diff --git a/GraphTea-linux.sh b/GraphTea-linux.sh
index 0860eb02..afd1fe01 100755
--- a/GraphTea-linux.sh
+++ b/GraphTea-linux.sh
@@ -1,5 +1,3 @@
 #!/bin/bash
 
-cd binary
-java -jar graphtea-main.jar
-cd ..
+java -jar binary/graphtea-main.jar
diff --git a/GraphTea-mac.sh b/GraphTea-mac.sh
index 0860eb02..afd1fe01 100755
--- a/GraphTea-mac.sh
+++ b/GraphTea-mac.sh
@@ -1,5 +1,3 @@
 #!/bin/bash
 
-cd binary
-java -jar graphtea-main.jar
-cd ..
+java -jar binary/graphtea-main.jar
diff --git a/src/scripts/build.xml b/build.xml
similarity index 94%
rename from src/scripts/build.xml
rename to build.xml
index 20ecbf0d..e8376252 100644
--- a/src/scripts/build.xml
+++ b/build.xml
@@ -33,7 +33,7 @@
        		developplugin
      ====================================================================== -->
 
-<project name="GraphTea" default="make binary" basedir="..">
+<project name="GraphTea" default="make binary">
     <description>
         The ant build file of GraphTea Project.
     </description>
@@ -46,9 +46,10 @@
             <pathelement location="${basedir}"/>
         </path>
         <pathconvert property="xdir" refid="zdir" targetos="unix"></pathconvert>
-        <property name="scripts.dir" value="${xdir}/scripts"/>
-        <property name="build.dir" value="${xdir}/../../build"/>
-        <property name="dist.dir" value="${xdir}/../binary"/>
+        <property name="scripts.dir" value="${xdir}/src/scripts"/>
+        <property name="build.dir" value="${xdir}/build"/>
+        <property name="dist.dir" value="${xdir}/binary"/>
+        <property name="src.dir" value="${xdir}/src"/>
         <path id="project.lib">
             <fileset dir="${scripts.dir}/lib" includes="**/*.*"/>
         </path>
@@ -63,7 +64,7 @@
           target: compile
          ================================= -->
     <target name="compile" depends="depends" description="--> The ant build file of GraphTea Project.">
-        <javac srcdir="${xdir}" destdir="${build.dir}">
+        <javac srcdir="${src.dir}" destdir="${build.dir}">
             <classpath>
                 <path refid="project.lib"/>
             </classpath>
@@ -71,7 +72,7 @@
             <!--<exclude name="graphtea/gui/plugins/developplugin/content/**"/>-->
         </javac>
         <copy todir="${build.dir}">
-            <fileset dir="${xdir}">
+            <fileset dir="${src.dir}">
                 <include name="graphtea/**/*.*"/>
                 <exclude name="**/*.java"/>
                 <exclude name="**/*.~*"/>
@@ -99,6 +100,7 @@
                 <attribute name="SplashScreen-Image" value="icon.PNG"/>
             </manifest>
             <fileset dir="${build.dir}">
+                <exclude name="**/*.psd"/>
                 <include name="graphtea/platform/**/*.*"/>
             </fileset>
         </jar>
@@ -269,7 +271,7 @@
         <!--<include name="**/*.*"/>-->
         <!--</fileset>-->
         <!--</copy>-->
-        <copy todir="${dist.dir}/lib">
+        <copy todir="${dist.dir}/lib" failonerror="false">
             <fileset dir="${scripts.dir}/lib">
                 <include name="**/*.*"/>
             </fileset>
@@ -286,16 +288,11 @@
             <pathelement location="${basedir}"/>
         </path>
         <pathconvert property="xdir" refid="zdir" targetos="unix"></pathconvert>
-        <property name="scripts.dir" value="${xdir}/scripts"/>
-        <property name="build.dir" value="${xdir}/../../build"/>
-        <property name="dist.dir" value="${xdir}/../binary"/>
-        <delete>
-            <!--<fileset dir="${build.dir}" includes="**/*.*"/>-->
-            <fileset dir="${dist.dir}" includes="**/*.*"/>
-        </delete>
-        <available file="${dist.dir}" property="dist.dir.present"></available>
-        <delete dir="${temp.dir}" />
-
+        <property name="scripts.dir" value="${xdir}/src/scripts"/>
+        <property name="build.dir" value="${xdir}/build"/>
+        <property name="dist.dir" value="${xdir}/binary"/>
+        <delete failonerror="false" dir="${dist.dir}" />
+        <delete failonerror="false" dir="${build.dir}" />
     </target>
 
     <!-- =================================-->
@@ -338,7 +335,6 @@
             <!--</fileset>-->
         <!--</zip>-->
         <!--<copyfile src="${basedir}/../docs/javadoc.zip" dest="${basedir}/../binary/javadoc.zip"/>-->
-        <deltree dir="${basedir}/../developer_resources/javadoc"/>
 
     <!--</target>-->
 
diff --git a/make.sh b/make.sh
index a99f93f2..49ed7ab3 100755
--- a/make.sh
+++ b/make.sh
@@ -1,5 +1,2 @@
-cd src/scripts
 ant
-cd ../../binary
-java -jar graphtea-main.jar
-cd ..
+java -jar binary/graphtea-main.jar
diff --git a/src/graphtea/platform/Application.java b/src/graphtea/platform/Application.java
index 06cca3f8..c8e126c3 100644
--- a/src/graphtea/platform/Application.java
+++ b/src/graphtea/platform/Application.java
@@ -87,7 +87,15 @@ public BlackBoard init() {
      */
     public void loadExtensions(BlackBoard blackboard) {
         ExtensionClassLoader.cl = getExtensionsClassLoader();
-        ExtensionClassLoader e = new ExtensionClassLoader("extensions");
+        String path = null;
+        try {
+            path = new File(getClass().getProtectionDomain().getCodeSource().getLocation().toURI().getPath()).getParent();
+            System.out.println(path);
+        } catch (Exception e1) {
+            e1.printStackTrace();
+        }
+
+        ExtensionClassLoader e = new ExtensionClassLoader(path + File.separator + "extensions");
         for (String c : e.classesData.keySet()) {
             try {
                 Class s = getExtensionsClassLoader().loadClass(c);
diff --git a/src/graphtea/platform/plugin/Plugger.java b/src/graphtea/platform/plugin/Plugger.java
index 4388e5e9..d3ceaa51 100644
--- a/src/graphtea/platform/plugin/Plugger.java
+++ b/src/graphtea/platform/plugin/Plugger.java
@@ -69,7 +69,15 @@ public Plugger(BlackBoard blackboard) {
      * to <code>classLoader</code>
      */
     public void plug() {
-        File f = new File("plugins");
+        File directory = null;
+        try {
+            directory = new File(getClass().getProtectionDomain().getCodeSource().getLocation().toURI().getPath()).getParentFile();
+            System.out.println(directory);
+        } catch (Exception e1) {
+            e1.printStackTrace();
+        }
+
+        File f = new File(directory, "plugins");
         if (f.isDirectory() && f.canRead()) {
             for (File ff : f.listFiles()) {
                 if (ff.isFile() && "jar".equalsIgnoreCase(getExtension(ff))) {
@@ -81,7 +89,7 @@ public void plug() {
             System.out.println("------------------------------------------------------------");
             if (first != null) {
                 int libCount = 0;
-                File libf = new File("lib");
+                File libf = new File(directory, "lib");
                 ArrayList<URL> libURLs = new ArrayList<URL>();
                 if (libf.isDirectory() && libf.canRead()) {
                     for (File ff : libf.listFiles()) {
@@ -111,7 +119,7 @@ public void plug() {
                     i++;
                 }
                 try {
-                    urls[i] = new File("extensions").toURL();
+                    urls[i] = new File(directory, "extensions").toURL();
                 } catch (MalformedURLException e) {
                     ExceptionHandler.catchException(e);
                 }
@@ -122,8 +130,10 @@ public void plug() {
             } else
                 System.out.println("Can't Load Any Plugin!");
             System.out.println("------------------------------------------------------------");
-        } else
-            System.out.println("There is no directory with name plugins.");
+        } else {
+            System.out.println("There is no directory named \"plugins\" in " +
+                    directory.getAbsolutePath());
+        }
     }
 
     /**
diff --git a/src/scripts/lib/Jama-1.0.1.jar b/src/scripts/lib/Jama-1.0.1.jar
deleted file mode 100644
index 4c76beca..00000000
Binary files a/src/scripts/lib/Jama-1.0.1.jar and /dev/null differ
diff --git a/src/scripts/lib/README b/src/scripts/lib/README
new file mode 100644
index 00000000..5e262efd
--- /dev/null
+++ b/src/scripts/lib/README
@@ -0,0 +1,5 @@
+Debian systems don't need this directory, since they ship bsh.jar and
+jama.jar in /usr/share/java/.
+
+Instead of patching build.xml, solely keep this README to make git happy
+(git doesn't track empty directories).
diff --git a/src/scripts/lib/bsh-2.0b4.jar b/src/scripts/lib/bsh-2.0b4.jar
deleted file mode 100644
index 36fe03d7..00000000
Binary files a/src/scripts/lib/bsh-2.0b4.jar and /dev/null differ