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java.util.logger.Logging: keeping logger.properties file outside the jar file

In my project I have a properties file which I use to set the level of logging. Now when I export my project as a jar and use it to run the project on a remote machine (linux), I cannot set the level. Is there a way to keep the properties file outside the jar file such that I can set the level and make the jar read that properties file. (preferred using environment variable)

There are several ways to achieve this, for example:
Configure your IDE to export resources outside the JAR: usually I don't consider this option since the specific solution depends by the developer's IDE
Use a generic build tool, for example Ant, and specify in the build.xml file which properties files should be packaged outside the jar
Integrate your project with Maven and customize the package goal in order to copy some specific properties file outside jar
From your question I guess you are exporting the JAR from your IDE, but as I stated above the solution depends by the IDE. For this reason, in order to adopt an IDE independent solution, I would suggest to use Ant. This would allow you to solve this and many similar issues that could arise in the future.
You can get Ant here: just download and unpackage it in any folder, it takes a couple of minutes. Then add a reference to Ant bin directory in your PATH variable (not strictly necessary but suggested) and create a sample build.xml file. Here it is a template example:
<project name="template" default="compile" basedir=".">
<description>Build file template</description>
<property name="project.name" value="myProject"/>
<property name="driver.log" value="log4j-1.2.15.jar"/>
<property name="driver.database" value="ojdbc6.jar"/>
<property name="library.home" value="lib"/>
<property name="env.type" value="dev"/>
<property name="src.version" value="Demo" />
<property name="src.folder" value="root/folder/template"/>
<property name="src.package" value="root.folder.template"/>
<property name="src.home" value="${basedir}/src/${src.folder}"/>
<property name="dist.home" value="${basedir}/dist"/>
<property name="build.home" value="${basedir}/build"/>
<property name="docs.home" value="${basedir}/docs"/>
<!-- Setting the classpath necessary to compile -->
<path id="compile.classpath">
<pathelement location="${library.home}/${driver.log}"/>
<pathelement location="${library.home}/${driver.database}"/>
</path>
<!-- DELETE the class files from the ${build.home} directory tree -->
<target name="clean" description="Clean up the build folder">
<delete dir="${build.home}"/>
<delete dir="${dist.home}"/>
</target>
<!-- CREATE the build directory structure used by compile -->
<target name="init" description="Creates the necessary directories">
<mkdir dir="${dist.home}"/>
<mkdir dir="${build.home}"/>
</target>
<!-- COMPILE the project and copy all necessary resources -->
<!-- Options: <compilerarg value="-Xlint"/> -->
<target name="compile" depends="init" description="Compile the sources">
<javac srcdir="${src.home}" destdir="${build.home}" includeantruntime="false">
<classpath refid="compile.classpath"/>
</javac>
<copy todir="${build.home}/${src.folder}/resources">
<fileset dir="${src.home}/resources">
<include name="messages_list.properties"/>
<include name="messages_list_en.properties"/>
</fileset>
</copy>
<copy file="${src.home}/resources/log4j_${env.type}.properties" tofile="${build.home}/${src.folder}/resources/log4j_${project.name}.properties"/>
<copy file="${src.home}/resources/configuration_${env.type}.properties" tofile="${build.home}/${src.folder}/resources/${project.name}_config.properties"/>
</target>
<!-- Creates the DISTRIBUTABLE JAR package and add 3d part libraries -->
<target name="dist" description="Create the distributable JAR archive">
<jar destfile="${dist.home}/${project.name}.jar">
<fileset dir="${build.home}">
<exclude name="place_holder\"/>
</fileset>
<!-- Setting MANIFEST properties -->
<manifest>
<section name="${ant.project.name} - ver. ${src.version}">
<attribute name="Built_By" value="${user.name}"/>
<attribute name="Created" value="${ts}"/>
</section>
<attribute name="Main-Class" value="package.mine.MainClass"/>
<attribute name="Class-Path" value=". lib/${driver.log} lib/${driver.database}"/>
</manifest>
</jar>
<!-- Adding third part libraries -->
<mkdir dir="${dist.home}/lib"/>
<copy file="${library.home}/${driver.database}" todir="${dist.home}/lib"/>
<copy file="${library.home}/${driver.log}" todir="${dist.home}/lib"/>
</target>
<tstamp><format property="ts" pattern="dd/MM/yyyy HH:mm:ss" /></tstamp>
</project>
Remark: in the template above you should replace the sample JARS (log4j and the OJDBC driver) with the actual JARS needed by your project. Then you can customize the copy task in order to place the properties files where you wish. You can copy those file in any directory you like, as long as such path appears in the application's classpath.

Why combine all jars together?

I have create RESTful web service based on the JAX-RS and used Jersey embedded web server. My ant script compiles code successfully while it gives me error ClassNotFoundException when I run my main class. So after doing research I came up with solution & here it goes java build ant file with external jar files . What I did was created a bundled jar file try to execute that & it works perfectly fine. I want to know the reason behind :
why this solution works ?
Why I should combine all jar file ?
Is it similar to war file which we create following J2EE architecture otherwise war will not be extracted by server ( say TOMCAT ) & in my case jar file for Jersey embedded HTTP server?
EDIT:
Here is my ant build.xml file
<property name="lib.dir" value="${user.dir}/lib"/>
<property name="build.dir" value="${user.dir}/build"/>
<property name="build.lib.dir" value="${build.dir}/lib"/>
<property name="build.classes.dir" value="${build.dir}/classes"/>
<property name="src.dir" value="${user.dir}/src/main/java"/>
<property name="main.class" value="com.assignment.ConsoleServer"/>
<path id="classpath">
<fileset dir="${lib.dir}" includes="**/*.jar"/>
</path>
<target name="clean">
<delete dir="${build.dir}"/>
</target>
<target name="init" depends="clean">
<!-- Create the build directory structure used by compile -->
<mkdir dir="${build.dir}"/>
<mkdir dir="${build.classes.dir}"/>
</target>
<target name="copy_jars" depends="init" >
<copy todir="${build.lib.dir}" >
<fileset dir="${lib.dir}">
<include name="**/*.jar" />
</fileset>
</copy>
</target>
<target name="compile" depends="copy_jars">
<javac srcdir="${src.dir}" destdir="${build.classes.dir}" classpathref="classpath" includeantruntime="false"/>
</target>
<target name="jar" depends="compile">
<jar destfile="${build.dir}/${ant.project.name}.jar" basedir="${build.classes.dir}">
<manifest>
<attribute name="Main-Class" value="${main.class}"/>
</manifest>
<zipgroupfileset dir="${lib.dir}" includes="*.jar"/>
</jar>
</target>
<target name="run" depends="jar">
<java fork="true" classname="${main.class}">
<classpath>
<path refid="classpath"/>
<path location="${build.dir}/${ant.project.name}.jar"/>
</classpath>
</java>
</target>
Here is my folder structure
P.S. I am not java expert so pardon me if this question is stupid.

Why this solution works?
In your particular case, you probably didn't include all of the necessary dependencies in your deployment in your previous. (It is not clear from your question how you were originally doing the deployment.)
Now you have put all of the application and dependent class files, etc into one JAR file, and presumably you are deploying / running that file. It works because now it has everything that it needs to run ... which it didn't before.
Why I should combine all jar file?
In your case I suspect that it was not strictly necessary. There was probably a way to "deploy" all of the dependencies without combining them into a single JAR file.
However, there is one case where a "uber-jar" has advantages. That is when the JAR is intended to be an "executable" JAR, and you want to be able to distribute / install it as a single file. (And executable JAR
file can refer to external JARs, etc, but the way that you have to do
it is "fragile".)
Is it similar to war file ... ?
Sort of, though a WAR file contains JAR files ... and typically other kinds of resources that the web-container understands.

The solution works because you packed all you service classes and depending libraries in one jar. That jar and everything inside will be in the class path and visible to your execution virtual machines class loader.
If you leave your depending libraries out your Jersey Web server needs to have them on it's class path, then you wouldn't get ClassNotFoundExcpetion
You shouldn't pack web application in single jar. You should crate war file where you dependencies will be placed inside WEB-INF/lib. You would easily then deploy that war on any application server. Switching to Maven instead of Ant can help a lot.
EDIT: After you added more details to description and ant
If you don't want to use fat-jar you can either
modify your antjava task to specify classpath that will reference
all external libraries (basically telling ant how to build
-classpath parameter for java -jar command
even better, modify your javac ant task by making complete Manifest file that specifies Class-Path correctly, take a better
look at the solution (at the bottom) of the answer you linked (java build ant file with external jar files)
For completness reference on Manifest here

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.

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.

How to include the lib folder in the manifest classpath in Netbeans

A library that my java application uses needs looks for a file (log4j.xml) in the class path. I use netbeans to manage my project, but I can't find a way to include the lib/ folder.
Netbeans automatically creates a MANIFEST.MF file inside the application jar and also creates a folder called lib/ which includes all dependencies. This manifest specifies a Class-Path attribute that overrides any -cp argument provided on the command line. I can select an arbitrary folder in netbeans' library panel, but it creates a sub folder in the manifest's classpath. I'd like all dependencies and the log4j.xml file inside the lib/ folder.
Hopefully it's possible to do this in the IDE. I include a snippet of the auto-generated build-impl.xml file.
<target depends="init,compile,-pre-pre-jar,-pre-jar" if="manifest.available+main.class+mkdist.available" name="-do-jar-with-libraries">
<property location="${build.classes.dir}" name="build.classes.dir.resolved"/>
<pathconvert property="run.classpath.without.build.classes.dir">
<path path="${run.classpath}"/>
<map from="${build.classes.dir.resolved}" to=""/>
</pathconvert>
<pathconvert pathsep=" " property="jar.classpath">
<path path="${run.classpath.without.build.classes.dir}"/>
<chainedmapper>
<flattenmapper/>
<globmapper from="*" to="lib/*"/>
</chainedmapper>
</pathconvert>
<taskdef classname="org.netbeans.modules.java.j2seproject.copylibstask.CopyLibs" classpath="${libs.CopyLibs.classpath}" name="copylibs"/>
<copylibs compress="${jar.compress}" jarfile="${dist.jar}" manifest="${manifest.file}" runtimeclasspath="${run.classpath.without.build.classes.dir}">
<fileset dir="${build.classes.dir}"/>
<manifest>
<attribute name="Main-Class" value="${main.class}"/>
<attribute name="Class-Path" value="${jar.classpath}"/>
</manifest>
</copylibs>
<echo>To run this application from the command line without Ant, try:</echo>
<property location="${dist.jar}" name="dist.jar.resolved"/>
<echo>java -jar "${dist.jar.resolved}"</echo>
</target>
Thanks.

Instead of editing the build-impl.xml file you should add this entry to the build.xml file. When you modify anything in your project pertaining to the building of that project, it will generate a new build-impl.xml file.
Here is an example of what I put in my build.xml file:
<target depends="init" name="-do-clean">
<delete dir="${build.dir}"/>
<delete file="${dist.jar}"/>
<delete dir="${dist.dir}/lib"/>
<delete dir="${dist.dir}/resources"/>
</target>
Since I put this in the build.xml file, it will override the "-do-clean" section of the build-impl.xml file which contains:
<target depends="init" name="-do-clean">
<delete dir="${build.dir}"/>
<delete dir="${dist.dir}" followsymlinks="false" includeemptydirs="true"/>
</target>
Furthermore, since it is in the build.xml it won't be modified by Netbeans.

I found a way to acheive this modifying the build-impl.xml.
I changed:
<attribute name="Class-Path" value="${jar.classpath}"/>
to:
<attribute name="Class-Path" value="${jar.classpath} /lib"/>
The problem is that netbeans will overwrite it since this file is automatically generated.

You can simply turn off project option Build/Packaging/Copy Dependent Library and manualy edit manifest.mf in root folder of your project (which is a template for manifest in jar file).

It seems that your problem is the "globmapper" that stores your log4j.xml file in /lib - you'd want it on the "/" or the jar.