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Index: docs/dev/metacat/source/replication.rst
===================================================================
--- docs/dev/metacat/source/replication.rst	(revision 6869)
+++ docs/dev/metacat/source/replication.rst	(revision 6870)
@@ -61,9 +61,9 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 To add, remove, or alter servers on your home server's Replication list, or to 
 activate and customize the Delta-T handler, use the Replication control panel, 
-which is accessed at the following URL::
+which is accessed via the Metacat Administration interface at the following URL::
  
-   http://somehost.somelocation.edu/context/style/skins/dev/replControl.html
+   http://somehost.somelocation.edu/context/admin
    
 "http://somehost.somelocation.edu/context" should be replaced with the name 
 of your Metacat server and context (e.g., http://knb.ecoinformatics.org/knb/). 
@@ -79,29 +79,27 @@
 remove a replication server after replication has occurred is to remove the 
 certificates. 
 
-Also note that you must SCP partner certificates to your machine; you cannot 
-use the "Download Certificate from" option on the Control Panel. For more 
-information about creating and installing certificates, please see Generating 
-and Exchanging Security Certificates.
-
 Generating and Exchanging Security Certificates
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Before you can take advantage of Metacat's replication feature, you must 
 generate security certificates on both the replication partner and home servers. 
-The certificates will be exchanged so that each machine understands that the 
-other has replication access.
+Depending on how the certificates are generated, the certificates may need to be
+exchanged so that each machine "trusts" that the other has replication access.
+Certificates that are purchased from a commercial and well-recognized 
+Certificate Authority do not need to be exchanged with the other replication
+partner before replication takes place.  Metacat replication relies on SSL with
+client certificate authentication enabled.  When a replication partner server 
+communicates with another replication partner, it presents a certificate that
+serves to verify and authenticate that the server is trusted.
 
-The process for generating certificates is different for Metacat servlets 
-running under Tomcat and those under Tomcat/Apache (the recommended configuration). 
-For instructions on generating and exchanging certificates on systems running 
-only Tomcat (and Java 6), see Generating a Certificate for Tomcat standalone 
-(no Apache).
+If you must generate a self-signed certificate, the partner replication server 
+will need the public certificate added to its existing Certificate Authorities. 
 
 Generate Certificates for Metacat running under Apache/Tomcat
 .............................................................
 Note: Instructions are for Ubuntu/Debian systems.
 
-1. Generate a certificate key using openssl. The key will be named 
+1. Generate a private key using openssl. The key will be named 
    ``<hostname>-apache.key``, where ``<hostname>`` is the name of your Metacat 
    server. Example values for the individual key fields are included in the
    table below.
@@ -144,9 +142,10 @@
    you'd like, but keep in mind that the file will be sent to the partner 
    machine used for replication. The certificate name should have enough 
    meaning that someone who sees it on that machine can figure out where it 
-   came from. 
+   came from and for what purpose it should be used. 
 
-3. Enter the certificate into Apache's security configuration. You must 
+3. Enter the certificate into Apache's security configuration. This will
+   be used to identify your server to a replication partner. You must 
    register the certificate in the local Apache instance. Note that the 
    security files may be in a different directory from the one used in the 
    instructions depending on how you installed Apache. Copy the certificate and 
@@ -157,10 +156,13 @@
      sudo cp <hostname>-apache.crt /etc/ssl/certs 
      sudo cp <hostname>-apache.key /etc/ssl/private 
 
-4. Apache needs to know about Metacat SSL. The helper file named "knb-ssl" has 
-   rules that tell Apache which traffic to route to the Metacat SSL port. Set up 
-   SSL by dropping the knb-ssl file into the sites-available directory and 
-   running ``a2ensite`` to enable the site: 
+4. Apache needs to be configured to request a “client certificate” when the 
+   replication API is utilized. The helper file named "knb-ssl" has default 
+   rules that configure Apache for SSL and client certificate authentication. 
+   Set up these SSL settings by copying the knb-ssl file into the ``sites-available`` 
+   directory, editing pertinent values to match your system and running 
+   ``a2ensite`` to enable the site. (Note: some settings in knb-ssl need to be 
+   changed to match the specifics of your system.) 
 
    ::
    
@@ -173,90 +175,34 @@
    
      sudo /etc/init.d/apache2 restart
 
-6. SCP ``<hostname>-apache.crt`` to the replication partner machine.
+6. If using a self-signed certificate, SCP ``<hostname>-apache.crt`` to the 
+   replication partner machine where it will be added as an additional 
+   Certificate Authority.
 
-Generating a Certificate for Tomcat standalone (no Apache)
-..........................................................
-If you are running Metacat under Tomcat (no Apache), generate keys in the Java 
-default key store.  The generated key is placed into the binary certificate's 
-file located at ``/etc/java-1.5.0-sun/security/cacerts``.
+If using self-signed certificates, after you have created and SCP'd a 
+certificate file to each replication partner, and received a certificate file 
+from each partner in return, both home and partner servers must add the 
+respective partner certificates as Certificate Authorities.
 
-1. Generate the key by running the following command (note that you must be 
-   logged in as the root user to use the keytool):
-   
-   ::
-    
-     keytool -genkey -alias <aliasname> -keyalg RSA -validity 800 -keystore /etc/java-1.6.0-sun/security/cacerts
 
-   ``<aliasname>`` is a unique name that you choose for this key. Something 
-   like "<hostname-tomcat>" might be appropriate, where ``<hostname-tomcat>`` 
-   is the name of the Metacat host. 
-
-2. The Password-keytool will ask for a password. If writing to a pre-existing 
-   keystore, you must know the password. If you are creating a new keystore, 
-   the password you enter will become the keystore password. 
-
-   Sample values when creating certificate: 
-
-   ::
-   
-     What is your first and last name? myserver.nceas.ucsb.edu (note: use the host name without port number) 
-     What is the name of your organizional unit? NCEAS 
-     What is the name of your organizional unit? UCSB 
-     What is the name of your City or Locality? Santa Barbara 
-     What is the name of your State or Province? California (note: this is spelled in full) 
-     What is the two-letter country code for this unit? US 
-
-3. Create a certificate by running the command:
-   
-   ::
-    
-     keytool -export -alias <aliasname> -file <outputfile>.cert -keystore /etc/java-1.6.0-sun/security/cacerts
-
-   ``<aliasname>`` is the same name you used when you created the key file. A 
-   file named ``<outputfile>.cert`` will be created in the directory from which 
-   you ran the keytool command. You can name the output file anything you like, 
-   but keep in mind that it will be sent to the partner machine used for 
-   replication. The filename should have enough meaning that someone who sees 
-   it on that machine can figure out where it came from. Again, something like 
-   "<hostname>-tomcat.cert" will suffice. 
-
-4. Edit the Tomcat server file at ``$TOMCAT_HOME/conf/server.xml`` to enable 
-   SSL in Tomcat.
-    
-   * Uncomment the section that starts with "<Connector port="8443" ...
-     (Note: Databased Information comments start with <!-- and end with -->). 
-
-   * Add two attribute to that section: 
-
-     ::
-     
-       keystoreFile="/etc/java-1.6.0-sun/security/cacerts"
-       keystorePass="<keystore_password>"
-
-     where ``<keystore_password>`` is the password you used when you created 
-     or accessed the keystore. 
- 
-5. SCP the certificate to the partner server.
-
 To import a certificate
 .......................
-1. Log in as a root user (the keytool must run as a root user)
+1. Copy it into the Apache directory
    
    ::
    
-     sudo su –
+     sudo cp <remotehostfilename> /etc/ssl/certs/
 
-2. Import the remote certificate by running: 
+2. Rehash the certificates for Apache by running: 
 
    ::
    
-     keytool -import -alias <remotehostalias> -file <remotehostfilename>.crt -keystore /etc/java-1.6.0-sun/security/cacerts
+     cd /etc/ssl/certs
+     sudo c_rehash
 
+
    where the ``<remotehostfilename>`` is the name of the certificate file 
    created on the remote partner machine and SCP'd to the home machine. 
-   The ``<remotehostalias>`` is the name the certificate will use in the 
-   keystore. The name should identify the remote host. 
 
 Update your Metacat database
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -272,8 +218,7 @@
 To update your Metacat database to use replication, select the "Add this server" 
 radio button from the Replication Control Panel, enter the partner server name, 
 and specify how the replication should occur (whether to replicate xml, data, 
-or use the local machine as a hub). Note that you cannot download certificates 
-using this interface.
+or use the local machine as a hub).
 
 To update the database using SQL
 ................................
Index: docs/dev/metacat/source/submitting.rst
===================================================================
--- docs/dev/metacat/source/submitting.rst	(revision 6869)
+++ docs/dev/metacat/source/submitting.rst	(revision 6870)
@@ -176,8 +176,7 @@
 wish to appear in the registry.
 
 Once you have saved your changes, you must restart Tomcat for them to come 
-into effect. To restart Tomcat, log in as the user that runs your Tomcat 
-server (often "tomcat") and type: /etc/init.d/tomcat5.5 restart or an 
+into effect. To restart Tomcat, type: ``sudo /etc/init.d/tomcat6 restart`` or an 
 equivalent command appropriate to your operating system. 
 
 .. figure:: images/screenshots/image037.jpg
@@ -794,9 +793,10 @@
 
 .. Note::
 
-  The EarthGrid/EcoGrid web service API is *deprecated* and will be removed from
-  a future version of Metacat.  Its functionality is being replaced by the 
-  standardized DataONE REST service interface.
+  The EarthGrid/EcoGrid web service API is *deprecated* as of Metacat 2.0.0 and 
+  will be removed from a future version of Metacat.  Its functionality is being 
+  replaced by the standardized DataONE REST service interface. The EarthGrid API
+  will be completely removed by the end of 2013.
    
 The EarthGrid (aka EcoGrid) provides access to disparate data on different 
 networks (e.g., KNB, GBIF, GEON) and storage systems (e.g., Metacat and SRB), 
@@ -867,6 +867,13 @@
 
 Creating Your Own Client
 ------------------------
+
+.. Note::
+
+  NOTE: The Client API (and underlying servlet implementation) has been 
+  deprecated as of Metacat 2.0.0. Future development should utilize the DataONE 
+  REST service methods. The Client API will be completely removed by the end of 2013.
+  
 Metacat's client API is available in Java and Perl (the Java interface is 
 described in this section and further detailed in the appendix). Some of the 
 API is also available in Python and Ruby. The API allows client applications 
@@ -876,7 +883,7 @@
 
 The Client API is defined by the interface edu.ucsb.nceas.metacat.client.Metacat, 
 and all operations are fully defined in the javadoc_ documentation. To use the 
-client API, include the ``metacat-client.jar``, ``utilities.jar``, and 
+client API, include the ``metacat-client.jar``, ``utilities.jar``, ``commons-io-2.0.jar``, and 
 ``httpclient.jar`` in your classpath. After including these classes, you can 
 begin using the API methods (see the next table). 
 
Index: docs/dev/metacat/source/intro.rst
===================================================================
--- docs/dev/metacat/source/intro.rst	(revision 6869)
+++ docs/dev/metacat/source/intro.rst	(revision 6870)
@@ -103,7 +103,7 @@
 * The appearance of Metacat's Web interface can be customized via skins. 
 * Metacat fully supports the DataONE Member Node interface, allowing Metacat deployments to easily participate in the DataONE federation
 
-.. figure:: images/screenshots/image007.jpg
+.. figure:: images/screenshots/image007.png
    :align: center
 
    Metacat's default home page. Users can customize the appearance using skins.
Index: docs/dev/metacat/source/images/screenshots/image031.png
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Index: docs/dev/metacat/source/geoserver.rst
===================================================================
--- docs/dev/metacat/source/geoserver.rst	(revision 6869)
+++ docs/dev/metacat/source/geoserver.rst	(revision 6870)
@@ -1,19 +1,17 @@
 Metacat's Use of Geoserver
 ==========================
 
-GeoServer 1.4.0, an open source Web Mapping Service (WMS) written in Java, is 
+GeoServer 2.0.2, an open source Web Mapping Service (WMS) written in Java, is 
 bundled with Metacat and can be used to render spatial data as web-deliverable 
-maps (see figure). Metacat uses Community MapBuilder (a pure HTML and JavaScript 
-application that uses AJAX and XSLT) to provide a web-based user interface for 
-interacting with the generated maps. You can use any WMS-compatible client 
-(e.g., ArcGIS, QGIS, JUMP, UDig, OpenLayers, Mapbender, Map Builder). Please 
-note the mapping functionality is only supported for Metacat servlets running 
-under Tomcat 6 or later. 
+maps. Metacat uses OpenLayers (http://openlayers.org/) to provide a web-based 
+user interface for interacting with the generated maps. You can use any 
+WMS-compatible client (e.g., ArcGIS, QGIS, JUMP, UDig, OpenLayers, Mapbender, 
+Map Builder). 
 
 IMPORTANT: Regardless of whether you plan on using the mapping functionality 
 you should, for security purposes, configure GeoServer so that it doesn't 
 use the default password. For instructions, please see 
-Geoserver Password Configuration.
+Geoserver Configuration.
 
 .. figure:: images/screenshots/image051.jpg
    :align: center
@@ -27,30 +25,28 @@
 
 Currently, GeoServer can be used with the following limitations:
 
-* The GeoServer will only map documents that are publicly available. This is 
+* GeoServer will only map documents that are publicly available. This is 
   because the mapping server's support for permissions control is not as 
   fine-grained as Metacat's.
-* The GeoServer can only access documents that conform to one chosen schema. 
-  This is because only one set of xpaths can be defined in the Metacat properties.
-* GeoServer 1.4, the version bundled with Metacat, does not support raster 
-  input (e.g., satellite imagery or digital elevation models). We suggest 
-  setting up UMN Mapserver if you aim to serve raster data. 
 
 Metacat developers plan to continue extending and improving Metacat's mapping 
 capabilities. If you are interested in contributing to those efforts, or if 
 you are interested in learning more about the architecture and future plans for 
-the mapping software.
+the mapping software, please contact the Metacat  development 
+team  (metacat-dev@ecoinformatics.org).
 
 Installing and Configuring
 --------------------------
-Metacat's GeoServer is automatically installed when Metacat is installed. If 
-you do NOT wish to run GeoServer, set the runSpatialOption property in the 
-``metacat.properties`` file (found in the source code's lib directory) to 
-false before building and deploying Metacat. 
+The GeoServer webapp should be installed as a sibling of Metacat. If you do 
+NOT wish to run GeoServer, the deployment can be skipped, but any skins that 
+use maps will not render correctly. (NOTE: Geoserver recommends using a PermGen 
+space setting of at least 128MB.). 
 
-The GeoServer bundled with Metacat comes with a world-countries base layer 
-and a default configuration that is already aware of Metacat's spatial cache. 
-To further configure GeoServer, use its Web-based configuration utility, 
+Metacat comes with a pre-configured data directory to be used by GeoServer. 
+This includes a world-countries base layer and a default configuration that 
+is already aware of Metacat's spatial cache. The Metacat configuration interface 
+is used to configure GeoServer to use this shared data directory. To further 
+configure GeoServer, use the Web-based configuration utility, 
 which is available at: http://your.server.com/context/geoserver.jsp 
 (e.g., http://knb.ecoinformatics.org/knb/geoserver.jsp). 
 
@@ -59,12 +55,11 @@
 * Adding a Map to a Web Page or Skin
 * Configuring the Size and Initial Extent of the Map
 * Configuring the Layout of the HTML Mapping Interface
-* Changing the Lat/Long Display to Degree-Minutes-Seconds
 * Configuring the "Select Location Drop-down Menu
 * Configuring the Visual Portrayal of Geospatial Data (e.g., symbology and color)
 * Adding Other Spatial Datasets to the Web Map
 
-.. figure:: images/screenshots/image053.jpg
+.. figure:: images/screenshots/image053.png
    :align: center
    
    GeoServer's Web-based administrative interface.
@@ -71,33 +66,27 @@
 
 Note: Some configurations may need to be made to the XML files as well.
 
-Community Mabuilder, which Metacat uses as the front-end for GeoServer's WMS 
-service, provides interface components or "widgets" (e.g., the map, a box zoom, 
-layer list, "Select Location" drop-down menu, scale bar, lat/long coordinates, 
-and a query form) that make it easy to deploy highly-functional Web mapping 
-applications with minimal coding. The WMS layers are configured through a Web 
-Map Context (WMC) document. This context document can be edited to customize 
-the initial extent of the map, the ordering and visibility of layers and, of 
-course, the source and name of the WMS layer.
+OpenLayers, which Metacat uses as the front-end for GeoServer's WMS service, 
+provides interface components or "widgets" (e.g., the map, a box zoom, layer 
+list, "Select Location" drop-down menu, scale bar, lat/long coordinates, and 
+a query form) that make it easy to deploy web-based mapping applications with 
+minimal coding.
 
-Mapbuilder has three main configuration files used to customize the map 
-interface (Table 5.1). If you plan to customize the map interface, you must 
-use a source code distribution of Metacat. Default configurations are in::
+OpenLayers has three main configuration files used to customize the map interface.
+Default configurations are in::
 
-  $METACAT/lib/style/common/spatial_templates/spatial1/
+  $METACAT/lib/style/common/spatial/
+  
++----------------------------------+---------------+-------------------------------------------------------------+
+| Document                         | Location      | Description                                                 |
++==================================+===============+=============================================================+
+| The named location file          | locations.jsp | The list of pre-defined locations (name and lat/lon bounds) |
++----------------------------------+---------------+-------------------------------------------------------------+
+| Main map rendering functions     | maps.js       | Defines the map, widgets and their behavior                 |
++----------------------------------+---------------+-------------------------------------------------------------+
+| The rendered map and page layout | map.jsp       | Loads the map and controls the HTML layout of the widgets.  |
++----------------------------------+---------------+-------------------------------------------------------------+
 
-+--------------------------------+-------------+---------------------------------------------------------------------+
-| Document                       | Location    | Description                                                         |
-+================================+=============+=====================================================================+
-| Web map context document (WMC) | context.xml | The WMC is used to customize the initial extent of the map,         |
-|                                |             | the order of the map layers, and the source and name of each layer. |
-+--------------------------------+-------------+---------------------------------------------------------------------+
-| Mapbuilder configuration file  | context.xml | Defines the Mapbuilder widgets and their behavior                   |
-+--------------------------------+-------------+---------------------------------------------------------------------+
-| The Map file                   | map.html    | Loads the Mapbuilder JavaScript library and controls the            |
-|                                |             | HTML layout of the widgets.                                         |
-+--------------------------------+-------------+---------------------------------------------------------------------+
-
 NOTE: By default, the first time Metacat is restarted, it generates a 
 "spatial cache" containing geographic information about documents in its 
 repository. This default behavior is specified in lib/metacat.properties, 
@@ -116,95 +105,62 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 To add a map to a Web page, simply include the map interface using an iframe:: 
 
-  <iframe scrolling="no" frameborder="0" width="736" height="520" 
-          src="/knb/style/common/spatial_templates/spatial1/map.html">
+  <iframe scrolling="no" frameborder="0" width="780" height="420" 
+          src="/knb/style/common/spatial/map.jsp">
   </iframe>
 
-The map URL, ``/knb/style/common/spatial_templates/spatial1/map.html``, is 
-the default map interface. If you plan to customize the map interface, copy 
-the spatial1 directory into your skin's directory (either the default or 
+The map URL, ``/knb/style/common/spatial/map.jsp``, is 
+the default map interface. If you plan to customize the map interface, copy
+the map.jsp file into your skin's directory (either the default or 
 customized skin directory). 
 
 ::
 
-  cp -r style/common/spatial_templates/spatial1 /style/skins/<myskin>/spatial
+  cp -r style/common/spatial/map.jsp /style/skins/<myskin>/spatial
 
-You can access the customized map with the URL: ``/knb/style/skins/<myskin>/spatial/map.html`` 
+You can access the customized map with the URL: ``/knb/style/skins/<myskin>/spatial/map.jsp`` 
 
 Configuring the Size and Initial Extent of the Map
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Before you configure the size and initial extent of the map, make sure that you 
-have copied the default spatial settings into your skin's directory (see :doc:`configuration`). 
-Once the settings have been copied, you can modify the map's initial extent in 
-the context settings: ``${skin.dir}/spatial/context.xml``. 
+have copied the map layout page into your skin's directory (See 
+:doc:`configuration` for directions). Once the file has been copied, you can 
+modify the map's initial extent in: ``${skin.dir}/spatial/map.jsp``.
 
-To change the map size and/or initial extent, edit the following lines::
+To change the map’s initial extent, edit the bounding box. The default is to 
+show the entire globe. The ``initMap()`` function should also be given the skin 
+name so that spatial search results can be correctly styled.
 
-  <Window width="720" height="360" />
-  <BoundingBox SRS="EPSG:4326" minx="-180" miny="-90" maxx="180" maxy="90" />
+::
 
-Where ``width`` and ``height`` specify the map size in pixels, ``minx/maxx`` 
-represent the range of longitudes and ``miny/maxy`` represent the range of latitudes. 
+  <script type="text/javascript">
+      function init() {
+         var bounds = new OpenLayers.Bounds(-180,-90,180,90); 
+         // make the map for this skin 
+         initMap("<%=GEOSERVER_URL%>", "<%=SERVLET_URL%>", "default", bounds);
+      }
+  </script>
 
+The size (height/width) of the map can be controlled by the ``#map`` CSS entry 
+included in the ``map.jsp`` page.
+
 Configuring the Layout of the HTML Mapping Interface
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Before you configure the size and initial extent of the map, make sure that 
-you have copied the default spatial settings into your skin's directory. 
-Once the settings have been copied, you can modify the layout here: 
-``${skin.dir}/spatial/map.html``.
+The size and initial extent of the map can be edited in : ${skin.dir}/spatial/map.jsp.
 
-``Map.html`` is a simple HTML file with a tabular layout. Map components are 
-abstracted into "widgets", blocks with a specific id (e.g., locationsSelect 
-and mainButtonBar), which can be reorganized within the table. 
-To customize the map extent and appearance, modify the Web map context 
-document (``context.xml``) and/or Mapbuilder's configuration file (``config.xml``). 
-Both files are in the spatial directory inside the skins folder.
+The map.jsp is a simple container that can be included in other more complex 
+pages if desired. It contains the map, widgets and location dropdown list.
 
-Changing the Lat/Long Display to Degree-Minutes-Seconds
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-By default, the map display shows the cursor's position in decimal degrees 
-(the preferred format for many GPS/GIS applications). To report coordinates as 
-degrees minutes-seconds, edit the spatial configuration file:
-
-1. If you have not already copied the default spatial settings into your skin's 
-   directory, do so now
-2. Open the ${skin.dir}/spatial/config.xml file.
-3. Edit the CursorTrack widget so that the content is the following: 
-
-::
-
-  <CursorTrack id="cursorTrack">
-     <mouseHandler>mainMap</mouseHandler>
-     <showDMS>true</showDMS>
-     <showLatLong>true</showLatLong>
-  </CursorTrack>
-
-4. Save and close the configuration file.
-
 Configuring the "Select Location" Drop-down Menu
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Before you configure the menu items, make sure that you have copied the default 
-spatial settings into your skin's directory. 
-
 The locations that appear in the "Select Location" drop-down menu are specified 
-in the ``${skin.dir}/spatial/named_locations.xml`` file. Each location is 
-defined as a ``gml:featureMember``. Edit the featureMember's ``gml:name`` and 
-``gml:coordinates`` fields to edit or add new locations. 
+in the ``locations.jsp`` file. The locations.jsp can be copied from the common 
+spatial template into your skin directory. Each location is defined as an 
+HTML ``<option/>`` tag. Edit the value and label to edit or add new locations.
 
 ::
 
-  <gml:featureMember>
-     <locationDef>
-          <gml:name>ACM Wilderness Field Station</gml:name>
-          <spatialKeyword>
-               <gml:location>
-                    <gml:Envelope srsName="http://www.opengis.net/gml/srs/epsg.xml#4326">
-                         <gml:coordinates>-91.956,47.87 -91.706,48.12</gml:coordinates>
-                    </gml:Envelope>
-               </gml:location>
-          </spatialKeyword>
-     </locationDef>
-  </gml:featureMember> 
+  <option value=“-149.725,68.475 -149.3254,68.725”> Arctic LTER (ARC)</option>
 
 Configuring the Visual Portrayal of Geospatial Data (e.g., symbology and color)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -213,9 +169,9 @@
 ``/lib/spatial/geoserver/data/styles/`` and are named data_points_style.sld and 
 data_bounds_style.sld, respectively. 
 
-You can find a more detailed tutorial on using SLD with GeoServer at::
+You can find a more detailed tutorial on using SLD with GeoServer in the GeoServer documentation::
 
-  http://geoserver.org/display/GEOSDOC/SLD+Intro+Tutorial.
+  http://docs.geoserver.org/
 
 Adding Other Spatial Datasets to the Web Map
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -230,94 +186,50 @@
 
 To register the data set and add it to the map:
 
-1. Point your browser to http://your.server/context/geoserver.jsp, log in to 
-   GeoServer, and navigate to the "Data Stores" configuration page 
-   under Config > Data > Stores. 
-2. Create a new Shapefile and assign it a DataStore ID. The DataStore ID can 
-   contain letters and numbers. It is just used internally, and should be 
-   unique. Click New.
+1. Point your browser to ``http://your.server/geoserver``, log in to GeoServer, 
+   and navigate to the "Data Stores" configuration page under ``Data > Stores``. 
+2. Create a new vector data source from a Shapefile in the “metacat” workspace.
 
-.. figure:: images/screenshots/image055.jpg
+.. figure:: images/screenshots/image055.png
    :align: center
    
    Creating a new shapefile using GeoServers web-based administrative interface.
 
-3. On the next screen, select the "metacat" namespace from the drop-down menu 
-   and point to the GIS data file on the file system, relative to:
-
-   ::
-
-     {tomcat.dir}/webapps/{context}/
-
-   The Description, if specified, is mostly used internally to provide other 
+3. The Description, if specified, is mostly used internally to provide other 
    administrators with information about the DataStore. Click Submit.
+4. Navigate to the "Layers" configuration page under Data > Layers. 
+   Add a new Layer from your new data source.
+5. You should also define a spatial reference system (SRS) number for the new 
+   layer. Most lat/long data is "4326". If your data is in another projection, 
+   determine its spatial reference system using the help links provided.
 
-4. Navigate to the "Feature Type" configuration page under 
-   Config > Data > Feature Type. Select your new data store from the 
-   drop-down menu. Click New.
-5. Style the layer using a style from the drop-down style menu, or click 
-   "Create new SLD" to create a new Style object and corresponding SLD 
-   (this option provides more control over the style). You should also define a 
-   spatial reference system (SRS) number for the new layer. 
-   Most lat/long data is "4326". If your data is in another projection,
-   determine its spatial reference system using the help links provided. 
-
-.. figure:: images/screenshots/image057.jpg
+.. figure:: images/screenshots/image057.png
    :align: center
    
-   GeoServer's FeatureType Editor. The Style and SRS settings discussed in step 5 are highlighted.
+   GeoServer's FeatureType configuration. The SRS settings discussed in step 5 are highlighted.
 
-6. Click "Apply" and "Save" 
-7. Try out the styled data set as a WMS layer using a URL like: 
+6. Style the layer using a style from the drop-down menu on the Publishing tab, 
+   or create a new SLD to create a new style object and corresponding SLD 
+   (this option provides more control over the style). 
+7. Try out the styled data set as a WMS layer using a the Layer Preview.
 
-   ::
+.. figure:: images/screenshots/image058.png
+   :align: center
+   
+   GeoServer's Layer Preview allows you to see an OpenLayer rendering of the new layer.
 
-     http://your.server/context/wms?VERSION=1.1.1&REQUEST=GetMap&SERVICE=WMS&LAYERS=metacat:newLayer&SRS=EPSG:4326&BBOX=-180,-90,180,90&WIDTH=720&HEIGHT=360&FORMAT=image/gif&STYLES=&TRANSPARENT=TRUE&UNIQUEID= 
-
-   Where your.server/context is the name of your server and context (e.g., 
-   http://knb.ecoinformatics.org/knb) and newLayer is the name of the new layer. 
-   The other parameters control which part of the layer is displayed.
-
-   If data is properly displayed, add the map to your map context document (Step 8).
-
-8. Locate the Web map context document (usually {skin}/spatial/context.xml) and 
-   open the file in a text editor.
-9. Locate the Layer entry for an existing layer next to which you wish to stack 
-   your layer (the first layers in the context are rendered at the bottom). 
-
-10. Create a new Layer entry, by copying and pasting the existing entry for the 
-    metacat data_points layer and editing the Layer Name and Title. The title 
-    is displayed in the map legend. Note: if you'd like to use transparency, 
-    leave the image format set to image/gif (IE pre-7 has trouble with PNG 
-    transparency).
-
-    ::
-    
-      <Layer queryable="0" hidden="0">
-      <Server service="OGC:WMS" version="1.1.1"
-      title="DatasetPoints">
-        <OnlineResource xlink:type="simple" xlink:href="../../../../wms" />
-      </Server>
-      <Name>metacat:data_points</Name>
-      <Title>Dataset Points</Title>
-      <SRS>EPSG:4326</SRS>
-      <FormatList>
-        <Format current="1">image/gif</Format>
-      </FormatList>
-      </Layer>
-
-11. Point your browser to the map interface. Your new layer should appear with 
+8. Copy the default ``map.js`` file that assembles the map in OpenLayers 
+   (``style/common/spatial/map.js``) to your skin’s spatial directory.
+9. Edit the init() method to include your new layer in the map – either as an 
+   overlay or as a base layer.
+10. Point your browser to the map interface. Your new layer should appear with 
     the existing ones.
 
 Adding External Spatial Data Made Publically Available through WMS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 There are hundreds of sources of spatial data made publically available 
-through WMS. (check out http://wms-sites.com for good catalog). To add these 
-data sources to your map, locate your skin's context file 
-(``${skin.dir}/spatial/context.xml``) and add a new Layer by copying and 
-pasting an existing Layer and modifying as appropriate: modify the 
-OnlineResourceURL, Name, Title and Style to match the WMS layer you'd like to 
-use. See the mapbuilder Add WMS Tutorial for further details.
+through WMS (check out http://wms-sites.com for a good catalog). To add these 
+data sources to your map, add the layers in your skin’s ``spatial/map.js`` file.
 
 Spatial Queries
 ---------------
Index: docs/dev/metacat/source/install.rst
===================================================================
--- docs/dev/metacat/source/install.rst	(revision 6869)
+++ docs/dev/metacat/source/install.rst	(revision 6870)
@@ -18,7 +18,7 @@
 
   * In order to use the Metacat Registry (and for a more robust Web-serving environment in general), the Apache Web server should be installed with Tomcat and the two should be integrated. See the installing Apache for more information.
 
-* Java_ 6 (Note: Java 5 is deprecated)
+* `Java 6`_ (Note: Java 5 is deprecated)
 
 .. _PostgreSQL: http://www.postgresql.org/
 
@@ -30,7 +30,7 @@
 
 .. _Apache HTTPD Server: http://httpd.apache.org/
 
-.. _Java: http://www.oracle.com/technetwork/java/javaee/overview/index.html
+.. _Java 6: http://www.oracle.com/technetwork/java/javaee/overview/index.html
 
 System requirements for running Metacat:
 
@@ -58,13 +58,13 @@
 they are doing, here are the steps needed to install Metacat. Detailed
 instructions for each step are in the next section.
 
-1. Download and install prerequisites (Java_ 6, `Apache Tomcat`_ 6, PostgreSQL_, `Apache HTTPD Server`_), including the tomcat6 init.d script
+1. Download and install prerequisites (`Java 6`_, `Apache Tomcat`_ 6, PostgreSQL_, `Apache HTTPD Server`_)
 2. Create a database in PostgreSQL named 'metacat' and authorize access to it in ``pb_hba.conf`` for the user 'metacat'
 3. Log in to PostgreSQL and create the 'metacat' user
 4. Download Metacat from the `Metacat Download Page`_ and extract the archive
 5. ``sudo mkdir /var/metacat; sudo chown -R <tomcat_user> /var/metacat``
 6. ``sudo cp <metacat_package_dir>/knb.war <tomcat_app_dir>``
-7. ``sudo /etc/init.d/tomcat5.5 restart``
+7. ``sudo /etc/init.d/tomcat6 restart``
 8. Configure Metacat through the Web interface
 
 .. _Metacat Download Page: http://knb.ecoinformatics.org/software/metacat/
@@ -106,14 +106,12 @@
 knb.war            The Metacat Web archive file (WAR) 
 knb                The Web definition file used by Apache on Ubuntu/Debian 
                    Linux systems. 
-Knb.ssl            The SSL definition file used by Apache on Ubuntu/Debian 
+knb.ssl            The SSL definition file used by Apache on Ubuntu/Debian 
                    Linux systems.
 jk.conf            The JkMount configuration file used by Apache on 
                    Ubuntu/Debian Linux systems. 
 workers.properties The workers definition file used by Apache on Ubuntu/Debian 
                    Linux systems. 
-tomcat5.5          The Tomcat startup script for Tomcat 5.5 installed with 
-                   apt-get on Ubuntu/Debian Linux systems.
 authority          The optional LSID Server application WAR
 ================== ===========================================================
 
@@ -181,7 +179,7 @@
 also highly recommend that you install Apache Web server, as it provides a more
 robust Web-serving environment and is required by some Metacat functionality. 
 
-* Java_ 6
+* `Java 6`_
 * `Apache Tomcat`_ 
 * `Apache HTTPD Server`_ (Highly Recommended)
 * PostgreSQL_ Database (or Oracle_)
@@ -215,18 +213,10 @@
 
 If you are running Ubuntu_/Debian, get Tomcat by typing::
 
-  sudo apt-get install tomcat5.5
+  sudo apt-get install tomcat6
 
 Otherwise, get Tomcat from the `Apache Tomcat`_ page.
 
-Install the Metacat-friendly Tomcat start-up script by typing::
-
-  sudo /etc/init.d/tomcat5.5 stop
-  sudo mv /etc/init.d/tomcat5.5 /etc/init.d/tomcat5.5.bak
-  sudo cp <metacat_package_dir>/debian/tomcat5.5 /etc/init.d/tomcat5.5
-  sudo chmod +x /etc/init.d/tomcat5.5
-
-
 Apache HTTPD Server (Highly Recommended)
 ........................................
 Although you have the option of running Metacat with only the Tomcat server, we
@@ -352,7 +342,7 @@
   sudo /etc/init.d/apache2 restart
 
 
-PostgreSQL Database 
+PostgreSQL Database
 ...................
 Metacat has been most widely tested with PostgreSQL_ and we recommend using it.
 Instructions for installing and configuring Oracle are also included in the
@@ -486,7 +476,7 @@
 
 Ant should be installed on your system and the "ant" executable shell script
 should be available in the user's path. The latest Metacat release was tested
-with Ant 1.6.5. 
+with Ant 1.8.2. 
 
 Installing Metacat
 ~~~~~~~~~~~~~~~~~~
@@ -515,7 +505,7 @@
     sudo chown -R <tomcat_user> /var/metacat
 
 
-3)  Install the Metacat WAR in the Tomcat web-application directory. For instructions on downloading the Metacat WAR, please see Downloading Metacat.  Typically, Tomcat will look for its application files (WAR files) in the <tomcat_home>/webapps directory (e.g., /usr/share/tomcat5.5/webapps). Your instance of Tomcat may be configured to look in a different directory. We will refer to the Tomcat application directory as <tomcat_app_dir>.  NOTE: The name of the WAR file (e.g., knb.war) provides the application context, which appears in the URL of the Metacat (e.g., http://yourserver.com/knb/). To change the context, simply change the name of the WAR file to the desired name before copying it.  To install the Metacat WAR:
+3.  Install the Metacat WAR in the Tomcat web-application directory. For instructions on downloading the Metacat WAR, please see Downloading Metacat.  Typically, Tomcat will look for its application files (WAR files) in the <tomcat_home>/webapps directory (e.g., /usr/share/tomcat6/webapps). Your instance of Tomcat may be configured to look in a different directory. We will refer to the Tomcat application directory as <tomcat_app_dir>.  NOTE: The name of the WAR file (e.g., knb.war) provides the application context, which appears in the URL of the Metacat (e.g., http://yourserver.com/knb/). To change the context, simply change the name of the WAR file to the desired name before copying it.  To install the Metacat WAR:
 
   ::
 
@@ -526,7 +516,7 @@
 
   ::
 
-    /etc/init.d/tomcat5.5 restart
+    /etc/init.d/tomcat6 restart
 
 Congratulations! You have now installed Metacat. If everything is installed
 correctly, you should see the Authentication Configuration screen (Figure 2.1)
@@ -534,7 +524,7 @@
 http://knb.ecoinformatics.org/knb) into a browser. For more information about
 configuring Metacat, please see the Configuration Section.
 
-.. figure:: images/screenshots/image009.jpg
+.. figure:: images/screenshots/image009.png
    :align: center
 
    The Authentication Configuration screen appears the first time you open a 
@@ -552,7 +542,7 @@
 
   ::
 
-    /etc/init.d/tomcat5.5 stop
+    /etc/init.d/tomcat6 stop
 
 3. Back up the existing Metacat installation. Although not required, we highly recommend that you back up your existing Metacat to a backup directory (<backup_dir>) before installing a new one. You can do so by typing:
 
@@ -584,7 +574,7 @@
 
   ::
 
-    /etc/init.d/tomcat5.5 restart
+    /etc/init.d/tomcat6 restart
 
 
 7. Run your new Metacat servlet. Go to a Web browser and visit your installed
@@ -710,7 +700,7 @@
 
   ::
 
-    sudo cp <metacat_package_directory>/authority.war /usr/share/tomcat5.5/webapps
+    sudo cp <metacat_package_directory>/authority.war /usr/share/tomcat6/webapps
  
 2. Set up the LSID server by dropping the authority file into Apache's
    sites-available directory and running a2ensite to enable the site:
@@ -765,7 +755,7 @@
 
   ::
 
-    /etc/init.d/tomcat5.5 restart
+    /etc/init.d/tomcat6 restart
 
 5. If you are running Tomcat behind the Apache server (the recommended
    configuration), set up and enable the authority service site configurations by
@@ -824,7 +814,7 @@
 
 1. Browse to the KNB Software Download Page. In the Metacat section, select
    the link that looks like: metacat-bin-X.X.X.zip, where X.X.X is the latest
-   version of Metacat (e.g., 1.9.0).
+   version of Metacat (e.g., 2.0.0).
 
 2. Choose to download and Save the file locally. 
 
@@ -844,7 +834,7 @@
 Before you can install and run Metacat, you must ensure that a recent Java SDK,
 PostgreSQL and Tomcat are installed, configured, and running correctly. 
 
-* Java_ 6
+* `Java 6`_
 * `Apache Tomcat`_
 * PostgreSQL_ Database
 
@@ -873,7 +863,7 @@
 .............
 We recommend that you install Tomcat version 6.  To download and install Tomcat:
 
-1. Browse to: http://tomcat.apache.org/download-55.cgi 
+1. Browse to: http://tomcat.apache.org/
 2. Download the Tomcat core zip file 
 3. Extract Tomcat files to C:\Program Files\tomcat using the windows zip
    utility. 
Index: docs/dev/metacat/source/index.rst
===================================================================
--- docs/dev/metacat/source/index.rst	(revision 6869)
+++ docs/dev/metacat/source/index.rst	(revision 6870)
@@ -2,7 +2,7 @@
 Metacat Administrator's Guide
 =============================
 
-.. sidebar:: Version: 2.0.0 Release
+.. sidebar:: Version: 2.0.0
 
     .. image:: themes/readable/static/metacat-logo.png
        :height: 130pt
@@ -12,6 +12,7 @@
         http://bugzilla.ecoinformatics.org
 
     License: GPL
+    Release Date: January 20, 2012
 
 Metacat is a repository for data and metadata (documentation about data) that helps 
 scientists find, understand and effectively use data sets they manage or that 
Index: docs/dev/metacat/source/configuration.rst
===================================================================
--- docs/dev/metacat/source/configuration.rst	(revision 6869)
+++ docs/dev/metacat/source/configuration.rst	(revision 6870)
@@ -73,7 +73,7 @@
 If you make changes to the authentication settings, you must restart Tomcat to 
 put them into effect.
 
-.. figure:: images/screenshots/image013.png
+.. figure:: images/screenshots/image009.png
    :align: center
 
    Configuring Authentication Values.
@@ -118,7 +118,7 @@
 In the log-in screen enter your user name and password and click 
 the "Login" button.
 
-.. figure:: images/screenshots/image015.jpg
+.. figure:: images/screenshots/image015.png
    :align: center
 
    Logging into Metacat.
@@ -169,6 +169,10 @@
 version of Metacat, you must restart the Tomcat server for the changes to 
 take effect.
 
+.. Note::
+   
+   Need to update this next figure!
+   
 .. figure:: images/screenshots/image019.png
    :align: center
 
@@ -294,44 +298,43 @@
 
    Upgrading an existing database.
 
-Geoserver Password Configuration (Highly Recommended)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Geoserver Configuration (Highly Recommended)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. sidebar:: Manual Geoserver Update
 
   Alternatively, you can change the Geoserver username and password manually by 
   directly logging in to the Geoserver. To configure the credentials manually: 
 
-  1. Go to the Geoserver admin page: http://<your_context_url>/geoserver.jsp. 
+  1. Go to the Geoserver admin page: http://<your_context_url>/geoserver/ 
   2. Log in using the default username and password ( admin / geoserver ) 
   3. Navigate to the Password Change Page.  Enter a new user and password and click Submit. 
   4. Click Apply then Save to save your new password. 
-
-  Note that once you change the Geoserver credentials manually, you cannot use 
-  the Metacat configuration tool to change it again (until a new Metacat 
-  upgrade or installation).
   
 Metacat comes bundled with a Web Mapping Service called Geoserver, which 
 converts spatial data into Web-deliverable map images. Geoserver installs with 
-a default administrative username and password. We highly recommend that you 
-change the default log-in information so that only local administrators can make 
-changes to your Geoserver. For more information about Geoserver, 
+a default administrative username and password. *We highly recommend that you 
+change the default credentials so that only local administrators can make 
+changes to your Geoserver.* For more information about Geoserver, 
 see :doc:`geoserver`.
 
 When you choose the Geoserver Configuration link from the main configuration 
-screen, Metacat will prompt you for a new user name and password. After you 
-enter the new credentials, the Metacat server contacts the embedded Geoserver s
-erver and updates the log-in settings.
+screen, Metacat will prompt you for a few important details about your Geoserver 
+installation. The data directory and context settings allow Geoserver and 
+Metacat to share the same spatial data store and render maps within Metacat skins. 
+The security configuration prompts for a new admin password. After you enter 
+the new settings, Metacat writes the information to the Geoserver deployment.
 
-If you wish to reset the Geoserver credentials at another time, click the 
-Bypass button. The Geoserver will remain configured with the default user name 
-and password, and the main configuration screen will display the "bypassed" 
-status beside the Geoserver settings. You will be able to run Metacat, just as 
-if the settings were configured.
+The default settings are typically appropriate for most Metacat deployments, 
+but if you wish to skip the Geoserver configuration, click the Bypass button. 
+Geoserver (if deployed) will remain with a default configuration and the main 
+Metacat configuration screen will display the "bypassed" status beside the 
+Geoserver settings. You will be able to run Metacat, but maps will not be 
+rendered.
 
 .. figure:: images/screenshots/image031.png
    :align: center
 
-   Resetting the Geoserver password.
+   Configuring Geoserver.
 
 Additional Configuration
 ------------------------
@@ -356,8 +359,8 @@
   <CONTEXT_DIR>/WEB_INF/metacat.properties
 
 Where ``<CONTEXT_DIR>`` is the directory in which the Metacat application code 
-lives (e.g., ``/usr/share/tomcat5.5/webapps/knb``). The path is a combination 
-of the Web application directory (e.g., ``/usr/share/tomcat5.5/webapps/``) and 
+lives (e.g., ``/var/lib/tomcat6/webapps/knb``). The path is a combination 
+of the Web application directory (e.g., ``/var/lib/tomcat6/webapps/``) and 
 the Metacat context directory (e.g., ``knb``). Both values depend upon how your 
 system was set up during installation.
 
@@ -415,7 +418,7 @@
 
   ::
   
-    /etc/init.d/tomcat5.5 restart
+    /etc/init.d/tomcat6 restart
 
 Navigate to Metacat's Configuration utility  and select the Configure Skins 
 option. Your custom skin should appear as a choice in the skins list. Change 
