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How to force ant javac task to overwrite the class file in the destination directory?

Here is a very simplified version of what I am trying to achieve. I have two directories, Directory1 and Directory2. Both directories contain Java source files. Some of the files in Directory2 can have the same fully qualified class name as the files in Directory1.
Using ant, the files are compiled to a directory called CompileDirectory, first from Directory1 and then from Directory2. I want the files in Directory2 to be compiled and overwrite the compiled class files from Directory1. However, ant seems to ignore the classes that have the same fully qualified class name.
Here's a simple example -
Directory structure
$ ls -R
.:
build.xml CompileDirectory Directory1 Directory2
./CompileDirectory:
./Directory1:
A.java
./Directory2:
A.java
build.xml
<project name="TestProject" default="build" basedir=".">
<target name="build" depends="javac1, javac2" />
<target name="javac1">
<javac srcdir="${basedir}/Directory1" destdir="CompileDirectory" includeantruntime="false"/>
</target>
<target name="javac2">
<javac srcdir="${basedir}/Directory2" destdir="CompileDirectory" includeantruntime="false"/>
</target>
</project>
Ant run
$ ant -buildfile build.xml
Buildfile: ...(path).../build.xml
javac1:
[javac] Compiling 1 source file to ...(path).../CompileDirectory
javac2:
build:
BUILD SUCCESSFUL
Total time: 0 seconds
As can be seen, the javac2 target above does nothing.
When I run the Java program, I see that the class file is the one from Directory1.
$ cd CompileDirectory/
$ java A
I am class A from directory 1
Is there a way to force the javac task in the javac2 target to compile the source file in Directory2 and overwrite the class file in the CompileDirectory?

It has to do with timestamp of files and whether the compiler thinks the source is newer than class file.
<project name="TestProject" default="build" basedir=".">
<target name="build" depends="javac1, touch2, javac2" />
<target name="javac1">
<javac srcdir="${basedir}/Directory1" destdir="CompileDirectory" includeantruntime="false"/>
</target>
<target name="touch2">
<sleep seconds="2" />
<touch datetime="now">
<fileset dir="${basedir}/Directory2" />
</touch>
</target>
<target name="javac2">
<javac srcdir="${basedir}/Directory2" destdir="CompileDirectory" includeantruntime="false"/>
</target>
</project>

Other possible way to avoid this is create a stage directory and compile the classes there and copy back to original directory using overwrite option.
<project name="TestProject" default="build" basedir=".">
<target name="build" depends="javac1, javac2, copy1" />
<target name="javac1">
<javac srcdir="${basedir}/Directory1" destdir="CompileDirectory" includeantruntime="false"/>
</target>
<target name="javac2">
<javac srcdir="${basedir}/Directory2" destdir="CompileDirectory1" includeantruntime="false"/>
</target>
<target name="copy1">
<copy overwrite="on" todir="CompileDirectory">
<fileset dir="CompileDirectory1">
<include name ="**/*.*"/>
</fileset>
</copy>
</target>

Class org.eclipse.jdt.core.JDTCompilerAdapter could not be loaded because of an invalid dependency

I am creating a java agent that will be used to to do some bytecode modification to some classes org.eclipse.jdt.core.JDTCompilerAdapter is one of them. I am using javassit to modify some the execute() method of org.eclipse.jdt.core.JDTCompilerAdapter. So I have included ecj as in my agent project (using gradle)
compile group: 'org.eclipse.jdt.core.compiler' ,name: 'ecj', version :'4.3.1'
As I need to use some classes from ecj.
The goal of the agent is to intercept the calls to execute method, modify the execute method to add some calls to some of my classes in the aim of triggering some processing.
I am testing the agent against a Simple java project with 2 classes. the project is builded with ant and uses JDTCompilerAdapter as a compiler.
Here is the build.xml file
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project basedir="." default="build" name="TestProject">
<property file="build.properties" />
<property name="debuglevel" value="source,lines,vars"/>
<property name="target" value="1.7"/>
<property name="source" value="1.7"/>
<path id="PClasspath">
<pathelement location="bin"/>
</path>
<target name="init">
<mkdir dir="bin"/>
<copy includeemptydirs="false" todir="bin">
<fileset dir="src">
<exclude name="**/*.java"/>
</fileset>
</copy>
</target>
<target name="clean">
<delete dir="bin"/>
</target>
<target depends="clean" name="cleanall"/>
<target depends="init" name="build">
<javac debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}">
<src path="src"/>
<classpath refid="PClasspath"/>
</javac>
</target>
<!--
<target description="copy Eclipse compiler jars to ant lib directory" name="init-eclipse-compiler">
<copy todir="${ant.library.dir}">
<fileset dir="${ECLIPSE_JDT_CORE}" includes="*.jar"/>
</copy>
</target>-->
<target name="build-e" >
<property name="build.compiler" value="org.eclipse.jdt.core.JDTCompilerAdapter"/>
<antcall target="build"/>
</target>
The agent is to be used when building a project.
So for testing the agent I use this command:
java -jar agent-wrapper.jar --outdir ./out --exec ./build_wrapper.sh
build_wrapper.sh contains this (I have added ecj dependency so I could compile the project with JDTCompilerAdapter as I have in bulid.xml <property name="build.compiler" value="org.eclipse.jdt.core.JDTCompilerAdapter"/> :
../ant/bin/ant -lib ../eclipse/plugins/ecj-4.3.1.jar build-e
The idea is that the agent-wrapper will parse the argument (outdir is used to generate some stuff and exec is a script used to launch a the build of my test project) get the command to be executed from build_wrapper.sh (in this case ../ant/bin/ant -lib ../eclipse/plugins/ecj-4.3.1.jar build-e) and add it self as java agent to the command.
The problem occurs during the execution of the agent. Here is the output:
java -jar custom-agent.jar --outdir ./out --exec ./build_wrapper.sh [10:18:53]
Picked up JAVA_TOOL_OPTIONS: -javaagent:/Users/dev/TestAgent/project/custom-agent.jar=OUTDIR=/Users/dev/TestAgent/project/./out
objc[30474]: Class JavaLaunchHelper is implemented in both /Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home/jre/bin/java and /Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home/jre/lib/libinstrument.dylib. One of the two will be used. Which one is undefined.
Buildfile: /Users/dev/TestAgent/project/build.xml
build-e:
init:
[mkdir] Created dir: /Users/dev/TestAgent/project/bin
build:
BUILD FAILED
/Users/dev/TestAgent/project/build.xml:47: The following error occurred while executing this line:
/Users/dev/TestAgent/project/build.xml:32: Class org.eclipse.jdt.core.JDTCompilerAdapter could not be loaded because of an invalid dependency.
Total time: 2 seconds
abnormal termination, exit code: 1
When I don't use ecj-4.3.1.jar inside my agent project, the build runs well I intercept the call to execute() method but I can't use the other classes from ecj jar.

The show stopper error is "Class org.eclipse.jdt.core.JDTCompilerAdapter could not be loaded because of an invalid dependency."
First hint at the fault might be found from reading this link
http://help.eclipse.org/mars/index.jsp?topic=%2Forg.eclipse.jdt.doc.user%2Ftasks%2Ftask-ant_javac_adapter.htm
The second hint might be that one of the jars required for running the JDTCompilerAdapter is missing.
To get the JDTCompilerAdapter to work I copied both the JDTCompilerAdapter.jar and org.eclipse.jdt.core.jar into the ant/lib folder.
There are differences based on version of eclipse and the version of java which are documented in the link mentioned above.

Could not find or load main class Java

Good evening Stack Overflow!
I started learning Java quite a few days ago, but not using an IDE once my computer is a bit slow. So, I decided to use Sublime Text, and compile things using ant on the cmd, since it seems to be the most reasonable thing to do.
Today I started ( at least tried ) to follow along a series of LWJGL tutorials (which are really cool), from ThinMatrix, but I can't manage to solve an error which I get every time I try to compile the 'project'.
This is the structure of my project:
LWJGL
src
com
game
test
MainGameLoop.java
renderEngine
DisplayManager.java
build.xml
And ladies and gentlemen... the build.xml (following Ant's official HelloWorld tutorial):
<project name="LWJGL" basedir="." default="main">
<property name="src.dir" value="src"/>
<property name="build.dir" value="build"/>
<property name="classes.dir" value="${build.dir}/classes"/>
<property name="lib.dir" value="lib"/>
<property name="jar.dir" value="${build.dir}/jar"/>
<property name="main-class" value="com.game.test.MainGameLoop"/>
<path id="classpath">
<fileset dir="${lib.dir}" includes="**/*.jar" />
</path>
<target name="clean">
<delete dir="${build.dir}"/>
</target>
<target name="compile">
<mkdir dir="${classes.dir}"/>
<javac srcdir="${src.dir}" destdir="${classes.dir}" includeantruntime="false" classpathref="classpath" />
</target>
<target name="jar" depends="compile">
<mkdir dir="${jar.dir}"/>
<jar destfile="${jar.dir}/${ant.project.name}.jar" basedir="${classes.dir}">
<manifest>
<attribute name="Main-Class" value="${main-class}"/>
</manifest>
</jar>
</target>
<target name="run" depends="jar">
<java jar="${jar.dir}/${ant.project.name}.jar" fork="true">
<jvmarg value="-Djava.library.path=lib/natives-win" />
</java>
</target>
<target name="clean-build" depends="clean,jar"/>
<target name="main" depends="clean,run"/>
Every time I run ant on the command line, inside the root folder of my project, I get this:
[java] Error: Could not find or load main class com.game.test.MainGameLoop
[java] Java Result: 1
I'm struggling to understand what is the root problem of this, I kinda sexually abused Google Search trying to find an answer on Java forums, Blogs, and even here...
I don't usually like populating Stack Overflow with noob questions, but I have to admit I don't know what to do.
Thanks in advance!

Your code depends on libraries. You have successfully added the libraries in the classpath to compile your code, and have thus successfully created an executable jar files containing your classes. But these classes depend on libraries to run. And when running the jar file, you don't secify anywhere that Java should look for classes in libraries in addition to your jar file.
See Generate manifest class-path from <classpath> in Ant for how to add a Class-Path entry to the manifest of your executbale jar file. Beware: the paths of the libraries must be relatie to the path of the jar.
Ant is a bit outdated. If I were you, I'd try using gradle, which has a neat application plugin doing all that for you, and much more.

I finally managed to solve this problem that I was struggling with by the help from a good friend of mine. There are two tricky points:
First, when specifying the "Main-Class" in the manifest section, just use the following format "packageName.className", and there is no need to specify the "build" or "source" folders!
Second, try and zip all the jar files that your "jar" file is going to depend on using "zipgroupfileset"
This image shows how I have commented out the "Class-Path" attribute that I would use for addressing the dependencies of the project, and have replaced it with the "zipgroupfileset". I hope that help you as well.

Small thing that can cause this issue is using uppercase letters in file extension. For example you can't use MainGameLoop.Java, The correct extension should be all lowercase like below.
MainGameLoop.java
Please check that first.

Classpath, Compile, and Run with Ant?

I'm completely new to Ant and need to add a couple jars to my classpath, compile a couple .java files, and run a junit test, all in Ant. I've been looking at a few online tutorials and manuals, but can't seem to wrap my head around the entire xml writing process.
All the previously-written code resides in a single directory called XXX.
In XXX there are two jars I need to add to my classpath with export CLASSPATH=$CLASSPATH:jar1:jar2, two java files I compile with javac *.java, one of which contains several junit tests that I run with java org.junit.runner.JUnitCore Tests. The build.xml would reside in XXX as well (I believe).
So far I have the following for just compiling, although I think there's a lot missing.
<?xml version="1.0"?>
<project name="EtlAutomation" default="compile" basedir=".">
<property name="src" value="${basedir}"/>
<target name="compile">
<!-- Compile .java files -->
<javac srcdir="${src}" destdir="${src}"/>
</target>
</project>
What else do I need to add to compile *.java in the current directory? How can I run the export CLASSPATH command, and finally the junit commend?
I'm not asking for anyone to write my code, but it would be appreciated. If anyone knows a good beginner tutorial for a unix environment, that would be awesome. I'm a total beginner with ant so I'll take what I can get.

Here is a previous question addressing this. And this may work for you:
<project name="EtlAutomation" default="compile" basedir=".">
<property name="src" value="${basedir}"/>
<path id="compile.classpath">
<fileset dir="./">
<include name="*.jar"/>
</fileset>
</path>
<target name="compile" >
<javac destdir="${src}" srcdir="${src}">
<classpath refid="compile.classpath"/>
</javac>
</target>
<target name="run" depends="compile">
<junit>
<classpath refid="compile.classpath" />
<test name="TestExample" />
</junit>
</target>
</project>

How can I build my jar file so that users who use the library will be able to see the javadoc in Eclipse

I'm working on a small library for our in-company use, and have been heavily documenting it. Now I'm building my jar with the following code:
<project name="commonutils" default="compile" basedir=".">
<property name="src" location="src" />
<property name="build" location="buildDirecotry" />
<target name="compile">
<delete file="${ant.project.name}.jar" />
<mkdir dir="${build}"/>
<javac srcdir="${src}" destdir="${build}" debug="on" target="1.5">
<classpath>
<pathelement location="lib/build/server.zip" />
<pathelement path="${java.class.path}/"/>
</classpath>
</javac>
<jar basedir="${build}" destfile="${ant.project.name}.jar" />
<delete dir="${build}" />
</target>
</project>
Which works fine, it builds my jar file with all the src files in it, but when I include the jar file in another project I no-longer have any of my javadoc comments. Using JDDecompiler I cannot see the comments in the class file, although I'm not sure if its the java compiler that's stripping them or JD.
My question is: How can I build my jar file so that users who use the library will be able to see the javadoc in Eclipse.

If you include the source files in the jar (each class and java file in the same package-directory) it should work.
<target name="jar.noCompile.src">
<jar destfile="${ant.project.name}.jar">
<fileset dir="${build}"/>
<fileset dir="${src}" includes="**/*.java"/>
</jar>
</target>

AFAIK the documentation is an Eclipse feature. You have to configure it manually. In your build generate the documentation (usually into folder 'javadoc') and package it with the JAR. Once someone wants to use your library, he/she has to go into Java Build Path select libraries, add yours, click next to it to open the tree node and then double click on Javadoc location to configure it.