, extensible \textbf{Developer} 
+top-level menu. This menu is shown in Figure
+\ref{fig:devmenu} and provides custom actions that enable efficient scientific
+application development for both novice and expert users of a given science
+code.
+
+The Developer Menu is completely customizable through Eclipse Extension Points.
+Specifically, ICE exposes a new extension point:
+\emph{org.eclipse.ice.developer.code}. This extension point provides the means
+to specify details about a scientific code: its name, category (Framework,
+Nuclear, Other, etc\ldots), and where its repository is hosted, just to name a
+few. This point also enables the addition of \emph{commands} that point to some
+custom subclass of \emph{org.eclipse.core.commands.AbstractHandler} that
+performs some task related to the development of the code.
+
+With these extensions exposed as part of an ICE product execution, ICE
+handles all the complexity of picking them up and populating the Developer Menu
+dynamically at runtime. This feature is shown in Figure \ref{fig:devcloneice},
+with an ICE category for ICE development, and another for scientific frameworks.
+This process is exactly how ICE developers work on ICE itself - by pulling down
+the ICE binary and leveraging the Developer Menu to clone and build ICE, all
+within ICE. ICE also provides these hooks for other scientific codes, like the
+Multiphysics Object Oriented Simulation Environment (MOOSE) for general
+finite-element simulations. ICE provides a hook for cloning MOOSE and for
+forking a templated repository for MOOSE Application development.
+
+\begin{figure}[h]
+\includegraphics[width=\textwidth]{figures/menu.png}
+\caption{The Developer Menu ICE and MOOSE Actions}
+\label{fig:devcloneice}
+\end{figure}
+
+Extending the Developer Menu is easy, and relies on simply creating a new plugin
+and exposing a new extension. Let's see how to do this task in detail:
+
+\subsection*{Extending the ICE Developer Menu}
+For this tutorial, we are going to create a hook into the Developer menu to
+clone a scientific code called Fern. Fern is an application that provides an
+efficient nuclear reaction network solver. It is hosted at
+\url{https://github.com/jayjaybillings/fern}. 
+
+To get started, we need to download the ICE plugins to our workspace, which we
+can actually do through the Developer menu (pretty cool to use the Developer 
+menu to extend the Developer menu!). Click Developer $>$ ICE $>$ Clone ICE to 
+get all of ICE's plugins into the workspace. With ICE cloned to the workspace, 
+we can now begin to extend the Developer menu. First, we will need to create a
+new plugin. 
+
+\subsubsection*{Create a New Plugin Project}
+Creating a new plugin for an extension to the ICE Developer menu is simple, just
+click File $>$ New $>$ Plugin Project (or Other, then select Plugin Project).
+When the wizard opens, name your new plugin with something similar to Figure
+\ref{fig:newplugin} and deselect the Generate an activation button. On the next
+page, simply uncheck the create a plugin from template button and click Finish. 
+\begin{figure}[h]
+\includegraphics[width=\textwidth]{figures/combinedplugin.png}
+\caption{Creating a new Plugin Project}
+\label{fig:newplugin}
+\end{figure}
+
+When the MANIFEST.MF file editor opens up, add the
+\emph{org.eclipse.ice.developer} plugin as a Required Plugin on the Dependencies
+tab.
+
+\subsubsection*{Create a New ICE Developer Extension}
+Now let's create a new Extension to connect ICE and the Developer Menu
+with a Clone Fern action. To do so, go to the Extensions tab of the
+plugin MANIFEST file and click add. ICE provides an
+org.eclipse.ice.developer.code extension point that lets users define various
+details about their codes. 
+% \ref{fig:createExtPt} and click Finish.
+% \begin{figure}[h]
+% \includegraphics[width=\textwidth]{figures/extensionPt.png}
+% \caption{Create a new ICE Scientific Code Extension}
+% \label{fig:createExtPt}
+% \end{figure}
+
+You will then be presented with the view in Figure \ref{fig:config1}. Enter a
+descriptive ID and Name for this extension and click Save. 
+\begin{figure}[h]
+\includegraphics[width=\textwidth]{figures/extptconfig1.png}
+\caption{Configure the ID and Name of this Code Extension.}
+\label{fig:config1}
+\end{figure}
+
+To define your scientific application, right click on the
+org.eclipse.ice.developer.code extension in the All Extensions section and
+select New $>$ Code in the context menu. This action will present you with the
+view in Figure \ref{fig:config2} where you can select the code category, code
+display name, the repository URL, and the branch you would like to work with. 
+
+\begin{figure}[h]
+\includegraphics[width=\textwidth]{figures/comb.png}
+\caption{Create a new Code description for this extension.}
+\label{fig:config2}
+\end{figure}
+
+To create a new developer action for your code, right click the code element of
+the extension tree and select New $>$ Command. You will then be presented
+with the view at the top of Figure \ref{fig:config2} where you can input the
+name of this action and the AbstractHandler subclass that performs the action.
+ICE provides a default GitCloneHandler that you may select. For this tutorial,
+select that and click Save. You should now have a view similar to the bottom of
+Figure \ref{fig:config2}.
+
+% \begin{figure}[h]
+% \includegraphics[width=.9\textwidth]{figures/extptconfig4.png}
+% \caption{Create a new command for this code extension.}
+% \label{fig:config4}
+% \end{figure}
+
+\subsubsection*{Setup ICE to Run with the New Plugin}
+To see this new Developer command in action, we need to launch a new instance of
+ICE. This can be done by opening the Run Configurations Wizard in Run $>$ Run
+Configurations. Under the Eclipse Applications element in the tree on the left,
+select the ICE launch configuration for your OS. Open the Plugins tab and add
+your new developer plugin (see Figure \ref{fig:launch}) by enabling it. Then,
+click Run to launch ICE with your developer plugin. 
+\begin{figure}[h]
+\includegraphics[width=\textwidth]{figures/launch.png}
+\caption{Add your plugin to the run configuration.}
+\label{fig:launch}
+\end{figure}
+With ICE running, navigate to the Developer menu and select Nuclear $>$ Fern $>$
+Clone Fern (see Figure \ref{fig:clonefern}).
+\begin{figure}[h]
+\includegraphics[width=\textwidth]{figures/cloned.png}
+\caption{Use the Developer Menu to Clone ICE.}
+\label{fig:clonefern}
+\end{figure}
+
+This will kick off the action you specified to clone the Fern repository and
+pull in any Eclipse projects to the workspace, as shown in Figure
+% \ref{fig:result}
+% \begin{figure}[h]
+% \includegraphics[width=\textwidth]{figures/result.png}
+% \label{fig:result}
+% \end{figure}
+\end{document}

docs/dynamicUI/.gitignore

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+/dynamicU.synctex.gz
+/bin/
+/tmp/

docs/dynamicUI/.project

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docs/dynamicUI/.texlipse

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docs/dynamicUI/src/.gitignore

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