Moved all dependencies to a local repository and created an overview

file for JavaDoc.

.gitignore

@@ -2,3 +2,4 @@
 /.settings/
 /.classpath
 /minimalSysBio.xml
+/.project

lib/de/zbit/SysBio/1390/SysBio-1390.pom

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>de.zbit</groupId>
+  <artifactId>SysBio</artifactId>
+  <version>1390</version>
+  <description>POM was created from install:install-file</description>
+</project>

lib/de/zbit/SysBio/maven-metadata-local.xml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<metadata>
+  <groupId>de.zbit</groupId>
+  <artifactId>SysBio</artifactId>
+  <versioning>
+    <release>1390</release>
+    <versions>
+      <version>1390</version>
+    </versions>
+    <lastUpdated>20160411192438</lastUpdated>
+  </versioning>
+</metadata>

lib/org/sbgn/0.2/sbgn-0.2.pom

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>org</groupId>
+  <artifactId>sbgn</artifactId>
+  <version>0.2</version>
+  <description>POM was created from install:install-file</description>
+</project>

lib/org/sbgn/maven-metadata-local.xml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<metadata>
+  <groupId>org</groupId>
+  <artifactId>sbgn</artifactId>
+  <versioning>
+    <release>0.2</release>
+    <versions>
+      <version>0.2</version>
+    </versions>
+    <lastUpdated>20160411192817</lastUpdated>
+  </versioning>
+</metadata>

lib/org/sbml/JSBML/2492/JSBML-2492.pom

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>org.sbml</groupId>
+  <artifactId>JSBML</artifactId>
+  <version>2492</version>
+  <description>POM was created from install:install-file</description>
+</project>

lib/org/sbml/JSBML/maven-metadata-local.xml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<metadata>
+  <groupId>org.sbml</groupId>
+  <artifactId>JSBML</artifactId>
+  <versioning>
+    <release>2492</release>
+    <versions>
+      <version>2492</version>
+    </versions>
+    <lastUpdated>20160411190120</lastUpdated>
+  </versioning>
+</metadata>

pom.xml

@@ -57,6 +57,17 @@
     </developer>
   </developers>
 
+  <!-- =================================================================== -->
+  <!-- Repositories -->
+  <!-- =================================================================== -->
+  <repositories>
+    <repository>
+      <id>in-project</id>
+      <name>In project repository</name>
+      <url>file://${project.basedir}/lib</url>
+    </repository>
+  </repositories>
+
   <!-- =================================================================== -->
   <!-- Dependencies                                                        -->
   <!-- =================================================================== -->
@@ -72,15 +83,15 @@
     </dependency>
 
     <dependency>
-      <!-- mvn install:install-file -Dfile=/path/to/jsbml.jar -DgroupId=org.sbml -DartifactId=JSBML -Dversion=REVISION_NUMBER -Dpackaging=jar -->
+      <!-- mvn install:install-file -Dfile=./lib/jsbml.jar -DgroupId=org.sbml -DartifactId=JSBML -Dversion=2492 -Dpackaging=jar -DlocalRepositoryPath=./lib/ -->
       <groupId>org.sbml</groupId>
       <artifactId>JSBML</artifactId>
       <version>2492</version>
       <scope>compile</scope>
     </dependency>
 
     <dependency>
-      <!-- mvn install:install-file -Dfile=/path/to/libSBGN.jar -DgroupId=org -DartifactId=sbgn -Dversion=0.2 -Dpackaging=jar -->
+      <!-- mvn install:install-file -Dfile=./lib/org.sbgn-with-dependencies.jar -DgroupId=org -DartifactId=sbgn -Dversion=0.2 -Dpackaging=jar -DlocalRepositoryPath=./lib/ -->
       <groupId>org</groupId>
       <artifactId>sbgn</artifactId>
       <version>0.2</version>
@@ -94,7 +105,7 @@
     </dependency>
 
     <dependency>
-      <!-- mvn install:install-file -Dfile=/path/to/sysbio.jar -DgroupId=de.zbit -DartifactId=SysBio -Dversion=REVISION_NUMBER -Dpackaging=jar -->
+      <!-- mvn install:install-file -Dfile=./lib/sysbio.jar -DgroupId=de.zbit -DartifactId=SysBio -Dversion=1390 -Dpackaging=jar -DlocalRepositoryPath=./lib/ -->
       <groupId>de.zbit</groupId>
       <artifactId>SysBio</artifactId>
       <version>1390</version> <!-- SVN revision -->
@@ -186,4 +197,23 @@
 
   </build>
 
+
+  <!-- =================================================================== -->
+  <!-- Building project documentation files                                -->
+  <!-- =================================================================== -->
+
+  <!-- see https://maven.apache.org/plugins/maven-javadoc-plugin/examples/javadoc-resources.html -->
+  <reporting>
+    <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-javadoc-plugin</artifactId>
+        <version>2.10.3</version>
+        <configuration>
+          <overview>${basedir}/overview.html</overview>
+        </configuration>
+      </plugin>
+    </plugins>
+  </reporting>
+
 </project>

src/main/javadoc/overview.html

@@ -0,0 +1,9 @@
+<html>
+
+  <head>
+  </head>
+
+  <body>
+  </body>
+
+</html>