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Posted to dev@rya.apache.org by mi...@apache.org on 2015/11/24 20:31:26 UTC

[3/3] incubator-rya git commit: RYA-3 Changing Manual to Markdown; linking README

RYA-3 Changing Manual to Markdown; linking README


Project: http://git-wip-us.apache.org/repos/asf/incubator-rya/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-rya/commit/ce4a10ff
Tree: http://git-wip-us.apache.org/repos/asf/incubator-rya/tree/ce4a10ff
Diff: http://git-wip-us.apache.org/repos/asf/incubator-rya/diff/ce4a10ff

Branch: refs/heads/develop
Commit: ce4a10ff5eafa2b85cb6829e5876956d5dd2278a
Parents: 2a6f730
Author: Aaron Mihalik <mi...@alum.mit.edu>
Authored: Sun Nov 22 12:27:56 2015 -0500
Committer: Aaron Mihalik <mi...@alum.mit.edu>
Committed: Sun Nov 22 16:17:24 2015 -0500

----------------------------------------------------------------------
 README.md                                       |  230 +--
 extras/rya.manual/pom.xml                       |  274 +--
 extras/rya.manual/src/main/java/temp/TempJ.java |   29 -
 extras/rya.manual/src/main/webapp/.livereload   |   19 -
 .../WEB-INF/scalate/layouts/default.scaml       |   97 --
 .../webapp/WEB-INF/scalate/layouts/print.ssp    |  778 ---------
 .../rya.manual/src/main/webapp/WEB-INF/web.xml  |   50 -
 extras/rya.manual/src/main/webapp/_banner.ssp   |    8 -
 .../rya.manual/src/main/webapp/_navigation.conf |   24 -
 .../rya.manual/src/main/webapp/_quicklinks.ssp  |    5 -
 extras/rya.manual/src/main/webapp/alx.conf      |   59 -
 .../src/main/webapp/build-source.conf           |   19 -
 .../src/main/webapp/css/pygmentize.css          |  134 --
 .../src/main/webapp/css/scalate/console.css     |   71 -
 extras/rya.manual/src/main/webapp/css/style.css | 1588 ------------------
 extras/rya.manual/src/main/webapp/eval.conf     |   56 -
 extras/rya.manual/src/main/webapp/images/bg.png |  Bin 244 -> 0 bytes
 .../src/main/webapp/images/bg02-blue-left.png   |  Bin 1068 -> 0 bytes
 .../src/main/webapp/images/bg02-blue-right.png  |  Bin 1114 -> 0 bytes
 .../main/webapp/images/bg02-white-left-nogr.png |  Bin 951 -> 0 bytes
 .../webapp/images/bg02-white-right-nogr.png     |  Bin 958 -> 0 bytes
 .../src/main/webapp/images/big-bullet.png       |  Bin 285 -> 0 bytes
 .../src/main/webapp/images/left-box-bottom.png  |  Bin 588 -> 0 bytes
 .../src/main/webapp/images/left-box-right.png   |  Bin 213 -> 0 bytes
 .../src/main/webapp/images/left-box-top.png     |  Bin 466 -> 0 bytes
 .../rya.manual/src/main/webapp/images/logo.png  |  Bin 18119 -> 0 bytes
 .../rya.manual/src/main/webapp/images/logo2.png |  Bin 9271 -> 0 bytes
 extras/rya.manual/src/main/webapp/index.conf    |    4 -
 extras/rya.manual/src/main/webapp/infer.conf    |   13 -
 .../src/main/webapp/loadPrecomputedJoin.conf    |   27 -
 extras/rya.manual/src/main/webapp/loaddata.conf |  117 --
 extras/rya.manual/src/main/webapp/overview.conf |    4 -
 .../rya.manual/src/main/webapp/querydata.conf   |  115 --
 .../rya.manual/src/main/webapp/quickstart.conf  |   42 -
 .../rya.manual/src/main/webapp/sm-addauth.conf  |   98 --
 .../src/main/webapp/sm-firststeps.conf          |   55 -
 extras/rya.manual/src/main/webapp/sm-infer.conf |  313 ----
 .../src/main/webapp/sm-namedgraph.conf          |  129 --
 .../src/main/webapp/sm-simpleaqr.conf           |   54 -
 .../src/main/webapp/sm-sparqlquery.conf         |   58 -
 .../src/main/webapp/sm-updatedata.conf          |   56 -
 extras/rya.manual/src/site/markdown/_index.md   |   23 +
 extras/rya.manual/src/site/markdown/alx.md      |   61 +
 .../src/site/markdown/build-source.md           |   15 +
 extras/rya.manual/src/site/markdown/eval.md     |   58 +
 extras/rya.manual/src/site/markdown/index.md    |   24 +
 extras/rya.manual/src/site/markdown/infer.md    |   14 +
 .../src/site/markdown/loadPrecomputedJoin.md    |   28 +
 extras/rya.manual/src/site/markdown/loaddata.md |  121 ++
 extras/rya.manual/src/site/markdown/overview.md |    5 +
 .../rya.manual/src/site/markdown/querydata.md   |  116 ++
 .../rya.manual/src/site/markdown/quickstart.md  |   41 +
 .../rya.manual/src/site/markdown/sm-addauth.md  |   98 ++
 .../src/site/markdown/sm-firststeps.md          |   59 +
 extras/rya.manual/src/site/markdown/sm-infer.md |  332 ++++
 .../src/site/markdown/sm-namedgraph.md          |  136 ++
 .../src/site/markdown/sm-simpleaqr.md           |   54 +
 .../src/site/markdown/sm-sparqlquery.md         |   58 +
 .../src/site/markdown/sm-updatedata.md          |   62 +
 .../src/site/resources/js/fixmarkdownlinks.js   |    6 +
 extras/rya.manual/src/site/site.xml             |   45 +
 61 files changed, 1486 insertions(+), 4396 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
index 04628cc..bc548a0 100644
--- a/README.md
+++ b/README.md
@@ -2,10 +2,14 @@
 
 ## Overview
 
-RYA is a scalable RDF Store that is built on top of a Columnar Index Store (such as Accumulo, Hbase(not currently supported)). It is implemented as an extension to OpenRdf to provide easy query mechanisms (SPARQL, SERQL, etc) and Rdf data storage (RDF/XML, NTriples, etc).
+RYA is a scalable RDF Store that is built on top of a Columnar Index Store (such as Accumulo). It is implemented as an extension to OpenRdf to provide easy query mechanisms (SPARQL, SERQL, etc) and Rdf data storage (RDF/XML, NTriples, etc).
 
 RYA stands for RDF y(and) Accumulo.
 
+## Rya Manual
+
+A copy of the Rya Manual is located [here](extras/rya.manual/src/site/markdown/index.md).  The material in the manual and below may be out of sync.
+
 ## Upgrade Path
 
 Since the data encodings changed in the 3.2.2 release, you will need to run the Upgrade322Tool MapReduce job to perform the upgrade.
@@ -13,7 +17,10 @@ Since the data encodings changed in the 3.2.2 release, you will need to run the
 1. Build the project with -Pmr to build the mapreduce artifacts
 2. Make sure to clone the rya tables before doing the upgrade
 3. Run
-    <pre> hadoop jar accumulo.rya-mr.jar mvm.rya.accumulo.mr.upgrade.Upgrade322Tool -Dac.instance={} -Dac.username={} -Dac.pwd={} </pre>
+    
+```
+hadoop jar accumulo.rya-mr.jar mvm.rya.accumulo.mr.upgrade.Upgrade322Tool -Dac.instance={} -Dac.username={} -Dac.pwd={}
+```
 
 ## Quick Start
 
@@ -22,41 +29,42 @@ This tutorial will outline the steps needed to get quickly started with the Rya
 ### Prerequisites
 
 * Columnar Store (either Accumulo) The tutorial will go forward using Accumulo
-* Rya code (Git: git@github.com:texeltek/rya.git)
-* Maven 2.2 +
+* Rya code (Git: git://git.apache.org/incubator-rya.git)
+* Maven 3.0 +
 
 ### Building from Source
 
 Using Git, pull down the latest code from the url above.
 
-Run the command to build the code {{mvn clean install}}
-
-If all goes well, the build should be successful and a war should be produced in {{web/web.rya/target/web.rya.war}}
+Run the command to build the code `mvn clean install`
 
-Note: To perform a build of the geomesa/lucene indexing, run the build with the profile 'indexing' (-P indexing)
+If all goes well, the build should be successful and a war should be produced in `web/web.rya/target/web.rya.war`
 
-Note: If you are building on windows, you will need hadoop-common 2.6.0's {{winutils.exe}} and {{hadoop.dll}}.  You can download it from [here](https://github.com/amihalik/hadoop-common-2.6.0-bin/archive/master.zip).  This build requires the [Visual C++ Redistributable for Visual Studio 2015 (x64)](https://www.microsoft.com/en-us/download/details.aspx?id=48145).   Also you will need to set your path and Hadoop home using the commands below:
+Note: To perform a build of the geomesa/lucene indexing, run the build with the profile 'indexing' `mvn clean install -P indexing`
 
-    set HADOOP_HOME=c:\hadoop-common-2.6.0-bin
-    set PATH=%PATH%;c:\hadoop-common-2.6.0-bin\bin
+Note: If you are building on windows, you will need hadoop-common 2.6.0's `winutils.exe` and `hadoop.dll`.  You can download it from [here](https://github.com/amihalik/hadoop-common-2.6.0-bin/archive/master.zip).  This build requires the [Visual C++ Redistributable for Visual Studio 2015 (x64)](https://www.microsoft.com/en-us/download/details.aspx?id=48145).   Also you will need to set your path and Hadoop home using the commands below:
 
-### Deployment
+```
+set HADOOP_HOME=c:\hadoop-common-2.6.0-bin
+set PATH=%PATH%;c:\hadoop-common-2.6.0-bin\bin
+```
 
-(Using tomcat)
+### Deployment Using Tomcat
 
 Unwar the above war into the webapps directory.
 
-To point the web.rya war to the appropriate Accumulo instance, make a properties file {{environment.properties}} and put it in the classpath. Here is an example:
+To point the web.rya war to the appropriate Accumulo instance, make a properties file `environment.properties` and put it in the classpath. Here is an example:
 
-    instance.name=accumulo  #Accumulo instance name
-    instance.zk=localhost:2181  #Accumulo Zookeepers
-    instance.username=root  #Accumulo username
-    instance.password=secret  #Accumulo pwd
-    rya.tableprefix=triplestore_  #Rya Table Prefix
-    rya.displayqueryplan=true  #To display the query plan
+```
+instance.name=accumulo  #Accumulo instance name
+instance.zk=localhost:2181  #Accumulo Zookeepers
+instance.username=root  #Accumulo username
+instance.password=secret  #Accumulo pwd
+rya.tableprefix=triplestore_  #Rya Table Prefix
+rya.displayqueryplan=true  #To display the query plan
+```
 
-
-Start the Tomcat server. {{./bin/startup.sh}}
+Start the Tomcat server. `./bin/startup.sh`
 
 ## Usage
 
@@ -64,29 +72,31 @@ Start the Tomcat server. {{./bin/startup.sh}}
 
 #### Web REST endpoint
 
-The War sets up a Web REST endpoint at {{http://server/web.rya/loadrdf}} that allows POST data to get loaded into the Rdf Store. This short tutorial will use Java code to post data.
+The War sets up a Web REST endpoint at `http://server/web.rya/loadrdf` that allows POST data to get loaded into the Rdf Store. This short tutorial will use Java code to post data.
 
 First, you will need data to load and will need to figure out what format that data is in.
 
 For this sample, we will use the following N-Triples:
 
-    <http://mynamespace/ProductType1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://mynamespace/ProductType> .
-    <http://mynamespace/ProductType1> <http://www.w3.org/2000/01/rdf-schema#label> "Thing" .
-    <http://mynamespace/ProductType1> <http://purl.org/dc/elements/1.1/publisher> <http://mynamespace/Publisher1> .
-
+```
+<http://mynamespace/ProductType1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://mynamespace/ProductType> .
+<http://mynamespace/ProductType1> <http://www.w3.org/2000/01/rdf-schema#label> "Thing" .
+<http://mynamespace/ProductType1> <http://purl.org/dc/elements/1.1/publisher> <http://mynamespace/Publisher1> .
+```
 
 Save this file somewhere $RDF_DATA
 
 Second, use the following Java code to load data to the REST endpoint:
 
-    import java.io.BufferedReader;
-    import java.io.InputStream;
-    import java.io.InputStreamReader;
-    import java.io.OutputStream;
-    import java.net.URL;
-    import java.net.URLConnection;
+``` JAVA
+import java.io.BufferedReader;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.net.URL;
+import java.net.URLConnection;
 
-    public class LoadDataServletRun {
+public class LoadDataServletRun {
 
     public static void main(String[] args) {
         try {
@@ -120,8 +130,8 @@ Second, use the following Java code to load data to the REST endpoint:
             e.printStackTrace();
         }
     }
-    }
-
+}
+```
 
 Compile and run this code above, changing the references for $RDF_DATA and the url that your Rdf War is running at.
 
@@ -134,11 +144,13 @@ Bulk loading data is done through Map Reduce jobs
 ##### Bulk Load RDF data
 
   This Map Reduce job will read a full file into memory and parse it into statements. The statements are saved into the store. Here is an example for storing in Accumulo:
-{code}
+
+```
 hadoop jar target/accumulo.rya-3.0.4-SNAPSHOT-shaded.jar mvm.rya.accumulo.mr.fileinput.BulkNtripsInputTool -Dac.zk=localhost:2181 -Dac.instance=accumulo -Dac.username=root -Dac.pwd=secret -Drdf.tablePrefix=triplestore_ -Dio.sort.mb=64 /tmp/temp.ntrips
-{code}
+```
 
 Options:
+
 * rdf.tablePrefix : The tables (spo, po, osp) are prefixed with this qualifier. The tables become: (rdf.tablePrefix)spo,(rdf.tablePrefix)po,(rdf.tablePrefix)osp
 * ac.* : Accumulo connection parameters
 * rdf.format : See RDFFormat from openrdf, samples include (Trig, N-Triples, RDF/XML)
@@ -151,41 +163,41 @@ The argument is the directory/file to load. This file needs to be loaded into HD
 Here is some sample code to load data directly through the OpenRDF API. (Loading N-Triples data)
 You will need at least accumulo.rya-<version>, rya.api, rya.sail.impl on the classpath and transitive dependencies. I find that Maven is the easiest way to get a project dependency tree set up.
 
+``` JAVA
+final RdfCloudTripleStore store = new RdfCloudTripleStore();
+AccumuloRdfConfiguration conf = new AccumuloRdfConfiguration();
+AccumuloRyaDAO dao = new AccumuloRdfDAO();
+Connector connector = new ZooKeeperInstance("instance", "zoo1,zoo2,zoo3").getConnector("user", "password");
+dao.setConnector(connector);
+conf.setTablePrefix("rya_");
+dao.setConf(conf);
+store.setRdfDao(dao);
 
-            final RdfCloudTripleStore store = new RdfCloudTripleStore();
-            AccumuloRdfConfiguration conf = new AccumuloRdfConfiguration();
-            AccumuloRyaDAO dao = new AccumuloRdfDAO();
-            Connector connector = new ZooKeeperInstance("instance", "zkserver:port").getConnector("user", "password");
-            dao.setConnector(connector);
-            conf.setTablePrefix("rya_");
-            dao.setConf(conf);
-            store.setRdfDao(dao);
-
-            Repository myRepository = new RyaSailRepository(store);
-            myRepository.initialize();
-            RepositoryConnection conn = myRepository.getConnection();
+Repository myRepository = new RyaSailRepository(store);
+myRepository.initialize();
+RepositoryConnection conn = myRepository.getConnection();
 
-            //load data from file
-            final File file = new File("ntriples.ntrips");
-            conn.add(new FileInputStream(file), file.getName(),
-                    RDFFormat.NTRIPLES, new Resource[]{});
+//load data from file
+final File file = new File("ntriples.ntrips");
+conn.add(new FileInputStream(file), file.getName(),
+        RDFFormat.NTRIPLES, new Resource[]{});
 
-            conn.commit();
-
-            conn.close();
-            myRepository.shutDown();
+conn.commit();
 
+conn.close();
+myRepository.shutDown();
+```
 
 
 ### Query Data
 
 #### Web JSP endpoint
 
-Open a url to {{http://server/web.rya/sparqlQuery.jsp}}. This simple form can run Sparql.
+Open a url to `http://server/web.rya/sparqlQuery.jsp`. This simple form can run Sparql.
 
 ### Web REST endpoint
 
-The War sets up a Web REST endpoint at {{http://server/web.rya/queryrdf}} that allows GET requests with queries.
+The War sets up a Web REST endpoint at `http://server/web.rya/queryrdf` that allows GET requests with queries.
 
 For this sample, we will assume you already loaded data from the [loaddata.html] tutorial
 
@@ -193,13 +205,14 @@ Save this file somewhere $RDF_DATA
 
 Second, use the following Java code to load data to the REST endpoint:
 
-    import java.io.BufferedReader;
-    import java.io.InputStreamReader;
-    import java.net.URL;
-    import java.net.URLConnection;
-    import java.net.URLEncoder;
+``` JAVA
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.net.URLConnection;
+import java.net.URLEncoder;
 
-    public class QueryDataServletRun {
+public class QueryDataServletRun {
 
     public static void main(String[] args) {
         try {
@@ -224,8 +237,8 @@ Second, use the following Java code to load data to the REST endpoint:
             e.printStackTrace();
         }
     }
-    }
-
+}
+```
 
 Compile and run this code above, changing the url that your Rdf War is running at.
 
@@ -233,54 +246,55 @@ Compile and run this code above, changing the url that your Rdf War is running a
 
 Here is a code snippet for directly running against Accumulo with the code. You will need at least accumulo.rya.jar, rya.api, rya.sail.impl on the classpath and transitive dependencies. I find that Maven is the easiest way to get a project dependency tree set up.
 
+``` JAVA
+Connector connector = new ZooKeeperInstance("instance", "zoo1,zoo2,zoo3").getConnector("user", "password");
 
-            Connector connector = new ZooKeeperInstance("cbinstance", "zkserver:port").getConnector("cbuser", "cbpassword");
+final RdfCloudTripleStore store = new RdfCloudTripleStore();
+AccumuloRyaDAO crdfdao = new AccumuloRyaDAO();
+crdfdao.setConnector(connector);
 
-            final RdfCloudTripleStore store = new RdfCloudTripleStore();
-            AccumuloRyaDAO crdfdao = new AccumuloRyaDAO();
-            crdfdao.setConnector(connector);
+AccumuloRdfConfiguration conf = new AccumuloRdfConfiguration();
+conf.setTablePrefix("rts_");
+conf.setDisplayQueryPlan(true);
+crdfdao.setConf(conf);
+store.setRdfDao(crdfdao);
 
-            AccumuloRdfConfiguration conf = new AccumuloRdfConfiguration();
-            conf.setTablePrefix("rts_");
-            conf.setDisplayQueryPlan(true);
-            crdfdao.setConf(conf);
-            store.setRdfDao(crdfdao);
+InferenceEngine inferenceEngine = new InferenceEngine();
+inferenceEngine.setRdfDao(crdfdao);
+inferenceEngine.setConf(conf);
+store.setInferenceEngine(inferenceEngine);
 
-            InferenceEngine inferenceEngine = new InferenceEngine();
-            inferenceEngine.setRdfDao(crdfdao);
-            inferenceEngine.setConf(conf);
-            store.setInferenceEngine(inferenceEngine);
+Repository myRepository = new RyaSailRepository(store);
+myRepository.initialize();
 
-            Repository myRepository = new RyaSailRepository(store);
-            myRepository.initialize();
-
-            String query = "select * where {\n" +
-                                "<http://mynamespace/ProductType1> ?p ?o.\n" +
-                                "}";
-            RepositoryConnection conn = myRepository.getConnection();
-            System.out.println(query);
-            TupleQuery tupleQuery = conn.prepareTupleQuery(
-                    QueryLanguage.SPARQL, query);
-            ValueFactory vf = ValueFactoryImpl.getInstance();
+String query = "select * where {\n" +
+                    "<http://mynamespace/ProductType1> ?p ?o.\n" +
+                    "}";
+RepositoryConnection conn = myRepository.getConnection();
+System.out.println(query);
+TupleQuery tupleQuery = conn.prepareTupleQuery(
+        QueryLanguage.SPARQL, query);
+ValueFactory vf = ValueFactoryImpl.getInstance();
 
-            TupleQueryResultHandler writer = new SPARQLResultsXMLWriter(System.out);
-            tupleQuery.evaluate(new TupleQueryResultHandler() {
+TupleQueryResultHandler writer = new SPARQLResultsXMLWriter(System.out);
+tupleQuery.evaluate(new TupleQueryResultHandler() {
 
-                int count = 0;
+    int count = 0;
 
-                @Override
-                public void startQueryResult(List<String> strings) throws TupleQueryResultHandlerException {
-                }
+    @Override
+    public void startQueryResult(List<String> strings) throws TupleQueryResultHandlerException {
+    }
 
-                @Override
-                public void endQueryResult() throws TupleQueryResultHandlerException {
-                }
+    @Override
+    public void endQueryResult() throws TupleQueryResultHandlerException {
+    }
 
-                @Override
-                public void handleSolution(BindingSet bindingSet) throws TupleQueryResultHandlerException {
-                    System.out.println(bindingSet);
-                }
-            });
+    @Override
+    public void handleSolution(BindingSet bindingSet) throws TupleQueryResultHandlerException {
+        System.out.println(bindingSet);
+    }
+});
 
-            conn.close();
-            myRepository.shutDown();
+conn.close();
+myRepository.shutDown();
+```

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/pom.xml
----------------------------------------------------------------------
diff --git a/extras/rya.manual/pom.xml b/extras/rya.manual/pom.xml
index 2e27b9f..f79359a 100644
--- a/extras/rya.manual/pom.xml
+++ b/extras/rya.manual/pom.xml
@@ -11,284 +11,26 @@
 
     <artifactId>rya.manual</artifactId>
     <name>RYA Manual</name>
-    <packaging>war</packaging>
-
-    <properties>
-        <must-succeed>false</must-succeed>
-        <manual.dir>${project.build.directory}/${project.artifactId}</manual.dir>
-        <manual>${manual.dir}/${project.artifactId}-${project.version}</manual>
-        <netbeans.hint.deploy.server>Tomcat60</netbeans.hint.deploy.server>
-        <jetty-port>8080</jetty-port>
-        <jetty-war-dir>${project.build.directory}/webapp/</jetty-war-dir>
-        <scalate.version>1.7.1</scalate.version>
-        <scala.version>2.11.1</scala.version>
-        <wikitext.version>1.3</wikitext.version>
-        <scalate.editor>${env.SCALATE_EDITOR}</scalate.editor>
-        <scalate.mode>production</scalate.mode>
-        <scalate.workdir>${project.build.directory}/scalateWorkDir</scalate.workdir>
-        <maven.wagon.version>1.0-beta-6</maven.wagon.version>
-        <remoteTomcatManager>http://10.40.190.248:8080/manager</remoteTomcatManager>
-    </properties>
-
-    <dependencies>
-        <dependency>
-            <groupId>org.scalatra.scalate</groupId>
-            <artifactId>scalate-wikitext_2.11</artifactId>
-            <version>${scalate.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>ch.qos.logback</groupId>
-            <artifactId>logback-classic</artifactId>
-            <version>0.9.24</version>
-        </dependency>
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-api</artifactId>
-            <version>1.6.0</version>
-        </dependency>
-        <dependency>
-            <groupId>org.scala-lang</groupId>
-            <artifactId>scala-library</artifactId>
-            <version>${scala.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.scala-lang</groupId>
-            <artifactId>scala-compiler</artifactId>
-            <version>${scala.version}</version>
-        </dependency>
-    </dependencies>
+    <packaging>jar</packaging>
 
     <build>
         <plugins>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-resources-plugin</artifactId>
-                <executions>
-                    <execution>
-                        <id>filter</id>
-                        <phase>generate-resources</phase>
-                        <goals>
-                            <goal>copy-resources</goal>
-                        </goals>
-                        <configuration>
-                            <outputDirectory>${project.build.directory}/webapp</outputDirectory>
-                            <resources>
-                                <resource>
-                                    <directory>src/main/webapp</directory>
-                                    <filtering>true</filtering>
-                                </resource>
-                            </resources>
-                        </configuration>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <groupId>org.codehaus.mojo</groupId>
-                <artifactId>build-helper-maven-plugin</artifactId>
-                <version>1.7</version>
-                <executions>
-                    <execution>
-                        <id>add-source</id>
-                        <phase>generate-resources</phase>
-                        <goals>
-                            <goal>add-source</goal>
-                        </goals>
-                        <configuration>
-                            <sources>
-                                <source>${project.build.directory}/webapp</source>
-                            </sources>
-                        </configuration>
-                    </execution>
-                    <!--execution>
-                        <id>attach-artifacts</id>
-                        <phase>install</phase>
-                        <goals>
-                            <goal>attach-artifact</goal>
-                        </goals>
-                        <configuration>
-                            <artifacts>
-                                <artifact>
-                                    <file>${manual}.html</file>
-                                    <type>html</type>
-                                </artifact>
-                            </artifacts>
-                        </configuration>
-                    </execution-->
-                </executions>
-            </plugin>
-            <plugin>
-                <groupId>org.scalatra.scalate</groupId>
-                <artifactId>maven-scalate-plugin_2.11</artifactId>
-                <version>${scalate.version}</version>
-                <executions>
-                    <execution>
-                        <id>generate-htmls</id>
-                        <phase>compile</phase>
-                        <goals>
-                            <goal>sitegen</goal>
-                        </goals>
-                        <configuration>
-                            <webappDirectory>${project.build.directory}/webapp</webappDirectory>
-                        </configuration>
-                    </execution>
-                </executions>
-                <configuration>
-                    <target>${basedir}/src/main/webapp</target>
-                </configuration>
+                <artifactId>maven-site-plugin</artifactId>
                 <dependencies>
                     <dependency>
-                        <groupId>org.apache.maven.wagon</groupId>
-                        <artifactId>wagon-ssh</artifactId>
-                        <version>${maven.wagon.version}</version>
-                    </dependency>
-                    <dependency>
-                        <groupId>org.fusesource.wikitext</groupId>
-                        <artifactId>confluence-core</artifactId>
-                        <version>${wikitext.version}</version>
+                        <groupId>org.apache.maven.doxia</groupId>
+                        <artifactId>doxia-module-markdown</artifactId>
+                        <version>1.6</version>
                     </dependency>
                 </dependencies>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-war-plugin</artifactId>
                 <configuration>
-                    <webResources>
-                        <resource>
-                            <directory>${project.build.directory}/webapp/</directory>
-                        </resource>
-                    </webResources>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.codehaus.mojo</groupId>
-                <artifactId>tomcat-maven-plugin</artifactId>
-                <version>1.1</version>
-                <configuration>
-                    <url>${remoteTomcatManager}</url>
-                </configuration>
-                <!--executions>
-                    <execution>
-                        <id>redeploy-war</id>
-                        <phase>deploy</phase>
-                        <goals>
-                            <goal>redeploy</goal>
-                        </goals>
-                    </execution>
-                </executions-->
-            </plugin>
-            <plugin>
-                <groupId>org.mortbay.jetty</groupId>
-                <artifactId>jetty-maven-plugin</artifactId>
-                <version>7.1.5.v20100705</version>
-                <configuration>
-                    <!--webAppConfig>
-                        <contextPath>${project.artifactId}</contextPath>
-                    </webAppConfig-->
-                    <!-- When editing the conf files, you can comment this line to run
-                        mvn jetty:run
-                       to have a live web site
-                    -->
-                    <webAppSourceDirectory>${jetty-war-dir}</webAppSourceDirectory>
-
-                    <systemProperties>
-                        <systemProperty>
-                            <name>scalate.editor</name>
-                            <value>${scalate.editor}</value>
-                        </systemProperty>
-                        <systemProperty>
-                            <name>scalate.workdir</name>
-                            <value>${scalate.workdir}</value>
-                        </systemProperty>
-                        <systemProperty>
-                            <name>scalate.mode</name>
-                            <value>${scalate.mode}</value>
-                        </systemProperty>
-                    </systemProperties>
-                </configuration>
+                    <inputEncoding>UTF-8</inputEncoding>
+                    <outputEncoding>UTF-8</outputEncoding>
+                </configuration> 
             </plugin>
         </plugins>
     </build>
-
-    <reporting>
-        <plugins>
-            <plugin>
-                <groupId>org.scalatra.scalate</groupId>
-                <artifactId>maven-scalate-plugin</artifactId>
-                <version>${scalate.version}</version>
-            </plugin>
-        </plugins>
-    </reporting>
-
-    <profiles>
-        <profile>
-            <id>live</id>
-            <properties>
-                <jetty-war-dir>${basedir}/src/main/webapp/</jetty-war-dir>
-                <scalate.mode>development</scalate.mode>
-            </properties>
-        </profile>
-        <profile>
-            <id>pdf-manual</id>
-            <build>
-                <plugins>
-                    <plugin>
-                        <groupId>org.apache.maven.plugins</groupId>
-                        <artifactId>maven-antrun-plugin</artifactId>
-                        <executions>
-                            <execution>
-                                <id>attach-manual</id>
-                                <phase>install</phase>
-                                <goals>
-                                    <goal>run</goal>
-                                </goals>
-                                <configuration>
-                                    <tasks>
-                                        <mkdir dir="${manual.dir}" />
-                                        <move file="${project.build.directory}/sitegen/manual.html" tofile="${manual}.html" />
-                                        <echo message="Generating PDF using Prince XML (http://www.princexml.com/)" />
-                                        <exec executable="prince">
-                                            <arg value="${manual}.html" />
-                                            <arg value="${manual}.pdf" />
-                                            <arg value="--log" />
-                                            <arg value="${project.build.directory}/prince.log" />
-                                        </exec>
-                                    </tasks>
-                                </configuration>
-                            </execution>
-                        </executions>
-                    </plugin>
-                    <plugin>
-                        <groupId>org.codehaus.mojo</groupId>
-                        <artifactId>build-helper-maven-plugin</artifactId>
-                        <executions>
-                            <execution>
-                                <id>attach-artifacts</id>
-                                <phase>install</phase>
-                                <goals>
-                                    <goal>attach-artifact</goal>
-                                </goals>
-                                <configuration>
-                                    <artifacts>
-                                        <artifact>
-                                            <file>${manual}.pdf</file>
-                                            <type>pdf</type>
-                                        </artifact>
-                                    </artifacts>
-                                </configuration>
-                            </execution>
-                        </executions>
-                    </plugin>
-
-                </plugins>
-            </build>
-        </profile>
-        <profile>
-            <id>release</id>
-            <properties>
-                <must-succeed>true</must-succeed>
-            </properties>
-        </profile>
-    </profiles>
-
 </project>
 

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/src/main/java/temp/TempJ.java
----------------------------------------------------------------------
diff --git a/extras/rya.manual/src/main/java/temp/TempJ.java b/extras/rya.manual/src/main/java/temp/TempJ.java
deleted file mode 100644
index be473e4..0000000
--- a/extras/rya.manual/src/main/java/temp/TempJ.java
+++ /dev/null
@@ -1,29 +0,0 @@
-package temp;
-
-/*
- * #%L
- * RYA Manual
- * %%
- * Copyright (C) 2014 Rya
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-/**
-* Marker class so that target/classes directory gets generated
-* and the bundle plugin does not fail
-*/
-public class TempJ {
-	
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/src/main/webapp/.livereload
----------------------------------------------------------------------
diff --git a/extras/rya.manual/src/main/webapp/.livereload b/extras/rya.manual/src/main/webapp/.livereload
deleted file mode 100644
index b185045..0000000
--- a/extras/rya.manual/src/main/webapp/.livereload
+++ /dev/null
@@ -1,19 +0,0 @@
-# Lines starting with pound sign (#) are ignored.
-
-# additional extensions to monitor
-#config.exts << 'haml'
-
-# exclude files with NAMES matching this mask
-#config.exclusions << '~*'
-# exclude files with PATHS matching this mask (if the mask contains a slash)
-#config.exclusions << '/excluded_dir/*'
-# exclude files with PATHS matching this REGEXP
-#config.exclusions << /somedir.*(ab){2,4}.(css|js)$/
-
-# reload the whole page when .js changes
-#config.apply_js_live = false
-# reload the whole page when .css changes
-#config.apply_css_live = false
-
-# wait 100ms for more changes before reloading a page
-#config.grace_period = 0.1

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/src/main/webapp/WEB-INF/scalate/layouts/default.scaml
----------------------------------------------------------------------
diff --git a/extras/rya.manual/src/main/webapp/WEB-INF/scalate/layouts/default.scaml b/extras/rya.manual/src/main/webapp/WEB-INF/scalate/layouts/default.scaml
deleted file mode 100644
index 8b27470..0000000
--- a/extras/rya.manual/src/main/webapp/WEB-INF/scalate/layouts/default.scaml
+++ /dev/null
@@ -1,97 +0,0 @@
-
--@ var body: String
--@ var title : String = "Rya Manual"
-- response.setContentType("text/html")
-
--# Only include the console if it's available and the engine is in dev mode.
-- val include_console = engine.isDevelopmentMode && engine.resourceLoader.exists("/org/fusesource/scalate/console/console_head.scaml")
-
-!!! Basic
-%html(lang="en")
-  %head
-    %meta(http-equiv="Content-Type" content="text/html; charset=utf-8")
-    %meta(name="description" content="description goes here")
-    %meta(name="keywords" content="keywords,goes,here")
-    %meta(name="author" content="The Team")
-
-    - if (include_console)
-      = include("/org/fusesource/scalate/console/console_head.scaml")
-
-    %link(href={uri("/css/style.css")} rel="stylesheet" type="text/css")
-    %link(href={uri("/css/pygmentize.css")} rel="stylesheet" type="text/css")
-
-    - if (include_console)
-      %link(href={uri("/css/scalate/console.css")} rel="stylesheet" type="text/css")
-
-    %title
-      = title
-  
-  %body
-    %table{:width => "100%", :cellpadding => "0", :cellspacing => "0"}
-      %tr{:width => "100%"}
-        %td#cell-0-0{:colspan => "2"}
-          &nbsp;
-        %td#cell-0-1
-          &nbsp;
-        %td#cell-0-2{:colspan => "2"}
-          &nbsp;
-      %tr{:width => "100%"}
-        %td#cell-1-0
-          &nbsp;
-        %td#cell-1-1
-          &nbsp;
-        %td#cell-1-2
-          %div{:style => "padding: 5px;"}
-            #banner
-              = include("/_banner.ssp")
-            #top-menu
-              %table{:border => "0", :cellpadding => "1", :cellspacing => "0", :width => "100%"}
-                %tr
-                  %td
-                    %div{:align => "left"}
-                  %td
-                    %div{:align => "right"}
-                      = include("/_quicklinks.ssp")
-        %td#cell-1-3
-          &nbsp;
-        %td#cell-1-4
-          &nbsp;
-      %tr{:width => "100%"}
-        %td#cell-2-0{:colspan => "2"}
-          &nbsp;
-        %td#cell-2-1
-          %table
-            %tr{:height => "100%", :valign => "top"}
-              %td{:height => "100%"}
-                #wrapper-menu-page-right
-                  #wrapper-menu-page-top
-                    #wrapper-menu-page-bottom
-                      #menu-page
-                        = include("_navigation.conf")
-              %td{:height =>"100%", :width => "100%"}
-                .wiki-content
-                  !~~ body
-        %td#cell-2-2{:colspan => "2"}
-          &nbsp;
-      %tr{:width => "100%"}
-        %td#cell-3-0
-          &nbsp;
-        %td#cell-3-1
-          &nbsp;
-        %td#cell-3-2
-          #footer
-            #site-footer
-              %br
-        %td#cell-3-3
-          &nbsp;
-        %td#cell-3-4
-          &nbsp;
-      %tr{:width => "100%"}
-        %td#cell-4-0{:colspan => "2"}
-          &nbsp;
-        %td#cell-4-1
-          &nbsp;
-        %td#cell-4-2{:colspan => "2"}
-          &nbsp;
-    - if (include_console)
-      = include("/org/fusesource/scalate/console/console.scaml")

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/src/main/webapp/WEB-INF/scalate/layouts/print.ssp
----------------------------------------------------------------------
diff --git a/extras/rya.manual/src/main/webapp/WEB-INF/scalate/layouts/print.ssp b/extras/rya.manual/src/main/webapp/WEB-INF/scalate/layouts/print.ssp
deleted file mode 100644
index 1676547..0000000
--- a/extras/rya.manual/src/main/webapp/WEB-INF/scalate/layouts/print.ssp
+++ /dev/null
@@ -1,778 +0,0 @@
-
-<%@ var body: String %>
-<%@ var title: String = "Rya Manual" %>
-<% escapeMarkup = false %>
-<!DOCTYPE html>
-<html>
-<head>
-  <style type="text/css">
-
-html {
-  margin: 0; padding: 0;
-  font: 10pt/1.26 "Gill Sans", sans-serif;
-}
-
-h1, h2, h3, h4, h5, h6 {
-  font-family: "Gill Sans", sans-serif;
-  margin: 2em 0 0.5em 0;
-  page-break-after: avoid;
-}
-
-h1 {
-  font-size: 2.0em;
-  font-weight: 900;
-
-  margin: 0;
-  margin-left:-2cm;
-  margin-top:-1cm;
-  margin-bottom:1.5cm;
-  top: 0cm;
-  left: 0cm;
-  padding: 2cm;
-  padding-top: 0cm;
-  padding-bottom: 1cm;
-  background: #888;
-  border-bottom-right-radius: 2cm;
-  page-break-before: always;
-  page-break-inside: avoid;
-}
-
-@media screen, handheld {
-h1 {
-  margin-top:1cm;
-  background-image: url("chapter-rounded-bottom.png");
-  background-repeat: no-repeat;
-  background-position: bottom right;
-}
-div.page-reset > h1 {
-  margin-top:0cm;
-}
-}
-
-
-h2 {
-  font-size: 1.2em;
-  text-transform: uppercase;
-  font-weight: bold;
-}
-
-h3 {
-  font-size: 1em;
-  font-weight: bold;
-}
-
-q::before {
-  content: "\201C";
-}
-
-q::after {
-  content: "\201D";
-}
-
-p { margin: 0 }
-p + p { text-indent: 1.3em ; margin-top: 0.2em; }
-p.sidenote + p, p.caption, p.art { text-indent: 0 }
-
-p.author {
-  margin-top: 2em;
-  text-indent: 0;
-  text-align: right;
-}
-
-a { text-decoration: none; color: black }
-
-/* cross-references */
-
-a.pageref::after { content: " on page " target-counter(attr(href), page); }
-a.chapref::before { content: " Chapter " target-counter(attr(href), chapter) ", "; }
-a.figref { content: " Figure " target-counter(attr(href), figure); }
-a.tableref { content: " Table " target-counter(attr(href), figure); }
-a.listingref { content: " Listing " target-counter(attr(href), listing); }
-
-/* sidenotes */
-
-.sidenote {
-  float: left;
-  clear: left;
-  margin: 0 0 1em -41%;
-  width: 37%;
-  font-size: 0.9em;
-  font-style: normal;
-  text-indent: 0;
-  text-align: right;
-  page-break-inside: avoid;
-}
-
-/* sidebars */
-
-div.sidebar {
-  float: top-next;
-  margin: 1.2em 0 1.2em 0;
-  border: thin solid;
-  background: #CCC;
-  padding: 0.5em 1em;
-  page-break-inside: avoid;
-  column-count: 2;
-  column-gap: 1.5em;
-}
-
-div.sidebar h2 {
-  margin-top: 0;
-}
-
-/* frontpage */
-
-.title p{
-	font-size:22pt;
-  	font-family: "Gill Sans", sans-serif;
-  	text-align: center;
-}
-
-.copyright-section {
-	text-align: center;
-	font-size: 9pt;
-	page-break-after: always;
-	margin-top: 50pt;
-	margin-bottom: 20pt;
-}
-
-.toc-title {
-	font-size:18pt;
-  	font-family: "Gill Sans", sans-serif;
-  	text-align: left;
-  	margin-left:20pt;
-  	margin-bottom: 40pt;
-
-}
-
-/* figures, tables, and listings */
-
-div.confluenceTableSmall th.confluenceTh {
-  font-size: 11px;
-}
-
-div.confluenceTableSmall td.confluenceTd {
-  font-size: 7px;
-}
-
-div.figure {
-  margin: 1em 0;
-  counter-increment: figure;
-}
-
-div.figure .caption, div.table .caption {
-  font-size: 0.9em;
-  font-style: italic;
-}
-
-div.figure .caption::before {
-  content: "Figure " counter(figure) ". ";
-  font-weight: bold;
-  font-style: normal;
-}
-
-div.table .caption::before {
-  content: "Table " counter(table) ". ";
-  font-weight: bold;
-  font-style: normal;
-}
-
-div.table {
-  margin: 1em 0;
-  counter-increment: table;
-}
-
-div.table th {
-  text-align: left;
-}
-
-table th, table td {
-  text-align: left;
-  padding-right: 1em;
-  page-break-inside: avoid;
-}
-
-table th {
-  border-top: thin solid;
-  border-bottom: thin solid;
-  padding-top: 0.2em;
-  padding-bottom: 0.2em;
-}
-table td {
-  border-top: none;
-  border-bottom: thin dotted;
-  padding-top: 0.2em;
-  padding-bottom: 0.2em;
-}
-
-div.Scrollbar {
-	display: none;
-}
-
-
-/* Weird div.codeHeader a b::before would be a better selection
-   but prince does not properly match it.. Firefox does. */
-div.codeHeader::before {
-  content: "Listing " counter(listing) ". ";
-  font-weight: bold;
-  font-style: normal;
-}
-div.codeHeader a b {
-  font-style: italic;
-  font-weight: normal;
-}
-div.codeHeader {
-  font-size: 0.9em;
-  counter-increment: listing;
-}
-div.code {
-	border: 1px dashed #c0c0c0;
-    font-size: 12px;
-	font-family: Courier;
-    margin: 5px;
-	line-height: 13px;
-	padding: 3px;
-	background-color: #f8f8f8;
-
-}
-
-
-@page {
-  margin: 2cm;
-  size: 7in 9.25in;
-
-  @footnotes {
-    border-top: thin solid black;
-    padding-top: 0.3em;
-    margin-top: 0.6em;
-  }
-}
-
-
-/* define default page and names pages: cover, blank, frontmatter */
-div.page-reset {
-    counter-reset: page 1;
-}
-
-@page :left {
-  @top-left-corner {
-    font-weight: 900; font: 9pt "Gill Sans", serif;
-    content: counter(page);
-    text-align: left;
-    margin-left: 1cm;
-    visibility: hidden;
-  }
-  @top-left {
-    font-weight: 900;
-    font: 9pt "Gill Sans", serif; white-space: pre; text-transform: uppercase; letter-spacing: 0.1em;
-    content: string(header, first);
-    visibility: hidden;
-  }
-  @bottom-left-corner {
-    font-weight: 900; font: 9pt "Gill Sans", serif;
-    content: counter(page);
-    text-align: left;
-    margin-left: 1cm;
-  }
-  @bottom-left {
-    font-weight: 900;
-    font: 9pt "Gill Sans", serif; white-space: pre; text-transform: uppercase; letter-spacing: 0.1em;
-    content: string(header, first);
-  }
-}
-
-@page :right {
-  @top-right-corner {
-    font-weight: 900; font: 9pt "Gill Sans", serif;
-    content: counter(page);
-    text-align: left;
-    margin-left: 1cm;
-    visibility: hidden;
-  }
-  @top-right {
-    font-weight: 900;
-    font: 9pt "Gill Sans", serif; white-space: pre; text-transform: uppercase; letter-spacing: 0.1em;
-    content: string(header, first)
-    visibility: hidden;
-  }
-  @bottom-right-corner {
-    font-weight: 900; font: 9pt "Gill Sans", serif;
-    content: counter(page);
-    text-align: right;
-    margin-right: 1cm;
-  }
-  @bottom-right {
-    font-weight: 900; font: 9pt "Gill Sans", serif;
-    white-space: pre; text-transform: uppercase; letter-spacing: 0.1em;
-    content: string(header, first)
-  }
-}
-
-/*
-  In theory we should be able to use the :first selector so taht
-  we can put the page numbering on the bottom of the first page of the chapter
-  but have the rest of the pages number at the top.  But this does not seem
-  to work.  See http://www.princexml.com/doc/6.0/page-selectors/
-
-  So for now just always number at the bottom :(
-*/
-/*
-div.chapter { page: bottom-number; }
-@page bottom-number :first {
-  @top-left {
-    visibility: hidden;
-  }
-  @bottom-left {
-    visibility: visible;
-  }
-  @top-right {
-    visibility: hidden;
-  }
-  @bottom-right {
-    visibility: visible;
-  }
-}
-*/
-
-@page cover { margin: 0; }
-
-@page frontmatter :left {
-  @bottom-left-corner {
-    content: counter(page, lower-roman);
-  }
-  @bottom-left-corner {
-    content: counter(page, lower-roman);
-  }
-}
-
-@page frontmatter :right {
-  @bottom-right-corner {
-    content: counter(page, lower-roman);
-  }
-  @bottom-right-corner {
-    content: counter(page, lower-roman);
-  }
-}
-
-@page blank :left {
-  @top-left { visibility: hidden; }
-  @bottom-left { visibility: hidden; }
-  @top-left-corner { visibility: hidden; }
-  @bottom-left-corner { visibility: hidden; }
-}
-
-@page blank :right {
-  @top-right { visibility: hidden; }
-  @bottom-right { visibility: hidden; }
-  @top-right-corner { visibility: hidden; }
-  @bottom-right-corner { visibility: hidden; }
-}
-
-/* footnotes */
-.footnote {
-  display: none;                   /* default rule */
-
-  display: prince-footnote;        /* prince-specific rules */
-  position: footnote;
-  footnote-style-position: inside;
-
-  counter-increment: footnote;
-  margin-left: 1.4em;
-  font-size: 90%;
-  line-height: 1.4;
-}
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http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/src/main/webapp/WEB-INF/web.xml
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diff --git a/extras/rya.manual/src/main/webapp/WEB-INF/web.xml b/extras/rya.manual/src/main/webapp/WEB-INF/web.xml
deleted file mode 100644
index 71398d6..0000000
--- a/extras/rya.manual/src/main/webapp/WEB-INF/web.xml
+++ /dev/null
@@ -1,50 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
-    Copyright (C) 2009-2010 the original author or authors.
-    See the notice.md file distributed with this work for additional
-    information regarding copyright ownership.
-
-    Licensed under the Apache License, Version 2.0 (the "License");
-    you may not use this file except in compliance with the License.
-    You may obtain a copy of the License at
-
-        http://www.apache.org/licenses/LICENSE-2.0
-
-    Unless required by applicable law or agreed to in writing, software
-    distributed under the License is distributed on an "AS IS" BASIS,
-    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-    See the License for the specific language governing permissions and
-    limitations under the License.
-
--->
-
-<web-app xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xmlns="http://java.sun.com/xml/ns/javaee" xmlns:web="http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd"
-	xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd"
-	version="2.5">
-
-  <display-name>MVM ALX Documentation</display-name>
-
-  <description>
-    MVM ALX Documentation
-  </description>
-
-  <filter>
-    <filter-name>TemplateEngineFilter</filter-name>
-    <filter-class>org.fusesource.scalate.servlet.TemplateEngineFilter</filter-class>
-  </filter>
-  <filter-mapping>
-    <filter-name>TemplateEngineFilter</filter-name>
-    <url-pattern>/*</url-pattern>
-  </filter-mapping>
-
-  <welcome-file-list>
-    <welcome-file>index.conf</welcome-file>
-  </welcome-file-list>
-
-  <error-page>
-    <error-code>500</error-code>
-    <location>/WEB-INF/scalate/errors/500.scaml</location>
-  </error-page>
-</web-app>

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/src/main/webapp/_banner.ssp
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diff --git a/extras/rya.manual/src/main/webapp/_banner.ssp b/extras/rya.manual/src/main/webapp/_banner.ssp
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--- a/extras/rya.manual/src/main/webapp/_banner.ssp
+++ /dev/null
@@ -1,8 +0,0 @@
-      <table border="0" cellpadding="0" cellspacing="0" width="100%">
-        <tr>
-          <td align="left" class="topbardiv" nowrap="">
-        <img border="0" src="${uri("/images/logo2.png")}" width="400px" height="100px"></img>
-</a>
-          </td>
-        </tr>
-      </table>

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/src/main/webapp/_navigation.conf
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diff --git a/extras/rya.manual/src/main/webapp/_navigation.conf b/extras/rya.manual/src/main/webapp/_navigation.conf
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index 6ab6ce8..0000000
--- a/extras/rya.manual/src/main/webapp/_navigation.conf
+++ /dev/null
@@ -1,24 +0,0 @@
-h3. [Home|index]
-
-h3. Rya
-- [Overview|./overview.html]
-- [Quick Start|./quickstart.html]
-- [Load Data|./loaddata.html]
-- [Query Data|./querydata.html]
-- [Evaluation Table|./eval.html]
-- [Pre-computed Joins|./loadPrecomputedJoin.html]
-- [Inferencing|./infer.html]
-
-h3. Samples
-- [Typical First Steps|./sm-firststeps.html]
-- [Simple Add/Query/Remove Statements|./sm-simpleaqr.html]
-- [Sparql query|./sm-sparqlquery.html]
-- [Adding Authentication|./sm-addauth.html]
-- [Inferencing|./sm-infer.html]
-- [Named Graph|./sm-namedgraph.html]
-- [Update data|./sm-updatedata.html]
-- [Alx|./alx.html]
-
-h3. Development
-- [Building From Source|./build-source.html]
-- [LTS Maven Settings XML|./maven-settings.html]
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/src/main/webapp/_quicklinks.ssp
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diff --git a/extras/rya.manual/src/main/webapp/_quicklinks.ssp b/extras/rya.manual/src/main/webapp/_quicklinks.ssp
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--- a/extras/rya.manual/src/main/webapp/_quicklinks.ssp
+++ /dev/null
@@ -1,5 +0,0 @@
-<p>
-<a href="${uri("/index.html")}" title="Home">Home</a>
-&#124;
-</p>
-

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/src/main/webapp/alx.conf
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diff --git a/extras/rya.manual/src/main/webapp/alx.conf b/extras/rya.manual/src/main/webapp/alx.conf
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--- a/extras/rya.manual/src/main/webapp/alx.conf
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@@ -1,59 +0,0 @@
-h1. Alx Rya Integration
-
-Alx is a modular framework for developing applications. Rya has mechanisms to integrate directly into Alx to provide other modules access to queries.
-
-Currently, the Alx Rya extension only allows interacting with an Accumulo store.
-
-h2. Prerequisites
-
-- Alx 1.0.5+ (we will refer to it at the ALX_HOME directory from now on)
-- alx.rya features xml (can be found in maven at mvn:mvm.rya/alx.rya/<version>/xml/features)
-
-h2. Steps
-
-1. Start up Alx
-2. features:addurl alx.rya features xml
-3. features:install alx.rya
-4. (optional) features:install alx.rya.console
-
-That's it. To make sure, run {{ls <alx.rya bundle id>}} and make sure something like this pops up:
-{code}
-mvm.rya.alx.rya (99) provides:
-------------------------------
-Bundle-SymbolicName = mvm.rya.alx.rya
-Bundle-Version = 3.0.4.SNAPSHOT
-objectClass = org.osgi.service.cm.ManagedService
-service.id = 226
-service.pid = mvm.rya.alx
-----
-...
-{code}
-
-h2. Using
-
-The bundle registers a Sail Repository, so you can interact with it directly as in the other code examples. Here is a quick groovy example of the usage:
-{code}
-import org.springframework.osgi.extensions.annotation.*;
-import org.openrdf.repository.*;
-import org.openrdf.model.ValueFactory;
-import static mvm.rya.api.RdfCloudTripleStoreConstants.*;
-
-class TstRepo {
-
-	@ServiceReference
-	public void setRepo(Repository repo) {
-		println repo
-		RepositoryConnection conn = repo.getConnection();
-		ValueFactory vf = VALUE_FACTORY;
-        def statements = conn.getStatements(vf.createURI("http://www.Department0.University0.edu"), null, null, true);
-        while(statements.hasNext()) {
-            System.out.println(statements.next());
-        }
-        statements.close();
-        conn.close();
-	}
-
-}
-{code}
-
-The bundle also registers a RyaDAO, so you can interact with the RyaDAO interface directly
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/src/main/webapp/build-source.conf
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diff --git a/extras/rya.manual/src/main/webapp/build-source.conf b/extras/rya.manual/src/main/webapp/build-source.conf
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+++ /dev/null
@@ -1,19 +0,0 @@
-h1. Building from Source
-
-h2. Prerequisites
-
-* Rya code
-* Maven 2.2 +
-
-h2. Building
-
-Using Git, pull down the latest code from the url above.
-
-Run the command to build the code {{mvn clean install}}
-
-If all goes well, here are the artifacts that you will be interested in:
-* Rya-WAR : web/web-rya/target/web.rya.war
-
-h3. Cloudbase
-
-To build cloudbase projects, run with the 'cloudbase' profile: {{mvn clean install -Pcloudbase}}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/src/main/webapp/css/pygmentize.css
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@@ -1,134 +0,0 @@
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http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/ce4a10ff/extras/rya.manual/src/main/webapp/css/scalate/console.css
----------------------------------------------------------------------
diff --git a/extras/rya.manual/src/main/webapp/css/scalate/console.css b/extras/rya.manual/src/main/webapp/css/scalate/console.css
deleted file mode 100644
index 4b2dfe7..0000000
--- a/extras/rya.manual/src/main/webapp/css/scalate/console.css
+++ /dev/null
@@ -1,71 +0,0 @@
-/**
- * Copyright (C) 2009-2010 the original author or authors.
- * See the notice.md file distributed with this work for additional
- * information regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#scalate-console {
-  position:fixed;
-  top:40px;
-  right:10px;
-  background: #FDFCAD;
-  padding:10px;
-  border: 1px solid #BDBD81;
-  font-family:Arial,Verdana,Helvetica,sans-serif;
-  font-size: 80%;
-  max-width: 400px;
-}
-
-#scalate-console .archetypes ul, #scalate-console .templates ul, #scalate-console .resources ul, #scalate-console .layouts ul   {
-  padding-left:20px;
-  overflow: auto;
-}
-
-#scalate-console .toggle {
-  text-align: right;
-}
-
-#scalate-console .toggle img {
-  vertical-align: middle;
-}
-
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-  margin: 10px;
-  overflow: auto;
-  background: white;
-}
-
-#scalate-console div.attributes table th {
-  text-align: left;
-  color: #993333;
-}
-#scalate-console div.attributes table td {
-  padding:2px;
-  border-top: 1px solid #BDBD81;
-}
-
-#scalate-console div.body {
-  margin: 10px;
-  overflow: auto;
-  max-height: 300px;
-  background: white;
-}
-
-#scalate-console div.systemProperties {
-  margin: 10px;
-  overflow: auto;
-  max-height: 300px;
-  background: white;
-}