Update usability and repo clarity

.gitignore

@@ -1,4 +1,5 @@
 /!!!temp/
+/heap/
 /AlgTest_JavaCard/nbproject/private/*
 /AlgTest_JavaCard/!uploader/*
 /AlgTest_JavaCard/build/*
@@ -7,18 +8,17 @@
 /AlgTest_JavaCard/src304/*
 /AlgTest_JavaCard/src305/*
 
-/AlgTest_JClient/nbproject/private/
+/AlgTest_JClient/nbproject/
 /AlgTest_JClient/build/*
 /AlgTest_JClient/test/*.jar
 /AlgTest_JClient/dist/*
-/AlgTest_JClient/nbproject/*
-
+/AlgTest_JClient/*.log
+/AlgTest_JClient/store/*
 
+/AlgTest_Process/nbproject/
 /AlgTest_Process/dist/*
 /AlgTest_Process/test-output/*
 /AlgTest_Process/build/*
-/AlgTest_Process/nbproject/private/*
-/AlgTest_Process/nbproject/*
 /AlgTest_Process/dist/*
 
 *.class

AlgTest_JClient/build.xml

@@ -1,31 +1,99 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project name="AlgTestJClient" default="default" basedir=".">
-    <description>Builds, tests, and runs the project AlgTestJClient.</description>
-    <import file="nbproject/build-impl.xml"/>
-          <target name="-post-jar">
-	     <!-- Copy newly build jar into test directory for simulator of smart cards-->
-             <copy file="${basedir}/dist/AlgTestJClient.jar" tofile="${basedir}/test/AlgTestJClient.jar"/>
-          </target>
-
+<project name="AlgTestJClient" default="jar" basedir=".">
+    <description>Builds, tests, and runs AlgTestJClient.</description>
+
+    <!-- Directories -->
+    <property name="src.dir"      value="src"/>
+    <property name="src.javacard" value="../AlgTest_JavaCard/src"/>
+    <property name="build.dir"    value="build"/>
+    <property name="classes.dir"  value="${build.dir}/classes"/>
+    <property name="dist.dir"     value="dist"/>
+    <property name="dist.jar"     value="${dist.dir}/AlgTestJClient.jar"/>
+    <property name="store.dir"    value="store"/>
+    <property name="main.class"   value="algtestjclient.AlgTestJClient"/>
+
+    <!-- Compile classpath -->
+    <path id="compile.classpath">
+        <fileset dir="libs/JNA"  includes="*.jar"/>
+        <fileset dir="libs"      includes="jcardsim-3.0.6.0.jar"/>
+        <fileset dir="../libs"   includes="jcommander-1.81.jar"/>
+    </path>
+
+    <path id="run.classpath">
+        <path refid="compile.classpath"/>
+        <pathelement location="${classes.dir}"/>
+    </path>
+
+    <target name="init">
+        <mkdir dir="${classes.dir}"/>
+        <mkdir dir="${dist.dir}"/>
+    </target>
+
+    <target name="compile" depends="init">
+        <javac destdir="${classes.dir}"
+               source="1.8" target="1.8"
+               encoding="UTF-8"
+               includeantruntime="false"
+               deprecation="false">
+            <src path="${src.javacard}"/>
+            <src path="${src.dir}"/>
+            <classpath refid="compile.classpath"/>
+        </javac>
+    </target>
+
+    <target name="jar" depends="compile">
+        <copy todir="${dist.dir}/lib">
+            <fileset dir="libs/JNA"  includes="*.jar"/>
+            <fileset dir="libs"      includes="jcardsim-3.0.6.0.jar"/>
+            <fileset dir="../libs"   includes="jcommander-1.81.jar"/>
+        </copy>
+        <path id="dist.classpath">
+            <fileset dir="${dist.dir}/lib" includes="*.jar"/>
+        </path>
+        <manifestclasspath property="manifest.cp" jarfile="${dist.jar}">
+            <classpath refid="dist.classpath"/>
+        </manifestclasspath>
+        <jar destfile="${dist.jar}" basedir="${classes.dir}">
+            <manifest>
+                <attribute name="Main-Class" value="${main.class}"/>
+                <attribute name="Class-Path" value="${manifest.cp}"/>
+            </manifest>
+        </jar>
+        <!-- Copy jar into test directory for card simulator -->
+        <copy file="${dist.jar}" tofile="test/AlgTestJClient.jar"/>
+    </target>
+
     <target name="package-for-store" depends="jar">
-       <property name="store.jar.name" value="AlgTestJClient"/>
-       <property name="store.dir" value="store"/>
-       <property name="store.jar" value="${store.dir}/${store.jar.name}.jar"/>
-       <echo message="Packaging ${application.title} into a single JAR at ${store.jar}"/>
-       <delete dir="${store.dir}"/>
-       <mkdir dir="${store.dir}"/>
-       <jar destfile="${store.dir}/temp_final.jar" filesetmanifest="skip">
-           <zipgroupfileset dir="dist" includes="*.jar"/>
-           <zipgroupfileset dir="dist/lib" includes="*.jar"/>
-           <manifest>
-               <attribute name="Main-Class" value="${main.class}"/>
-           </manifest>
-       </jar>
-       <zip destfile="${store.jar}">
-           <zipfileset src="${store.dir}/temp_final.jar"
-           excludes="META-INF/*.SF, META-INF/*.DSA, META-INF/*.RSA"/>
-       </zip>
-       <delete file="${store.dir}/temp_final.jar"/>
-   </target>
-
-</project>
+        <property name="store.jar" value="${store.dir}/AlgTestJClient.jar"/>
+        <echo message="Packaging into a single JAR at ${store.jar}"/>
+        <delete dir="${store.dir}"/>
+        <mkdir  dir="${store.dir}"/>
+        <jar destfile="${store.dir}/temp_final.jar" filesetmanifest="skip">
+            <zipgroupfileset dir="${dist.dir}"     includes="*.jar"/>
+            <zipgroupfileset dir="${dist.dir}/lib" includes="*.jar"/>
+            <manifest>
+                <attribute name="Main-Class" value="${main.class}"/>
+            </manifest>
+        </jar>
+        <zip destfile="${store.jar}">
+            <zipfileset src="${store.dir}/temp_final.jar"
+                        excludes="META-INF/*.SF, META-INF/*.DSA, META-INF/*.RSA"/>
+        </zip>
+        <delete file="${store.dir}/temp_final.jar"/>
+    </target>
+
+    <target name="run" depends="jar">
+        <java classname="${main.class}" fork="true">
+            <classpath refid="run.classpath"/>
+            <jvmarg value="-enableassertions"/>
+            <jvmarg value="-noverify"/>
+        </java>
+    </target>
+
+    <target name="clean">
+        <delete dir="${build.dir}"/>
+        <delete dir="${dist.dir}"/>
+        <delete dir="${store.dir}"/>
+    </target>
+
+</project>