Commit in projects/lcsim/trunk/site on MAIN
TODO+16-112855 -> 2856
pom.xml+13-42855 -> 2856
rebuild.sh+5added 2856
src/site/apt/build.apt+18-232855 -> 2856
            /distribution.apt+61added 2856
            /drivers.apt+12added 2856
            /features.apt+31added 2856
            /grid.apt+89added 2856
            /maven-repo.apt+83-32855 -> 2856
            /project-structure.apt+107added 2856
            /source-code.apt+1-12855 -> 2856
src/site/site.xml+23-72855 -> 2856
+459-49
6 added + 6 modified, total 12 files
updates and improvements to lcsim project website

projects/lcsim/trunk/site
TODO 2855 -> 2856
--- projects/lcsim/trunk/site/TODO	2013-12-14 22:02:58 UTC (rev 2855)
+++ projects/lcsim/trunk/site/TODO	2013-12-15 23:52:17 UTC (rev 2856)
@@ -6,26 +6,31 @@
 
 X lcsim Maven repository information
 
-explanation of Maven module structure
+X adding pom dependency to distribution
 
+X steering file usage; can point to the lcsim xml documentation page
+
+X list of Driver classes
+
+X instructions on running the software on the grid 
+
+X explanation of project module structure 
+
 software license
 
 news
 
 publications
 
-coding standards
+coding standards and Javadoc guidelines
 
-Eclipse instructions
+Eclipse project setup instructions
 
-Netbeans instructions
+Netbeans project setup instructions
 
-links e.g. to Confluence etc
+links page, such as ILC Confluence docs for further instruction and information
 
-instructions on running the software on the grid; should mostly be links to ILCDIRAC documentation
+description and links of other associated applications such as SLIC, PandoraPFA, slicPandora, LCFIVertexing (ick)
 
-steering file usage; can point to the lcsim xml documentation page
-
-----------------------------------------------------
-
-see freehep/trunk/site/src/site/apt/*.apt for examples and java.freehep.org for the output
+JAS instructions such as explanation of ~/.JAS3/extensions, how to install, how to run drivers, basic event display usage (can point to wiki),
+basic usage of event browser (also wiki) 

projects/lcsim/trunk/site
pom.xml 2855 -> 2856
--- projects/lcsim/trunk/site/pom.xml	2013-12-14 22:02:58 UTC (rev 2855)
+++ projects/lcsim/trunk/site/pom.xml	2013-12-15 23:52:17 UTC (rev 2856)
@@ -3,10 +3,9 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.lcsim</groupId>
     <artifactId>lcsim-site</artifactId>
-    <version>1.0-SNAPSHOT</version>
     <packaging>pom</packaging>
-    <name>LCSim Project Homepage</name>
-    <description>lcsim site</description>
+    <name>LCSim Project</name>
+    <description>Physics Event Reconstruction and Analysis in Java</description>
     <scm>
         <connection>scm:svn:svn://svn.freehep.org/lcdet/projects/lcsim/trunk/site</connection>
         <developerConnection>scm:svn:svn://svn.freehep.org/lcdet/projects/lcsim/trunk/site</developerConnection>
@@ -76,17 +75,26 @@
                             <report>index</report>
                             <report>issue-tracking</report>
                             <report>mailing-list</report>
+<!--
                             <report>modules</report>
                             <report>plugin-management</report>
                             <report>plugins</report>
+-->
                             <report>project-team</report>
-                            <report>scm</report>
                         </reports>
                     </reportSet>
                 </reportSets>
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-report-plugin</artifactId>
+                <version>2.16</version>
+                <configuration>
+                    <aggregate>true</aggregate>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-changes-plugin</artifactId>
                 <version>2.9</version>
                 <configuration>
@@ -127,6 +135,7 @@
                     <linkJavadoc>true</linkJavadoc>
                 </configuration>
             </plugin>
+
         </plugins>
     </reporting>
 </project>

projects/lcsim/trunk/site
rebuild.sh added at 2856
--- projects/lcsim/trunk/site/rebuild.sh	                        (rev 0)
+++ projects/lcsim/trunk/site/rebuild.sh	2013-12-15 23:52:17 UTC (rev 2856)
@@ -0,0 +1,5 @@
+#!/bin/sh
+rm -rf /scratch/staging/*
+#mvn site:site site:stage --non-recursive -DstagingDirectory=/scratch/staging/site/
+#mvn site:site site:deploy
+mvn site:site site:stage -Djava.awt.headless=true -DstagingDirectory=/work/scratch/site

projects/lcsim/trunk/site/src/site/apt
build.apt 2855 -> 2856
--- projects/lcsim/trunk/site/src/site/apt/build.apt	2013-12-14 22:02:58 UTC (rev 2855)
+++ projects/lcsim/trunk/site/src/site/apt/build.apt	2013-12-15 23:52:17 UTC (rev 2856)
@@ -6,23 +6,22 @@
 
 * Prerequisites
 
-    The following tools are required for building HPS Java software:
+    The following tools are required for building the software:
 
     * {{{http://subversion.tigris.org/}Subversion}}
       
-      This is the revision control system used by the experiment.  
-      Unix and OSX machines should have this installed by default.  
-      Windows users can install TortoiseSVN or the SVN command line tool.
+      This is a common revision control tool. Unix and OSX machines should have this installed by default.  
+      Windows users may install {{{http://tortoisesvn.net/}TortoiseSVN}} or the SVN command line tool.
       
     * {{{http://www.oracle.com/technetwork/java/javase/downloads/index.html}Java}}
       
       A valid JDK 1.7 installation is required for building and running the software.  
-      The commands java and javac must both work from the command line.
+      The commands "java" and "javac" must both work from the command line.
       
     * {{{http://maven.apache.org/}Maven}}
     
       This is the build tool used to create a local installation of the Java software.  
-      Any 3.x.x version should work fine.
+      Any 3.x.x version of Maven should work fine for building LCSim.
       
     []
 
@@ -40,8 +39,8 @@
       
     []
 
-    The instructions below which involve command line input assume a bash shell on Unix but those which don't involve Unix-specific
-    utilities will also work from a Windows command prompt.
+    The instructions below which involve command line input assume a bash shell on Unix, but those which don't use Unix-specific
+    utilities should also work from a Windows command prompt.
 
 * Downloading
 
@@ -50,25 +49,27 @@
 * Maven Overview
 
     LCSim projects are built using the Maven project management tool.  It provides facilities for compiling Java source code, 
-    as well as downloading a project's dependencies from remote repositories, among other {{{http://maven.apache.org/maven-features.html}features}}.
+    as well as downloading a project's dependencies from remote repositories, among other 
+    {{{http://maven.apache.org/maven-features.html}features}}.
 
 * Installing Maven 
 
- 	The command line 'mvn' tool can be installed by getting the latest release from the {{{http://maven.apache.org/download.cgi}download area}}.
+    The command line 'mvn' tool can be installed by getting the latest release from the {{{http://maven.apache.org/download.cgi}download area}}
+    using a web browser.
  	
- 	Or you may fetch it directly from the command, e.g. using a wget command such as:
+    Or you may fetch it directly, e.g. using a wget command such as:
  	
 +--
 wget http://mirror.cc.columbia.edu/pub/software/apache/maven/maven-3/3.1.1/binaries/apache-maven-3.1.1-bin.tar.gz
 +--
  	      
-    Once downloaded, untar the file into a directory on your system where you install local software:
+    Once downloaded, the file should be unpacked:
 	
 +--
 tar -zxvf apache-maven-3.1.1-bin.tar.gz
 +--
 
-    Now all that needs to be done is setting up your environment to find the command line tool:
+    The shell environment can be configured to find the command line tool:
    
 +--
 cd apache-maven-3.1.1/
@@ -76,19 +77,19 @@
 export PATH=$MAVEN_HOME/bin:$PATH
 +--   	     	
 
-    Finally, check that the command line client is accessible in your shell:
+    This command will check if the command line build tool is accessible in your shell:
     
 +--
 mvn -version
 +--
 
-   This should print out the local configuration starting with a line like:
+   That command should output the local configuration to the terminal, starting with a line like:
    
 +--
 Apache Maven 3.1.1
 +--
          
-   Now you are ready to build LCSim on your system.
+   Once Maven is successfully installed, LCSim can be built locally.
    
 * IDE Support
 
@@ -118,7 +119,7 @@
 target/${artifactId}-${version}.jar
 +--       
 
-    For instance, suppose you have compiled a local copy of the tracking module, then its artifact will show up at:
+    For instance, suppose the tracking module was built; its artifact will be located at:
         
 +--
 target/lcsim-tracking-3.0-SNAPSHOT.jar
@@ -208,9 +209,3 @@
     This will allow the LCSim repository to be used by all projects for resolving their dependencies.
 
     []
-    
-* Distribution Module
-
-    TODO
-    
-        
\ No newline at end of file

projects/lcsim/trunk/site/src/site/apt
distribution.apt added at 2856
--- projects/lcsim/trunk/site/src/site/apt/distribution.apt	                        (rev 0)
+++ projects/lcsim/trunk/site/src/site/apt/distribution.apt	2013-12-15 23:52:17 UTC (rev 2856)
@@ -0,0 +1,61 @@
+    ---
+LCSim - Distribution
+    ---
+
+Distribution
+
+* Dependency
+
+    The distribution jar can be used to include all LCSim modules in your project.
+
+    In order to depend on the distribution jar, include the following snippet in the dependencies 
+    section of your pom.xml file.
+
++--
+<dependency>
+    <groupId>org.lcsim</groupId>
+    <artifactId>lcsim-distribution</artifactId>
+    <version>3.0-SNAPSHOT</version>
+<dependency>
++--
+
+    The Nexus repository described in the {{{maven-repo.html}Maven Repository}} section can be 
+    used to see what versions of the distribution are available.
+
+* Downloading Distributions
+
+    The distribution jar may also be downloaded and run from the command line, as it is self-contained.
+
+    To find a distribution, go to the Nexus repository and type "lcsim-distribution" into the search box.
+    Then click on the {{{http://srs.slac.stanford.edu/nexus/service/local/artifact/maven/redirect?r=lcsim-maven2-snapshot&g=org.lcsim&a=lcsim-distribution&v=3.0-SNAPSHOT&e=jar&c=bin}bin jar}} link under the "Download" column. 
+
+* Running the Bin JAR    
+
+    Once the distribution jar has been downloaded locally, it can be run as follows:
+
++--
+java -jar lcsim-distribution-3.0-SNAPSHOT-bin.jar [arguments]    
++--
+
+    To see what options are available for command line usage, simply run the command without any arguments.
+    The following help text should show:
+
++--
+java -jar lcsim-bin.jar [options] steeringFile.xml
+usage:
+ -D    Define a variable with form [name]=[value]
+ -i    Add an LCIO input file to process
+ -n    Set the max number of events to process
+ -p    Load a properties file containing variable definitions
+ -q    Turn on quiet mode
+ -r    Use a steering resource rather than a file
+ -s    Set the number of events to skip
+ -v    Turn on verbose mode
+ -w    Rewrite the XML file with variables resolved
+ -x    Perform a dry run which does not process events
++--
+
+* Steering Files
+
+    The {{{https://confluence.slac.stanford.edu/display/ilc/lcsim+xml}LCSim XML documentation}} shows how to create steering files
+    for running algorithms from the command line.

projects/lcsim/trunk/site/src/site/apt
drivers.apt added at 2856
--- projects/lcsim/trunk/site/src/site/apt/drivers.apt	                        (rev 0)
+++ projects/lcsim/trunk/site/src/site/apt/drivers.apt	2013-12-15 23:52:17 UTC (rev 2856)
@@ -0,0 +1,12 @@
+    ---
+LCSim - Drivers
+    ---
+
+Drivers  
+
+    One of the most fundamental concepts in LCSim is the Driver, which is an algorithm that runs on event data.
+    Drivers may have child Drivers, so the entire algorithm structure is hierarchical.
+
+    The {{{apidocs/org/lcsim/util/Driver.html}Driver API documentation}} shows all the classes that derive from
+    this class under the "Direct Known Subclasses" section.  These may all be called from within LCSim steering
+    files.

projects/lcsim/trunk/site/src/site/apt
features.apt added at 2856
--- projects/lcsim/trunk/site/src/site/apt/features.apt	                        (rev 0)
+++ projects/lcsim/trunk/site/src/site/apt/features.apt	2013-12-15 23:52:17 UTC (rev 2856)
@@ -0,0 +1,31 @@
+    ---
+LCSim - Features
+    ---
+
+Features    
+
+    LCSim has the following major features:
+
+    * Physics event model including an abstract API and IO implementation using LCIO.
+    
+    * Driver framework for creating a hierarchical set of reconstruction and analysis algorithms.
+    
+    * Histogramming and Plotting using AIDA.
+    
+    * Calorimeter hit clustering.
+    
+    * Track finding and fitting with Seedtracker.
+    
+    * Detailed hierarchical detector and geometry description framework.
+    
+    * Batch processing using a flexible XML steering format.
+    
+    * Math utility library.
+    
+    * Vertexing with Billoir.
+    
+    * TRF track reconstruction framework.
+    
+    * HepRep output for binding to the Wired event display.
+    
+    * Plugin for JAS3 including an event browser, event display and binding to the record loop.

projects/lcsim/trunk/site/src/site/apt
grid.apt added at 2856
--- projects/lcsim/trunk/site/src/site/apt/grid.apt	                        (rev 0)
+++ projects/lcsim/trunk/site/src/site/apt/grid.apt	2013-12-15 23:52:17 UTC (rev 2856)
@@ -0,0 +1,89 @@
+    ---
+LCSim - Grid Usage
+    ---
+
+Grid Usage
+
+    Because it is packaged as standalone, runnable bin jar, LCSim is easily adapted for grid usage.
+
+* ILCDIRAC
+
+    The recommended way to run jobs with the application is using the {{{https://twiki.cern.ch/twiki/bin/view/CLIC/DiracUsage}ILCDIRAC}}
+    client, which wraps a suite of reconstruction and analysis tools with a structured Python API. 
+
+
+    The {{{https://twiki.cern.ch/twiki/bin/view/CLIC/DiracForUsers}DIRAC for Users}} guide shows how to configure jobs under
+    the "LCSIM" section.
+
+    The page {{{https://confluence.slac.stanford.edu/display/ilc/LCSim+Analysis+Jobs+on+the+Grid+with+DIRAC}LCSim Analysis Jobs on the Grid with DIRAC}}
+    on the SLAC Confluence Wiki gives a recipe for running a more complicated script.
+
+* Sample Script
+
+    The LCSim application is activated with the {{{http://lcd-data.web.cern.ch/lcd-data/doc/ilcdiracdoc/ILCDIRAC.Workflow.Modules.LCSIMAnalysis-module.html}LCSIMAnalysis module}}.
+
+    Below is a sample of how to use this class, which can be used as a starting point for writing your own scripts:
+
++--
+#!/usr/bin/env python
+
+"""
+Simple test job that runs a dummy lcsim job in ILCDIRAC.
+"""
+
+# MUST call this first
+from DIRAC.Core.Base import Script
+Script.parseCommandLine()
+
+# imports
+import sys
+from ILCDIRAC.Interfaces.API.NewInterface.Applications import *
+from ILCDIRAC.Interfaces.API.NewInterface.UserJob import *
+from ILCDIRAC.Interfaces.API.DiracILC import *
+from DIRAC.Resources.Catalog.FileCatalogClient import FileCatalogClient
+
+# job parameters
+repositoryFile = 'myrepo.cfg'
+outputSandbox = [ "*.log" ]
+inputSandbox = []
+jobName = 'lcsim_test'
+systemConfig = 'x86_64-slc5-gcc43-opt'
+cpuLimit = 100000
+inputFile = '/ilc/user/j/jeremy/slic_test/slic.slcio'
+
+# lcsim config
+lcsimVer = '3.0-SNAPSHOT'
+nEvts = 1
+xmlFile = 'template.lcsim'
+
+# setup ILCDIRAC
+dirac = DiracILC ( True , repositoryFile )
+
+# configure lcsim
+lcsim = LCSIM()
+lcsim.setVersion( lcsimVer )
+lcsim.setNumberOfEvents( nEvts )
+lcsim.setSteeringFile( xmlFile )
+
+# add lcsim to the job
+job = UserJob()
+result = job.append( lcsim )
+if not result['OK']:
+    print result['Message']
+    sys.exit(2)
+    
+# configure the job
+job.setOutputSandbox ( outputSandbox )
+job.setInputSandbox ( inputSandbox )
+job.setCPUTime( cpuLimit )
+job.setName( jobName )
+job.setJobGroup( jobName )
+job.setSystemConfig ( systemConfig )
+job.setInputData( [ inputFile ] )
+
+# submit job
+job.submit ( dirac )
++--
+
+    This is an example which only prints out the number of each event.  The DIRAC Wiki contains all the information for setting
+    up and configuring your actual analysis jobs in Python.

projects/lcsim/trunk/site/src/site/apt
maven-repo.apt 2855 -> 2856
--- projects/lcsim/trunk/site/src/site/apt/maven-repo.apt	2013-12-14 22:02:58 UTC (rev 2855)
+++ projects/lcsim/trunk/site/src/site/apt/maven-repo.apt	2013-12-15 23:52:17 UTC (rev 2856)
@@ -4,12 +4,42 @@
     
 Maven Repository
 
+* Remote Repositories
+
     LCSim module artifacts such as jar files are deployed to a remote repository where they are 
-    publically available for download, either manually or via a dependency in a POM file.
+    publically available for download, either manually or via a dependency in a POM file.  These repositories
+    have directory and file structures that allow Maven to find these dependencies when building dependent
+    projects.
 
+* Local Repository
+
+    When building, Maven will cache artifacts from remote repositories into a local repository so that
+    it does not need to fetch them from the internet every time.  By default, the location of the
+    local repository is <~/.m2/settings.xml> on Linux and OSX or the user home area on Windows.
+
+    This location can be configured differently via the settings file at <~/.m2/settings.xml>:
+
++--
+<settings>
+  ...
+  <localRepository>/path/to/local/repo/</localRepository>
+  ...
+</settings>
++--
+
+    Or it may be set from the command line for an individual build, as follows:
+
++--
+mvn -Dmaven.repo.local=/path/to/my/repo
++--
+
+    In fact, periodically removing and then rebuilding the local repository is a good idea, as it can 
+    make clear any possible dependency problems that might be otherwise hidden.
+
 * Repository Information
     
-    The following information can be put into the repositories section of your Maven project:
+    The following information can be put into the repositories section of your project's POM file
+    so that LCSim artifacts will be downloaded when found in the dependencies: 
     
 +--        
 <repository>
@@ -27,4 +57,54 @@
     The {{{http://www.sonatype.org/nexus/}Sonatype Nexus}} application is used to manage the repository.
     
     To search for jars, go to the {{{http://srs.slac.stanford.edu/nexus/index.html}SLAC SRS Nexus Application}} and
-    enter "lcsim" in the "Keyword Search" box, which will show the artifacts that are available.
\ No newline at end of file
+    enter "lcsim" in the "Keyword Search" box, which will show the artifacts that are available.
+
+* Snapshots
+
+    Maven has the concept of the snapshot version, which is a rolling release that is subject to change over time.
+    There can be many remote snapshot versions, because they are deployed automatically by the continuous integration system.
+
+    Artifacts of this type have long names including a unique identifer, such as:
+
++--
+lcsim-distribution-3.0-20131214.221640-10-bin.jar
++--
+
+    It is easy to spot snapshot dependencies in POM files as these have "SNAPSHOT" in the name, for instance:
+
++--
+<dependency>
+    <groupId>org.lcsim</groupId>
+    <artifactId>lcsim-distribution</artifactId>
+    <version>3.0-SNAPSHOT</version>
+<dependency>
++--
+
+    When referenced in this way, the latest version of the snapshot will be pulled automatically from the remote repository,
+    or a copy will be used from the local repository if it has a more recent timestamp.
+
+    Snapshot versions must be updated when releases are made, so after the "3.0" release is made, the snapshot version would
+    be changed to "3.1-SNAPSHOT" in anticipation of the "3.1" release.
+
+* Releases
+
+    Release versions point to artifacts that usually do not change once deployed to the remote repository.
+
+    These artifacts have short names including the release such as:
+
++--
+lcsim-distribution-3.0-bin.jar
++--
+
+    A dependency on that release would look like this in a POM file:
+
++--
+<dependency>
+    <groupId>org.lcsim</groupId>
+    <artifactId>lcsim-distribution</artifactId>
+    <version>3.0-SNAPSHOT</version>
+<dependency>
++--
+
+    Depending on release versions has the benefit that a project will not be affected by changes in the HEAD copy of the dependency
+    which are usually deployed automatically to remote repositories.

projects/lcsim/trunk/site/src/site/apt
project-structure.apt added at 2856
--- projects/lcsim/trunk/site/src/site/apt/project-structure.apt	                        (rev 0)
+++ projects/lcsim/trunk/site/src/site/apt/project-structure.apt	2013-12-15 23:52:17 UTC (rev 2856)
@@ -0,0 +1,107 @@
+    ---
+LCSim - Project Structure 
+    ---
+
+Project Structure
+
+* Modules
+
+    LCSim is structured as a series of Maven modules whose artifacts are combined together into a runnable bin jar
+    and a plugin for the JAS3 framework.  
+
+    The current HEAD version or "trunk" of all modules can be found at this location: 
+
++--
+svn://svn.freehep.org/lcdet/projects/lcsim/trunk/
++--
+
+    The top level POM that builds all the modules is found here:
+
++--
+svn://svn.freehep.org/lcdet/projects/lcsim/trunk/pom.xml
++--
+
+    Every module in the project is referenced from that configuration, so Maven commands that are executed from the "trunk" directory 
+    will actually operate on every module unless the "--non-recursive" option is used.  
+
+    This command run from "trunk" would build all the modules and execute the tests for them:
+
++--
+mvn clean install
++-- 
+
+    Usually when bootstrapping the software, this is the only command that should need to be executed
+    to get a working local copy of the application.
+
+* Distribution    
+
+    The distribution module is responsible for packaging all the jars together into a standalone runnable jar. 
+    It is referenced as a module in the primary POM described above so usually it does not need to be built
+    seperately.
+
+    But when a local copy of one or more modules contains source code changes that are not in the SVN and therefore deployed to the remote repository
+    via snapshots, the distribution module should be rebuilt in order to make a copy of the runnable bin jar that will contain these changes.
+
+    The distribution module is found here in SVN:
+
++--
+svn://svn.freehep.org/lcdet/projects/lcsim/trunk/distribution
++-- 
+
+    The standard 'mvn install' command can be used to both make the runnable bin jar as well as install your changes for JAS3 to load when it starts.
+
+* Parent POM Files
+
+    In order that each module need not include configuration information that is common to all of them, settings are kept in shared, parent POM files.
+
+    Most modules depend on the "lcsim-parent" artifact by including a section in their POM file such as:
+
++--
+<parent>
+    <groupId>org.lcsim</groupId>
+    <artifactId>lcsim-parent</artifactId>
+    <version>3.0-SNAPSHOT</version>
+    <relativePath>../parent/pom.xml</relativePath>
+</parent>
++--
+
+    Should modules be checked out individually, the parent POM usually needs to be installed manually so that the module can load
+    its settings.
+
+    The parent POM is located here:
+
++--
+svn://svn.freehep.org/lcdet/projects/lcsim/trunk/parent
++--
+
+    Additionally, for technical reasons, the parent POM itself has its own parent which contains information for the website.  This is
+    called "lcsim-site-parent" and it needs to be found by "lcsim-parent" when it builds.
+
+    The site-parent is found here:   
+
++--
+svn://svn.freehep.org/lcdet/projects/lcsim/trunk/site-parent
++--
+
+    Both of these modules can be built using the standard 'mvn install' command, and if installing manually, e.g. outside a full build
+    of all modules, site-parent should be built before parent.
+
+* Website
+
+    Most of the website configuration is found in this module:
+
++--
+svn://svn.freehep.org/lcdet/projects/lcsim/trunk/site
++--
+
+    The site POM file has its own list of modules that are included in the website.  (Some are not because they have no attached source code.)
+    This means that without the "--non-recursive" option, commands from the "site" directory will actually be run on each module as well
+    as site itself, to produce the full website including the top LCSim project page as well as module sub-pages.
+
+    It is possible to build a complete local working copy of the site by executing a command such as this:
+
++--
+mvn site:site site:stage -Djava.awt.headless=true -DstagingDirectory=/work/scratch/site
++--
+
+    Once this (rather long) build has completed, the URL "file:///work/scratch/site/index.html" should point to the top of the full LCSim website.

projects/lcsim/trunk/site/src/site/apt
source-code.apt 2855 -> 2856
--- projects/lcsim/trunk/site/src/site/apt/source-code.apt	2013-12-14 22:02:58 UTC (rev 2855)
+++ projects/lcsim/trunk/site/src/site/apt/source-code.apt	2013-12-15 23:52:17 UTC (rev 2856)
@@ -100,4 +100,4 @@
 +--
 svn list svn://svn.freehep.org/lcdet/projects/lcsim/branches/
 +--
-  
\ No newline at end of file
+  

projects/lcsim/trunk/site/src/site
site.xml 2855 -> 2856
--- projects/lcsim/trunk/site/src/site/site.xml	2013-12-14 22:02:58 UTC (rev 2855)
+++ projects/lcsim/trunk/site/src/site/site.xml	2013-12-15 23:52:17 UTC (rev 2856)
@@ -1,30 +1,46 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
-<project name="LCSim Project Homepage">
+<project name="LCSim Project">
 
     <body>
 
         <menu name="General">
+            <item name="Home" href="index.html"/>
+            <item name="Site Map" href="sitemap.html"/>
             <item name="Introduction" href="intro.html"/>
+            <item name="Features" href="features.html"/>
             <item name="Users" href="users.html"/>
             <item name="Team" href="team-list.html"/>
             <item name="Mailing List" href="mail-lists.html"/>
         </menu>
         
-        <menu name="For Users">
+        <menu name="Source Documentation">
+            <item name="Javadoc" href="apidocs/index.html"/>
+            <item name="Test Javadoc" href="testapidocs/index.html"/>
+            <item name="Source Xref" href="xref/index.html"/>
+            <item name="Test Source Xref" href="xref-test/index.html"/>
+        </menu>
+ 
+        <menu name="Project Information">
+            <item name="Project Dependencies" href="dependency-convergence.html"/>
             <item name="Bugs and Issues" href="issue-tracking.html"/>
+            <item name="Jira Report" href="jira-report.html"/>
         </menu>
 
+        <menu name="For Users">
+            <item name="Maven Repository" href="maven-repo.html"/>
+            <item name="Distribution" href="distribution.html" /> 
+            <item name="Analysis Drivers" href="drivers.html" />
+            <item name="Grid Usage" href="grid.html" />
+        </menu>
+
         <menu name="For Developers">
             <item name="Getting the Source Code" href="source-code.html"/>
             <item name="Building the Software" href="build.html"/>
-            <item name="LCSim Maven Repository" href="maven-repo.html"/>
+            <item name="Project Structure" href="project-structure.html"/>
             <item name="Continuous Integration" href="integration.html"/>
+            <item name="Surefire Test Report" href="surefire-report.html"/>
         </menu>
 
-<!--  
-        <menu ref="reports"/>
--->
-
     </body> 
 
 </project>
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