Index: docs/user/metacatconfigure.html
===================================================================
--- docs/user/metacatconfigure.html	(revision 4714)
+++ docs/user/metacatconfigure.html	(nonexistent)
@@ -1,371 +0,0 @@
-<!-- 
-  *   '$RCSfile$'
-  *     Purpose: web page describing the installation of Metacat
-  *   Copyright: 2008 Regents of the University of California and the
-  *               National Center for Ecological Analysis and Synthesis
-  *     Authors: Chad Berkley
-  *
-  *    '$Author$'
-  *    '$Date$'
-  *    '$Revision$'
-  *
-  *
-  -->
-  
-<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
-<html>
-
-<head>
-  <title>Metacat Configuration Instructions</title>
-  <link rel="stylesheet" type="text/css" href="./common.css">
-  <link rel="stylesheet" type="text/css" href="./default.css">
-</head>
-
-<body>
-
-<table class="tabledefault" width="100%">
-<tr><td rowspan="2"><img src="./images/KNBLogo.gif"></td>
-<td colspan="7">
-<div class="title">Metacat Configuration</div>
-</td>
-</tr>
-<tr>
-  <td><a href="/" class="toollink"> KNB Home </a></td>
-  <td><a href="/data.html" class="toollink"> Data </a></td>
-  <td><a href="/people.html" class="toollink"> People </a></td>
-  <td><a href="/informatics" class="toollink"> Informatics </a></td>
-  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
-  <td><a href="/education" class="toollink"> Education </a></td>
-  <td><a href="/software" class="toollink"> Software </a></td>
-</tr>
-</table>
-<hr>
-
-<div class="header1">Table of Contents</div>
-<div class="toc">
-  <div class="toc1"><a href="#Overview">Overview</a></div>
-      <div class="toc2"><a href="#MetacatConfiguration">Metacat Configuration</a></div> 
-      <div class="toc2"><a href="#ConfigurationRules">Configuration Rules</a></div>
-  <div class="toc1"><a href="#authConfig">Authentication Configuration</a></div>
-      <div class="toc2"><a href="#AuthOverview">Authentication Overview</a></div> 
-      <div class="toc2"><a href="#GetToAuthConfig">Getting to the Authentication Configuration</a></div> 
-      <div class="toc2"><a href="#ConfigAuthNoAuth">Changing Authentication Configuration Without Authentication</a></div>
-  <div class="toc1"><a href="#AdminLogin">Admin Log In</a></div>
-    <div class="toc2"><a href="#AdminLoginOverview">Admin Log In</a></div>
-    <div class="toc2"><a href="#LoggingIn">Logging In</a></div>
-  <div class="toc1"><a href="#MainConfig">Main Configuration Page</a></div>
-    <div class="toc2"><a href="#MainConfigOverview">Main Configuration Overview</a></div>
-  <div class="toc1"><a href="#GlobalConfig">Global Properties Configuration</a></div>
-    <div class="toc2"><a href="#GlobalConfigOverview">Global Properties Overview</a></div>
-    <div class="toc2"><a href="#AutoDetection">Property Auto-Detection</a></div>
-    <div class="toc2"><a href="#GlobalConfigBackup">Global Property Backup</a></div>  
-  <div class="toc1"><a href="#SkinsConfig">Skins Configuration</a></div>  
-    <div class="toc2"><a href="#SkinsConfigOverview">Skins Overview</a></div>
-    <div class="toc2"><a href="#ChoosingDefaultSkin">Choosing a Default Skin</a></div>
-    <div class="toc2"><a href="#ConfigOnlineRegistry">Configuring Online Registry</a></div>
-  <div class="toc1"><a href="#DatabaseConfig">Database Configuration</a></div>
-    <div class="toc2"><a href="#DatabaseConfigOverview">Database Configuration Overview</a></div>
-    <div class="toc2"><a href="#DatabaseNewInstall">New Database Installation</a></div>
-    <div class="toc2"><a href="#DatabaseUpgrade">Database Upgrade</a></div>
-  <div class="toc1"><a href="#GeoserverConfig">Geoserver Configuration</a></div>
-    <div class="toc2"><a href="#GeoserverUpdatePassword">Geoserver Password Update</a></div>
-    <div class="toc2"><a href="#GeoserverManualUpdate">Geoserver Manual Update</a></div>  
-  <div class="toc1"><a href="#CompleteConfig">Complete the Metacat Configuration</a></div>
-</div> 
-
-<a name="Overview"></a><div class="header1">Overview</div>
-<a name="MetacatConfiguration"></a><div class="header2">Metacat Configuration</div>
-  <p>As of version 1.9.0, Metacat configuration is done internally by the application.  When
-  Metacat (Tomcat) is started, it will check to see if it is configured.  If not, you will be 
-  automatically sent to the configuration pages. </p>
-  
-  <p>If the installation is new, or the previous version is before 1.9.0, you will 
-  need to pay close attention to the configuration values.  If you have upgraded 
-  Metacat, and the previous version is 1.9.0 or later, Metacat will pull existing 
-  values from a backup location.  You should still verify that the values are
-  correct.</p>
-  
-  <p>Get to Metacat on your server by entering into the browser:</p>
-  <div class="code">http://&lt;your_context_url&gt;</div>
-  <p>Where &lt;your_context_url&gt is the url where Metacat will be served followed
-  by the name of the war file(application context) that you installed.  For instance, 
-  the KNB production Metacat url is:</p>
-  <div class="code">http://knb.ecoinformatics.org/knb</div>
-  
-  <p>You can always go to the configuration screen from within Metacat by typing:
-  <div class="code">&lt;your_context_url&gt;/admin</div>
-  
-<a name="ConfigurationRules"></a><div class="header2">Configuration Rules</div>   
-  <p>The system will follow these rules in order to determine the order
-  that the configuration will occur:</p>
-  
-  <ul>
-    <li>
-      Is Authentication Configured? If not, show 
-      <a HREF="metacatconfigure.html#auth-config">Authentication Configuration Section</a>.  
-      You will need to have authorizaiton configured in order to define administrative accounts
-      and authenticate as one of these users.
-    </li>
-    <li>
-      Are you logged in as an administrative user?  If not, show 
-      <a HREF="metacatconfigure.html#admin-login">Administrator Login Page</a>.
-      You can only configure Metacat as an administrator.
-    </li>
-    <li>
-      Are main properties, skins or database unconfigured?  If so, show 
-      <a HREF="metacatconfigure.html#main-config">Main Configuration Page</a>
-      Note that you will not be able to select the database configuration utility 
-      until main properties have been configured.
-    </li>  
-    <li>
-      Are all sections configured?  If so, show 
-      <a HREF="metacatconfigure.html#main-config">Main Configuration Page</a> which
-      include instructions for going to Metacat server (or restarting Metacat if you 
-      are reconfiguring a running server).
-    </li> 
-  </ul>
-  
-  <p> See the following sections for descriptions of how each of these work.  For more
-  information on each field, click on the blue question mark icon to the right.</p>
-
-<a name="AuthConfig"></a><div class="header1">Authentication Configuration</div>
-<a name="AuthOverview"></a><div class="header2">Authentication Overview</div>
-  <p>Metacat uses LDAP as it's primary authentication mechanism, but you can define
-  your own mechanism by creating a java class that implements 
-  AuthInterface. The configuration values needed are Authentication Class, Authentication URL, 
-  Authentication Secure URL and Metacat Administrators.  You need 
-  to verify that the the Authentication URL and Authentication Secure URL are correct (fig 1).  
-  <span class="emphasis">You need to make sure that your user 
-  account is entered into the Metacat Administrators field.  You will not be allowed
-  to continue with configuration if this is missing.</span>
-
-  <img class="screenshot" src="./images/auth-config.png"/>
-  <div class="fig-text"> fig 1 </div>
-
-<a name="GetToAdminConfig"></a><div class="header2">Getting to the Authentication Configuration</div>
-  <p>You will automatically be sent to the Authentication Configuration page if this is a new
-  installation or upgrade.</p>
-  
-  <p>You can also get to the Administrative configuration from a running Metacat by typing:</p>
-  <div class="code">&lt;your_context_url&gt;/admin</div>
-  <p>You will be required to log in as an administrator and restart Metacat once you
-  make changes.</p>
-  
-  <a name="ConfigAuthNoAuth"></a><div class="header2">Changing Authentication Configuration Without Authentication</div>
-  <p>There is one exception to the log in rule.  That is when you need to change or add 
-  authentication information, but you can't authenticate using the existing setup.  For example:</p>
-  
-  <ul>
-    <li>The existing Metacat administrator is no longer available</li>
-    <li>You forgot the administrator password.</li>
-    <li>The configured authentication urls are unavailable and you need to configure new ones.</li>  
-  </ul>
-  
-  <p>In this case, you will need to edit the Metacat configuration file by hand and
-  make the changes.  This insures that only a person who has access to the Metacat
-  server and the configuration files on that server will be able to change the
-  administrator accounts</p>
-
-  <p>Stop Tomcat and edit the Metacat properties file at:</p>
-  <div class="code">&lt;webapp_dir&gt;/&lt;context_dir&gt;/WEB-INF/metacat.properties</div>
-  <p>where &lt;webapp_dir&gt; is the place that Tomcat looks for applications and 
-  &lt;context_dir&gt; is the name of the Metacat application (usually knb).  Change the 
-  following properties appropriately:</p>
-  
-  <ul>
-    <li>auth.administrators - a colon separated list of administrators</li>
-    <li>auth.url - the authenication server url</li>
-    <li>auth.surl - the authentication secure server url</li>  
-  </ul>
-  
-  <p>Save the metacat.properties file and start Tomcat.</p>
-  
-<a name="AdminLogin"></a><div class="header1">Admin Log In</div>
-<a name="AdminLoginOverview"></a><div class="header2">Admin Log In Overview</div>
-  <p>Once authentication has been configured, you will be required to login as an 
-  administrative user if you haven't already.  You will be taken to 
-  the administrator login screen (fig 2).  You can also get to the login
-  screen by choosing the "log in as different user" link at the bottom of
-  any configuration screen.</p>
-  
-  <img class="screenshot" src="./images/admin-login.png"/>
-  <div class="fig-text"> fig 2 </div>
-
-<a name="LoggingIn"></a><div class="header2">Logging In</div>
-<p>You need to log in with an account that was configured as an administrative
-user in the authentication configuration section.  If you did not set up the correct user 
-there, you will need to go through the 
-<a href="#ConfigAuthNoAuth">Changing Authentication Configuration Without Authentication</a>
-instructions to set up the user.</p>
-
-<p>Enter your user name.  This is one of the Metacat administrators that you 
-entered in authenticationuthentication configuration.  Enter your password and
-hit the "Login" button.  You should successfully log in.</p>
-
-<a name="MainConfig"></a><div class="header1">Main Configuration Page</div>
-<a name="MainConfigOverview"></a><div class="header2">Main Configuration Overview</div>
-  <p>The main configuration screen acts as a gateway into individual configuration
-  sections (fig 3).  You should see that the authentication is already configured.</p>  
-  
-  <p>Each section is listed with a status to the left which can be one of:</p>
-  <ul>
-    <li><font color="red">[unconfigured]</font> - the section has yet to be configured</li>
-    <li><font color="green">[configured]</font> - the section has been configured</li>
-    <li>
-      <font color="green">[bypassed]</font> - this is currently only used for Geoserver 
-      configuration.  The administrator can choose not to configure the Geoserver user/password.
-      In essence, the bypass status acts like the configured status.
-    </li>  
-  </ul>
-  
-  <p>To the right of each section is an option which can be one of:
-  <ul>
-    <li>Configure Now - click on this link to configure that section</li>
-    <li>Reconfigure Now - the section was already configured, but you can choose to reconfigure it.</li>
-    <li>
-      Configure Global Properties First - this section has a dependency on the global
-      properties section.  Once global properties is configured, the option to configure
-      this section should become available.
-    </li>  
-    <li>Version: X.X.X - this is used for the Database Installation/Upgrade section.  The system
-      detects the database schema version.  If that version is the same as the application version,
-      that version will be displayed (i.e. 1.9.0) and no further database configuration is
-      required.
-    </li>
-  </ul>
-  
-  <p>All sections must be in a configured or bypassed state in order to run Metacat.</p>
-  
-  <img class="screenshot" src="./images/main-config.png"/>
-  <div class="fig-text"> fig 3 </div>
-  
-<a name="GlobalConfig"></a><div class="header1">Global Properties Configuration</div>
-<a name="GlobalConfigOverview"></a><div class="header2">Global Properties Overview</div>
-  <p>Metacat global properties are the bulk of the core properties needed to run Metacat 
-  (fig 4).  For detailed instructions on setting these properties, refer to the blue 
-  question mark icon to the right of each property.  Be sure that each of these are set
-  appropriately.</p>
-  
-  <img class="screenshot" src="./images/global-config.png"/>
-  <div class="fig-text"> fig 4 </div>
-
-<a name="AutoDetection"></a><div class="header2">Property Auto-Detection</div> 
-   <p>The first time you install Metacat, the system will attempt to auto-detect
-   some values.  These are:</p>
-   
-  <ul>
-    <li>Metacat Context - Name of the context under which Metacat will run. This is the name 
-        of the Metacat war file that was deployed (minus the .war extension).</li>
-    <li>Server Name - The DNS name of the server where Metacat will be available, not including
-        port numbers or the http:// header.</li>
-    <li>HTTP Port - The non-secure port where Metacat will be available. </li>  
-    <li>HTTP SSL Port - The secure port where Metacat will be available.</li>
-    <li>Deploy Location - The directory where the application is deployed.</li>
-  </ul>
-  
-  <p>You should be extra careful that these were detected correctly.</p>
-  
-<a name="GlobalConfigBackup"></a><div class="header2">Global Property Backup</div>
-  <p>When you save global properties, they are saved in a backup file that is 
-  located in the following directory on linux:</p>
-  <div class="code">/var/metacat/.metacat</div>
-  and on windows:
-  <div class="code">C:\Program Files\metacat\.metacat</div>
-  <p>When you update Metacat, the system will look for these backed up properties
-  so you won't have to re-enter all the information from previous installs.</p>
-  
-<a name="SkinsConfig"></a><div class="header1">Skins Configuration</div>
-<a name="SkinsConfigOverview"></a><div class="header2">Skins Overview</div>
-  <p>Metacat allows for a customized look and feel for the Metacat front end and for the 
-  online data registry services.  There are two major functions provided by the
-  skins configuration.  The first is to choose which skin will be the default.  The
-  second will be to configure the look and feel of the online data registry pages.  For
-  more information on the online data registry option, refer to the 
-  <a href="./registry_installation.html">Metacat Registry Installation</a> documentation.</p>
-  
-  <p>Note that if you are not using the online registry, and you don't have a custom skin,
-  you can just save the default skins configuration and move on to the next configuration
-  section.</p>
-  
-<a name="ChoosingDefaultSkin"></a><div class="header2">Choosing a Default Skin</div> 
-  <p>There are several skins available to choose from in Metacat (fig 5).  If you have a 
-  skin that has been developed specifically for your instance of Metacat, you should
-  select the checkbox next to that skin.  When you do, the form will open up with 
-  several options for that skin (fig 6).  choose the 'Make "skin_name" default" radio selection.
-  You should see "(default)" appear next to that skin name.  Save the configuration
-  and that skin will be the one that appears when users visit your Metacat site.  Note
-  that if you do not have a custom skin, you should leave your skin as the "default" skin.</p>
-  
-  <img class="screenshot" src="./images/skins-config.png"/>
-  <div class="fig-text"> fig 5 </div>  
-
-<a name="ConfigOnlineRegistry"></a><div class="header2">Configuring Online Registry</div> 
-  <p>The online registry code provides a web interface for entering data into Metacat.  The
-  screens are somewhat configurable as far as which fields show up and which are required.
-  You should select each for which you want to activate the registry and then select the
-  appropriate fields for that skin.</p> 
-   
-  <img class="screenshot" src="./images/skins-config-2.png"/>
-  <div class="fig-text"> fig 6 </div>  
-  
-<a name="DatabaseConfig"></a><div class="header1">Database Configuration</div>
-<a name="DatabaseConfigOverview"></a><div class="header2">Database Configuration Overview</div>
-  <p>Metacat will detect the schema version of your database, and upgrade it if necessary.  Once the
-  global Metacat properties have been configured, the Database Installation/Upgrade link 
-  will become active on the main Metacat configuration page (see fig 3).</p>
-
-<a name="DatabaseNewInstall"></a><div class="header2">New Database Installation</div>
-  <p>If this is a installation of Metacat, the database install/upgrade utility will
-  inform you of this (fig 7).  It will list the sql scripts that will get run in order
-  to create a database schema for the version of Metacat that you are installing.  If
-  there is any question as to whether the database is new, you should choose to cancel.
-  When you choose to continue, the server will run the scripts you saw earlier.</p>
-  <img class="screenshot" src="./images/database-config.png"/>
-  <div class="fig-text"> fig 7 </div> 
- 
-<a name="DatabaseUpgrade"></a><div class="header2">Database Upgrade</div> 
-  <p>If this is an upgrade of Metacat, the database install/upgrade utility will
-  inform you of the current version of the database (fig 7).  It will list the sql scripts 
-  that will get run in order to update the database schema to the upgraded version of 
-  Metacat.  If there is any question as to whether the detected database schema version is 
-  correct, you should choose to cancel. When you choose to continue, the server will run 
-  the scripts you saw earlier.</p>
-  <img class="screenshot" src="./images/database-config-2.png"/>
-  <div class="fig-text"> fig 8 </div> 
- 
-<a name="GeoserverConfig"></a><div class="header1">Geoserver Configuration</div>
-<a name="GeoserverOverview"></a><div class="header2">Geoserver Configuration Overview</div> 
-  <p>Metacat comes bundled with a Web Mapping Service called Geoserver which 
-  converts spatial data into web-deliverable map images.  For more information, see the
-  <a href="./spatial_option.html">Metacat Spatial Option documentation</a>.  Geoserver 
-  installs with a default admin username and password.  You should change these so that
-  only local administrators can make changes to Geoserver.</p>
-<a name="GeoserverUpdatePassword"></a><div class="header2">Geoserver Password Update</div>
-  <p>When you choose the Geoserver Configuration link on the main configuratio page, you
-  will go to a page that will prompt you for a user name and password (fig 9).  When you 
-  enter a user name and password, the metacat server will contact the embedded Geoserver
-  server and change the login credentails.</p>
-  <p>You also have the option of choosing "bypass".  This will leave Geoserver configured
-  with the default user name and password.  The main configuration screen will show the 
-  bypassed status.  The system will interpret the bypassed status the same as the configured
-  status.</p>
-  <img class="screenshot" src="./images/geoserver-config.png"/>
-  <div class="fig-text"> fig 9 </div> 
-<a name="GeoserverManualUpdate"></a><div class="header2">Geoserver Manual Update</div>
-  <p>You also have the option of changeing the Geoserver username and password by logging
-  in directly to the Geoserver.  For more information on changing the credentials directly,
-  refer to the <a href="./geoserver-manual-configure.html">Geoserver Password Change documentation</a>.
-  Note that once you change the credentails manually, you will not be able to use the 
-  Metacat admin tool to change it again (until a new Metacat Upgrade or installation).
-<a name="CompleteConfig"></a><div class="header1">Complete the Metacat Configuration</div>  
-  At this point, all the sections of the main configuration should be in a configured or
-  bypassed state (fig 10).  If you are configuring because of a Metacat install or upgrade,
-  you will have the option to click on the "go to metacat" link and you should get taken
-  directly to the running version of Metacat.  Note that this may take some time depending
-  on the amount of data in your database, since Metacat goes through an indexing process
-  at start-up time.</p>
-  
-  <p>If you are reconfiguring an already running version of Metacat, you will not have the
-  option to go directly back to Metacat.  You will need to restart the server (Tomcat).</p>
-  <img class="screenshot" src="./images/main-config-2.png"/>
-  <div class="fig-text"> fig 10 </div> 
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Index: docs/dev/building-metacat.html
===================================================================
--- docs/dev/building-metacat.html	(revision 4714)
+++ docs/dev/building-metacat.html	(revision 4715)
@@ -65,7 +65,7 @@
   <li>build.tomcat.dir - Metacat will look for some HttpServlet libraries in the local
   Tomcat directories.  Make sure this value is set to your local Tomcat installation 
   directory.</li>
-  <li>dev.deploy.dir - the automated development build (dev-install) will deploy your
+  <li>app.deploy.dir - the automated installation build (install) will deploy your
   war file for you and clean up old application directories.  Make sure this is set
   to the directory where Tomcat looks for its applications.</li>
   <li>cvsroot - if your cvs user is different than the user you are using to build metacat, 
@@ -113,15 +113,16 @@
   </ul>
   
   <a name="AutomatedBuild"></a><div class="header1">Automated Build</div>
-  <p>There is an ant target called "dev-install" that was created specifically for
-  local develoment building and deploying.  What it does is:
+  <p>The ant "install" target controls deploying Metacat locally.  This can be 
+  used for source distributions or code that was checked out of the repository.
+  What is does is:</p>
   <ul>
   <li>Builds the Metacat project, resulting in a war file.</li>
-  <li>Moves the war file to the dev.deploy.dir that you set in build.properties</li>
-  <li>Removes the existing application directory from the dev.deploy.dir.</li>
+  <li>Moves the war file to the app.deploy.dir that you set in build.properties</li>
+  <li>Removes the existing application directory from the app.deploy.dir.</li>
   </ul>
   Typical usage would be something like:</p>
-  <div class="code">ant fullclean dev-install</div>
+  <div class="code">ant fullclean install</div>
   
   <a name="ManualBuild"></a><div class="header1">Manual Build</div>  
   <p>You can also build the Metacat war file and deploy manually.  To build and create the 
Index: docs/user/properties.html
===================================================================
--- docs/user/properties.html	(revision 4714)
+++ docs/user/properties.html	(revision 4715)
@@ -34,7 +34,7 @@
   </p>  
    
   <p> 
-     The most dynamic properties are modified using the internal <a href="./metacatconfigure.html">Metacat configuration utility </a>.
+     The most dynamic properties are modified using the internal <a href="./metacat-configure.html">Metacat configuration utility </a>.
      However, it may be necessary to manually edit a configuration file to update more static values.
   </p>   
    
@@ -48,7 +48,7 @@
        <li> <b>Set Method</b> - how does the value get set in the properties file.  There are
          two options:
          <ul>
-           <li> Configuration Utility - the value is set via the internal <a href="./metacatconfigure.html">Metacat configuration utility </a></li>
+           <li> Configuration Utility - the value is set via the internal <a href="./metacat-configure.html">Metacat configuration utility </a></li>
            <li> Manually - the value is set to a default that can only be changed by manually editing the configuration file. </li>
          </ul>  
        <li> <b>Example</b> - an example setting for the property.</li>
Index: docs/user/metacat-configure.html
===================================================================
--- docs/user/metacat-configure.html	(nonexistent)
+++ docs/user/metacat-configure.html	(revision 4715)
@@ -0,0 +1,411 @@
+<!-- 
+  *   '$RCSfile$'
+  *     Purpose: web page describing the installation of Metacat
+  *   Copyright: 2008 Regents of the University of California and the
+  *               National Center for Ecological Analysis and Synthesis
+  *     Authors: Chad Berkley
+  *
+  *    '$Author$'
+  *    '$Date$'
+  *    '$Revision$'
+  *
+  *
+  -->
+  
+<!DOCTYPE html PUBLIC "-//W3C//DTD html 4.0//EN">
+<html>
+
+<head>
+  <title>Metacat Configuration Instructions</title>
+  <link rel="stylesheet" type="text/css" href="./common.css">
+  <link rel="stylesheet" type="text/css" href="./default.css">
+</head>
+
+<body>
+
+<table class="tabledefault" width="100%">
+<tr><td rowspan="2"><img src="./images/KNBLogo.gif"></td>
+<td colspan="7">
+<div class="title">Metacat Configuration</div>
+</td>
+</tr>
+<tr>
+  <td><a href="/" class="toollink"> KNB Home </a></td>
+  <td><a href="/data.html" class="toollink"> Data </a></td>
+  <td><a href="/people.html" class="toollink"> People </a></td>
+  <td><a href="/informatics" class="toollink"> Informatics </a></td>
+  <td><a href="/biodiversity" class="toollink"> Biocomplexity </a></td>
+  <td><a href="/education" class="toollink"> Education </a></td>
+  <td><a href="/software" class="toollink"> Software </a></td>
+</tr>
+</table>
+<hr>
+
+<div class="header1">Table of Contents</div>
+<div class="toc">
+  <div class="toc1"><a href="#Overview">Overview</a></div>
+      <div class="toc2"><a href="#MetacatConfiguration">Metacat Configuration</a></div> 
+      <div class="toc2"><a href="#ConfigurationRules">Configuration Rules</a></div>
+  <div class="toc1"><a href="#authConfig">Authentication Configuration</a></div>
+      <div class="toc2"><a href="#AuthOverview">Authentication Overview</a></div> 
+      <div class="toc2"><a href="#GetToAuthConfig">Getting to the Authentication Configuration</a></div> 
+      <div class="toc2"><a href="#ConfigAuthNoAuth">Changing Authentication Configuration Without Authentication</a></div>
+  <div class="toc1"><a href="#AdminLogin">Admin Log In</a></div>
+    <div class="toc2"><a href="#AdminLoginOverview">Admin Log In</a></div>
+    <div class="toc2"><a href="#LoggingIn">Logging In</a></div>
+  <div class="toc1"><a href="#MainConfig">Main Configuration Page</a></div>
+    <div class="toc2"><a href="#MainConfigOverview">Main Configuration Overview</a></div>
+  <div class="toc1"><a href="#GlobalConfig">Global Properties Configuration</a></div>
+    <div class="toc2"><a href="#GlobalConfigOverview">Global Properties Overview</a></div>
+    <div class="toc2"><a href="#AutoDetection">Property Auto-Detection</a></div>
+    <div class="toc2"><a href="#GlobalConfigBackup">Global Property Backup</a></div>  
+  <div class="toc1"><a href="#SkinsConfig">Skins Configuration</a></div>  
+    <div class="toc2"><a href="#SkinsConfigOverview">Skins Overview</a></div>
+    <div class="toc2"><a href="#ChoosingDefaultSkin">Choosing a Default Skin</a></div>
+    <div class="toc2"><a href="#ConfigOnlineRegistry">Configuring Online Registry</a></div>
+  <div class="toc1"><a href="#DatabaseConfig">Database Configuration</a></div>
+    <div class="toc2"><a href="#DatabaseConfigOverview">Database Configuration Overview</a></div>
+    <div class="toc2"><a href="#DatabaseNewInstall">New Database Installation</a></div>
+    <div class="toc2"><a href="#DatabaseUpgrade">Database Upgrade</a></div>
+  <div class="toc1"><a href="#GeoserverConfig">Geoserver Configuration</a></div>
+    <div class="toc2"><a href="#GeoserverUpdatePassword">Geoserver Password Update</a></div>
+    <div class="toc2"><a href="#GeoserverManualUpdate">Geoserver Manual Update</a></div>  
+  <div class="toc1"><a href="#CompleteConfig">Complete the Metacat Configuration</a></div>
+</div> 
+
+<a name="Overview"></a><div class="header1">Overview</div>
+<a name="MetacatConfiguration"></a><div class="header2">Metacat Configuration</div>
+  <p>As of version 1.9.0, Metacat configuration is done internally by the application.  When
+  Metacat (Tomcat) is started, it will check to see if it is configured.  If not, you will be 
+  automatically sent to the configuration pages. </p>
+  
+  <p>If the installation is new, or the previous version is before 1.9.0, you will 
+  need to pay close attention to the configuration values.  If you have upgraded 
+  Metacat, and the previous version is 1.9.0 or later, Metacat will pull existing 
+  values from a backup location.  You should still verify that the values are
+  correct.</p>
+  
+  <p>Get to Metacat on your server by entering into the browser:</p>
+  <div class="code">http://&lt;your_context_url&gt;</div>
+  <p>Where &lt;your_context_url&gt is the url where Metacat will be served followed
+  by the name of the war file(application context) that you installed.  For instance, 
+  the KNB production Metacat url is:</p>
+  <div class="code">http://knb.ecoinformatics.org/knb</div>
+  
+  <p>You can always go to the configuration screen from within Metacat by typing:
+  <div class="code">&lt;your_context_url&gt;/admin</div>
+  
+<a name="ConfigurationRules"></a><div class="header2">Configuration Rules</div>   
+  <p>The system will follow these rules in order to determine the order
+  that the configuration will occur:</p>
+  
+  <ul>
+    <li>
+      Always prompt the user for the backup directories with the  
+      <a HREF="#BackupConfig">Backup Configuration Section</a>.  
+      You will need to have backup directories configured in order 
+      to continue with configuration.
+    </li>
+    <li>
+      Is Authentication Configured? If not, show 
+      <a HREF="#AuthConfig">Authentication Configuration Section</a>.  
+      You will need to have authorizaiton configured in order to define administrative accounts
+      and authenticate as one of these users.
+    </li>
+    <li>
+      Are you logged in as an administrative user?  If not, show 
+      <a HREF="#AdminLogin">Administrator Login Page</a>.
+      You can only configure Metacat as an administrator.
+    </li>
+    <li>
+      Are main properties, skins or database unconfigured?  If so, show 
+      <a HREF="#MainConfig">Main Configuration Page</a>
+      Note that you will not be able to select the database configuration utility 
+      until main properties have been configured.
+    </li>  
+    <li>
+      Are all sections configured?  If so, show 
+      <a HREF="#MainConfig">Main Configuration Page</a> which
+      include instructions for going to Metacat server (or restarting Metacat if you 
+      are reconfiguring a running server).
+    </li> 
+  </ul>
+  
+  <p> See the following sections for descriptions of how each of these work.  For more
+  information on each field, click on the blue question mark icon to the right.</p>
+
+<a name="BackupConfig"></a><div class="header1">Backup Configuration</div>
+  <a name="BackupOverview"></a><div class="header2">Backup Overview</div>
+  <p>Metacat backs up all configured values to a directory outside the application
+  installation directories.  This is so that we can preserve the configuration even
+  after you upgrade Metacat (and the application directories get removed).</p>
+  
+  <p>Since a new installation/upgrade won't know where this external directory is, it will
+  go through a discovery algorithm to give a best guess and pre-populate this value on the 
+  Backup Directory Configuration screen (see fig 1).  The algorithm is:
+  
+  <ul>
+  <li>Look for a saved backup location file in the user home dir - Is there a file named 
+    &lt;user_home&gt;/.metacat/backup-location for the user that started tomcat? if so, does 
+    it contain a single line which is a readable directory?  This directory was the backup 
+    directory used during a previous install.  Return that directory.</li>
+  <li>Look for an existing hidden (.metacat) directory in a default system directory.  Get 
+   the default base directory for the OS.  (See application.windowsBackupBaseDir and 
+   application.linuxBackupBaseDir in metacat.properties.)  If a directory called 
+   &lt;base_dir&gt;/metacat/.metacat exists, return &lt;base_dir&gt;/metacat.</li>
+  <li> Look for an existing hidden (.metacat) directory in the user directory. If a directory 
+    called &lt;user_home&gt;/.metacat exists for the user that started tomcat, return &lt;user_home&gt;.</li>
+  <li> Is the &lt;base_dir&gt; writable by the user that started tomcat?  If so, return &lt;base_dir&gt;</li>
+  <li> Does the &lt;user_home&gt; exist?  If so, return &lt;user_home&gt;</li>
+  <li> Otherwise, return null </li>
+  </ul>
+  <img class="screenshot" src="./images/backup-config.png"/>
+  <div class="fig-text"> fig 1 </div>  
+
+  <a name="ConfigBackup"></a><div class="header2">Configure Backup</div>
+  <p>If the pre-populated value is incorrect, you should change it to the correct
+  directory</p> 
+
+<a name="AuthConfig"></a><div class="header1">Authentication Configuration</div>
+  <a name="AuthOverview"></a><div class="header2">Authentication Overview</div>
+  <p>Metacat uses LDAP as it's primary authentication mechanism, but you can define
+  your own mechanism by creating a java class that implements 
+  AuthInterface. The configuration values needed are Authentication Class, Authentication URL, 
+  Authentication Secure URL and Metacat Administrators.  You need 
+  to verify that the the Authentication URL and Authentication Secure URL are correct (fig 2).  
+  <span class="emphasis">You need to make sure that your user 
+  account is entered into the Metacat Administrators field.  You will not be allowed
+  to continue with configuration if this is missing.</span>
+
+  <img class="screenshot" src="./images/auth-config.png"/>
+  <div class="fig-text"> fig 2 </div>
+
+<a name="GetToAdminConfig"></a><div class="header2">Getting to the Authentication Configuration</div>
+  <p>You will automatically be sent to the Authentication Configuration page if this is a new
+  installation or upgrade.</p>
+  
+  <p>You can also get to the Administrative configuration from a running Metacat by typing:</p>
+  <div class="code">&lt;your_context_url&gt;/admin</div>
+  <p>You will be required to log in as an administrator and restart Metacat once you
+  make changes.</p>
+  
+  <a name="ConfigAuthNoAuth"></a><div class="header2">Changing Authentication Configuration Without Authentication</div>
+  <p>There is one exception to the log in rule.  That is when you need to change or add 
+  authentication information, but you can't authenticate using the existing setup.  For example:</p>
+  
+  <ul>
+    <li>The existing Metacat administrator is no longer available</li>
+    <li>You forgot the administrator password.</li>
+    <li>The configured authentication urls are unavailable and you need to configure new ones.</li>  
+  </ul>
+  
+  <p>In this case, you will need to edit the Metacat configuration file by hand and
+  make the changes.  This insures that only a person who has access to the Metacat
+  server and the configuration files on that server will be able to change the
+  administrator accounts</p>
+
+  <p>Stop Tomcat and edit the Metacat properties file at:</p>
+  <div class="code">&lt;webapp_dir&gt;/&lt;context_dir&gt;/WEB-INF/metacat.properties</div>
+  <p>where &lt;webapp_dir&gt; is the place that Tomcat looks for applications and 
+  &lt;context_dir&gt; is the name of the Metacat application (usually knb).  Change the 
+  following properties appropriately:</p>
+  
+  <ul>
+    <li>auth.administrators - a colon separated list of administrators</li>
+    <li>auth.url - the authenication server url</li>
+    <li>auth.surl - the authentication secure server url</li>  
+  </ul>
+  
+  <p>Save the metacat.properties file and start Tomcat.</p>
+  
+<a name="AdminLogin"></a><div class="header1">Admin Log In</div>
+<a name="AdminLoginOverview"></a><div class="header2">Admin Log In Overview</div>
+  <p>Once authentication has been configured, you will be required to login as an 
+  administrative user if you haven't already.  You will be taken to 
+  the administrator login screen (fig 2).  You can also get to the login
+  screen by choosing the "log in as different user" link at the bottom of
+  any configuration screen.</p>
+  
+  <img class="screenshot" src="./images/admin-login.png"/>
+  <div class="fig-text"> fig 3 </div>
+
+<a name="LoggingIn"></a><div class="header2">Logging In</div>
+<p>You need to log in with an account that was configured as an administrative
+user in the authentication configuration section.  If you did not set up the correct user 
+there, you will need to go through the 
+<a href="#ConfigAuthNoAuth">Changing Authentication Configuration Without Authentication</a>
+instructions to set up the user.</p>
+
+<p>Enter your user name.  This is one of the Metacat administrators that you 
+entered in authenticationuthentication configuration.  Enter your password and
+hit the "Login" button.  You should successfully log in.</p>
+
+<a name="MainConfig"></a><div class="header1">Main Configuration Page</div>
+<a name="MainConfigOverview"></a><div class="header2">Main Configuration Overview</div>
+  <p>The main configuration screen acts as a gateway into individual configuration
+  sections (fig 4).  You should see that the authentication is already configured.</p>  
+  
+  <p>Each section is listed with a status to the left which can be one of:</p>
+  <ul>
+    <li><font color="red">[unconfigured]</font> - the section has yet to be configured</li>
+    <li><font color="green">[configured]</font> - the section has been configured</li>
+    <li>
+      <font color="green">[bypassed]</font> - this is currently only used for Geoserver 
+      configuration.  The administrator can choose not to configure the Geoserver user/password.
+      In essence, the bypass status acts like the configured status.
+    </li>  
+  </ul>
+  
+  <p>To the right of each section is an option which can be one of:
+  <ul>
+    <li>Configure Now - click on this link to configure that section</li>
+    <li>Reconfigure Now - the section was already configured, but you can choose to reconfigure it.</li>
+    <li>
+      Configure Global Properties First - this section has a dependency on the global
+      properties section.  Once global properties is configured, the option to configure
+      this section should become available.
+    </li>  
+    <li>Version: X.X.X - this is used for the Database Installation/Upgrade section.  The system
+      detects the database schema version.  If that version is the same as the application version,
+      that version will be displayed (i.e. 1.9.0) and no further database configuration is
+      required.
+    </li>
+  </ul>
+  
+  <p>All sections must be in a configured or bypassed state in order to run Metacat.</p>
+  
+  <img class="screenshot" src="./images/main-config.png"/>
+  <div class="fig-text"> fig 4 </div>
+  
+<a name="GlobalConfig"></a><div class="header1">Global Properties Configuration</div>
+<a name="GlobalConfigOverview"></a><div class="header2">Global Properties Overview</div>
+  <p>Metacat global properties are the bulk of the core properties needed to run Metacat 
+  (fig 5).  For detailed instructions on setting these properties, refer to the blue 
+  question mark icon to the right of each property.  Be sure that each of these are set
+  appropriately.</p>
+  
+  <img class="screenshot" src="./images/global-config.png"/>
+  <div class="fig-text"> fig 5 </div>
+
+<a name="AutoDetection"></a><div class="header2">Property Auto-Detection</div> 
+   <p>The first time you install Metacat, the system will attempt to auto-detect
+   some values.  These are:</p>
+   
+  <ul>
+    <li>Metacat Context - Name of the context under which Metacat will run. This is the name 
+        of the Metacat war file that was deployed (minus the .war extension).</li>
+    <li>Server Name - The DNS name of the server where Metacat will be available, not including
+        port numbers or the http:// header.</li>
+    <li>HTTP Port - The non-secure port where Metacat will be available. </li>  
+    <li>HTTP SSL Port - The secure port where Metacat will be available.</li>
+    <li>Deploy Location - The directory where the application is deployed.</li>
+  </ul>
+  
+  <p>You should be extra careful that these were detected correctly.</p>
+  
+<a name="GlobalConfigBackup"></a><div class="header2">Global Property Backup</div>
+  <p>When you save global properties, they are saved in a backup file that is 
+  located in the following directory on linux:</p>
+  <div class="code">/var/metacat/.metacat</div>
+  and on windows:
+  <div class="code">C:\Program Files\metacat\.metacat</div>
+  <p>When you update Metacat, the system will look for these backed up properties
+  so you won't have to re-enter all the information from previous installs.</p>
+  
+<a name="SkinsConfig"></a><div class="header1">Skins Configuration</div>
+<a name="SkinsConfigOverview"></a><div class="header2">Skins Overview</div>
+  <p>Metacat allows for a customized look and feel for the Metacat front end and for the 
+  online data registry services.  There are two major functions provided by the
+  skins configuration.  The first is to choose which skin will be the default.  The
+  second will be to configure the look and feel of the online data registry pages.  For
+  more information on the online data registry option, refer to the 
+  <a href="./registry_installation.html">Metacat Registry Installation</a> documentation.</p>
+  
+  <p>Note that if you are not using the online registry, and you don't have a custom skin,
+  you can just save the default skins configuration and move on to the next configuration
+  section.</p>
+  
+<a name="ChoosingDefaultSkin"></a><div class="header2">Choosing a Default Skin</div> 
+  <p>There are several skins available to choose from in Metacat (fig 6).  If you have a 
+  skin that has been developed specifically for your instance of Metacat, you should
+  select the checkbox next to that skin.  When you do, the form will open up with 
+  several options for that skin (fig 6).  choose the 'Make "skin_name" default" radio selection.
+  You should see "(default)" appear next to that skin name.  Save the configuration
+  and that skin will be the one that appears when users visit your Metacat site.  Note
+  that if you do not have a custom skin, you should leave your skin as the "default" skin.</p>
+  
+  <img class="screenshot" src="./images/skins-config.png"/>
+  <div class="fig-text"> fig 6 </div>  
+
+<a name="ConfigOnlineRegistry"></a><div class="header2">Configuring Online Registry</div> 
+  <p>The online registry code provides a web interface for entering data into Metacat.  The
+  screens are somewhat configurable as far as which fields show up and which are required.
+  You should select each for which you want to activate the registry and then select the
+  appropriate fields for that skin.</p> 
+   
+  <img class="screenshot" src="./images/skins-config-2.png"/>
+  <div class="fig-text"> fig 7 </div>  
+  
+<a name="DatabaseConfig"></a><div class="header1">Database Configuration</div>
+<a name="DatabaseConfigOverview"></a><div class="header2">Database Configuration Overview</div>
+  <p>Metacat will detect the schema version of your database, and upgrade it if necessary.  Once the
+  global Metacat properties have been configured, the Database Installation/Upgrade link 
+  will become active on the main Metacat configuration page (see fig 4).</p>
+
+<a name="DatabaseNewInstall"></a><div class="header2">New Database Installation</div>
+  <p>If this is a installation of Metacat, the database install/upgrade utility will
+  inform you of this (fig 8).  It will list the sql scripts that will get run in order
+  to create a database schema for the version of Metacat that you are installing.  If
+  there is any question as to whether the database is new, you should choose to cancel.
+  When you choose to continue, the server will run the scripts you saw earlier.</p>
+  <img class="screenshot" src="./images/database-config.png"/>
+  <div class="fig-text"> fig 8 </div> 
+ 
+<a name="DatabaseUpgrade"></a><div class="header2">Database Upgrade</div> 
+  <p>If this is an upgrade of Metacat, the database install/upgrade utility will
+  inform you of the current version of the database (fig 9).  It will list the sql scripts 
+  that will get run in order to update the database schema to the upgraded version of 
+  Metacat.  If there is any question as to whether the detected database schema version is 
+  correct, you should choose to cancel. When you choose to continue, the server will run 
+  the scripts you saw earlier.</p>
+  <img class="screenshot" src="./images/database-config-2.png"/>
+  <div class="fig-text"> fig 9 </div> 
+ 
+<a name="GeoserverConfig"></a><div class="header1">Geoserver Configuration</div>
+<a name="GeoserverOverview"></a><div class="header2">Geoserver Configuration Overview</div> 
+  <p>Metacat comes bundled with a Web Mapping Service called Geoserver which 
+  converts spatial data into web-deliverable map images.  For more information, see the
+  <a href="./spatial_option.html">Metacat Spatial Option documentation</a>.  Geoserver 
+  installs with a default admin username and password.  You should change these so that
+  only local administrators can make changes to Geoserver.</p>
+<a name="GeoserverUpdatePassword"></a><div class="header2">Geoserver Password Update</div>
+  <p>When you choose the Geoserver Configuration link on the main configuratio page, you
+  will go to a page that will prompt you for a user name and password (fig 10).  When you 
+  enter a user name and password, the metacat server will contact the embedded Geoserver
+  server and change the login credentails.</p>
+  <p>You also have the option of choosing "bypass".  This will leave Geoserver configured
+  with the default user name and password.  The main configuration screen will show the 
+  bypassed status.  The system will interpret the bypassed status the same as the configured
+  status.</p>
+  
+  <img class="screenshot" src="./images/geoserver-config.png"/>
+  <div class="fig-text"> fig 10 </div> 
+  
+<a name="GeoserverManualUpdate"></a><div class="header2">Geoserver Manual Update</div>
+  <p>You also have the option of changeing the Geoserver username and password by logging
+  in directly to the Geoserver.  For more information on changing the credentials directly,
+  refer to the <a href="./geoserver-manual-configure.html">Geoserver Password Change documentation</a>.
+  Note that once you change the credentails manually, you will not be able to use the 
+  Metacat admin tool to change it again (until a new Metacat Upgrade or installation).
+<a name="CompleteConfig"></a><div class="header1">Complete the Metacat Configuration</div>  
+  At this point, all the sections of the main configuration should be in a configured or
+  bypassed state (fig 11).  If you are configuring because of a Metacat install or upgrade,
+  you will have the option to click on the "go to metacat" link and you should get taken
+  directly to the running version of Metacat.  Note that this may take some time depending
+  on the amount of data in your database, since Metacat goes through an indexing process
+  at start-up time.</p>
+  
+  <p>If you are reconfiguring an already running version of Metacat, you will not have the
+  option to go directly back to Metacat.  You will need to restart the server (Tomcat).</p>
+  <img class="screenshot" src="./images/main-config-2.png"/>
+  <div class="fig-text"> fig 11 </div> 
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--- docs/user/metacat-windows-install.html	(revision 4714)
+++ docs/user/metacat-windows-install.html	(revision 4715)
@@ -157,7 +157,7 @@
 	</ul>
 	
   <a name="ConfigureMetacatInstall"></a><div class="header2">Configure Metacat</div> 
-  <p>Refer to the documentation on <a href="./metacatconfigure.html">Metacat Confguration</a>
+  <p>Refer to the documentation on <a href="./metacat-configure.html">Metacat Confguration</a>
   to complete your installation of Metacat.</p>
     
   <a name="QuickUpdate"></a><div class="header1">Quick Update</div>
@@ -195,7 +195,7 @@
     </ul>
 	
   <a name="ConfigureMetacatUpdate"></a><div class="header2">Configure Metacat</div> 
-    <p>Refer to the documentation on <a href="./metacatconfigure.html">Metacat Confguration</a>
+    <p>Refer to the documentation on <a href="./metacat-configure.html">Metacat Confguration</a>
     to complete your installation of Metacat.</p>
 
   <br>
