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How could I have Eclipse export files into a different location than their source?

I am writing a Bukkit plugin in Eclipse in which I separate different functions into different packages and export each package as its own jar file.
However, I would still like to keep these packages in the same project, rather than separating them into different Eclipse projects. These plugins each have files which must be in the root of the jar file, such as plugin.yml. I have moved each jar's files into their respective packages, but these files are put into plugin.jar\com\Preston159\plugin rather than in the root of the jar file (plugin.jar\), causing the plugin not to work.
Does Eclipse have any function to make these files automatically compress into the root of the jar file even though they are contained within the package in the source, or, is this something that I could solve by using Maven? My current solution to this problem is to move the files manually after exporting the jar, but this is becoming increasingly annoying.
EDIT:
The project builder XML I ended up using to complete this task can be found here

You would need to use a Build Tool. There are several supported by Eclipse. Ant and Maven are now built-in, but there are several build tools that run directly within Eclipse, but Eclipse can also be configured to run an external build tool as well.
Do a quick search on build.xml for examples of ANT build jobs.
Unless you're specifically required to use MAVEN for continuous integration, etc. then what you want to accomplish would be easily done with ANT.

Netbeans generating .jar file

When I clean and build, Netbeans generates a .jar file for my Java project, and it uses a "lib" folder which has all of my external Jar files that I use. Can I somehow tell Netbeans to package these Jar files into the .jar it makes? So that I can run my project as a stand-alone .jar file?
I am using Netbeans 7.1.1 on Mac OSX

The short answer is no, the long answer is complicated.
Firstly, Java does not support embedded Jars (ie, you cann't simply add the depended Jars into the main Jar).
Secondly, uncompressing all the Jars and merging them into one will overwrite any resources/classes that share the same path/name. This may not be an issue in small projects but is a major issue in large ones (we have this problem with the project I'm working on at work).
One solution is to use something like One-Jar, which basically uses it's own boot class loader to all you to reference Jars inbedded within a single Jar.
I've had issues with this when using our own custom classloader, but otherwise it seems to work well.
It includes Ant support, so you can include it in your projects Ant build script, if you not using Maven, otherwise, you'll need to devise your own build process

There is no options in netbeans to do that.
There are some other options that a quick search would help, but requires manual intervention.

Understanding External Jars in Eclipse

So I'm fairly new to Java and especially Eclipse, so please excuse my ignorance. I took a project from a server and copied it locally to my machine. When I opened the workspace, I had many errors due to it not being able to find the jars. This makes sense because I don't have the same dir structure as the server I copied from. So if I copy the same external jar's to my machine and get it to compile into a jar and copy it back to the server, will it work? Or will it fail because now the external jar's are in a different place than it is expecting?
Also, down the road should I put the external jars into regular jars to avoid this problem?

You should be OK. Java is using what is called classpath to locate dependencies. The classpath may be different on the development machines, but as long as all the dependencies are on the classpath in the production everything should work.
To avoid issues with the synchronisation of directory structures the most common way is to use Maven - it will manage all the dependencies for you (but you have to manage the pom.xml - the Maven's project descriptor). A little clumsier way is to have the dependencies in the project, however you may end up with many projects having to include same jars, and then there will be version conflicts and so on.
For small projects you can manage dependencies yourself, however larger projects will need a more thought through strategy (like Maven).
In regard to the executable jars, make sure the Class-Path entry in <jarfile>:\META-INF\MANIFEST.MF is correct, e.g. where it references other jars, those jars are going to be there in the production. For example, assume we have ourjar.jar and assume this is a snippet from its MANIFEST.MF:
Class-Path: lib/myteamjar.jar
It will then be expected that a following directory structure is in place:
lib/myteamjar.jar
ourjar.jar

No, the location of the external jars does not mater. What you want to do is put the external jars on your classpath. How you do it depends on how you are running your java code. If you are running it from the CLI using the java command, it takes the classpath as an argument. If you want your code to build/run in Eclipse, you need to right click on your project, select "Build Path" > "Configure Build Path..." Use the "Add JARs..." button to add jars that are part of a project you have open and "Add External JARs..." to add jars that reside outside of the project. See specific documentation for your tool for more details about classpaths.

I would not recommend Maven to somebody who is fairly new to Java and Eclipse. I would forget about Eclipse, too.
You have a packaging and CLASSPATH issue. Focus on that.
What kind of project are you talking about? The answer you get will depend on what type of app you're creating. Is it an executable JAR? Then the right way to do it is to package everything into a ZIP file that's laid out exactly as the CLASSPATH in the JAR manifest expects.
If it's a web app, the right thing is a WAR file, with all the JARs your app needs in the WEB-INF/lib directory.
If you package things properly, you should end up with a single package that has everything laid out the right way. You should be able to deploy it to the server and make it all work.

Generating a Jar in Eclipse including external library

I have a java application I've written in eclipse. It works fine there.
It works fine run from a command line in the directory where I export it to. In that directory is another directory containing two jar files that I need for the application, and the manifest file has a Class-path option specifying them.
I want a way to use eclipse to generate the necessary file(s) to package this application to run on another machine. Is that possible?
If I choose "create executable jar file", it creates this huge file; it does unpack and repack the two libraries, which I know is one way to get their functionality included. I would actually prefer it if they were left as their own jars somehow, but I am not certain eclipse can do that. More annoying is the fact that the executable jar file option puts lots of files from my eclipse project into that jar file. I don't see an option to choose what gets included there, though I do see a place to enter inclusion and exclusion "rules' in the project properties. Do those apply here? Is there somewhere else I go to select what does and does not get included in the "executable jar"?
If I choose "create jar" (ins of "create executable jar"), I don't see where there's an option to include these two jar files anywhere. Perhaps there is no place to include them where they could be used.
If possible, I do not want to use Ant, I do not want to use Maven, I do not want to download another tool. It seems to me that Eclipse already has all this information and I suspect it can already do this without having to go and learn yet another "nifty" tool.

Eclipse has its own Jar export wizard for generate a runnable jar packed with required library or with the required library in a folder aside the jar.
Going in File ---> Export then choose Java - Runnable Jar
You can then choose how pack the jar and how handling libraries :
You can also save the ant script for later modification or use ...

You actually should use Ant or Maven for your task, I see no other option. Ant is already packed with eclipse, you only need to install a JDK, not only a JRE.
Ant is very easy to learn and you can find billions of examples in the internet. With ant you can do exactly what you want.
Maven is the more up-to-date way to build and package jars and do much more other stuff. Maven also is a good choice for you.

I'll second a vote for Maven. Eclipse has a decent maven integration (m2eclipse). Then check out this answer for building the jar effectively using Maven2
Building a runnable jar with Maven 2

How to add source files of library jars?

I am using Eclipse IDE and its derivative like Spring IDE for Java development.
In a web application project, I add external jars like Spring MVC jars, Apache commons jars etc to the Web App library folder, hence they are automatically added to the build path. There are many jars in the Web App library folder.
I want to create folder in the project and add all the source files (zip/jar) of the libraries included in Web App library folder, so that I can navigate through the source of libraries from the Java editor window. Whenever I add a source zip/jar file to this folder, Eclipse should detect it and use it whenever I want to navigate to the source of a library.
Is the above possible in eclipse?
Note: I know how to add source files
for each individual jar by navigating
to the build path window and
specifying the source location. But
this is very crude way, and I need to
do for every library individually.
Also the drawback is that source path
is absolute, which means if I import
the project into another computer then
I need to create the source path or
even worse I might have to add the
source files individually again.

One way to automagically get the sources for the jars would be some kind of dependency management system. Most people would scream Maven (2/3) by now, but others exist and work well. Maven does have nice Eclipse integration, so that should be a plus.
The downside is that setting up a Maven project just for it's dependency management can seem overkill. Another point is that all the jars you depend on should be "Mavenized" as well.
As far as I know Eclipse wont automatically detect/scan source archive files and link them up to libraries in your workspace in the way you described it.

I agree with #Gressie on using Maven and the Eclipse Maven plugins -- as in that case it's just a matter of ticking a few boxes and Maven will do that for you.
If however your project is not Maven-ized, you can still do this in Eclipse but it's more tedious:
for each one of the jars in your project (which appear under the dependecies section) right click on it and select properties
in the dialog that pops up you have (at least) 2 locations you can configure: java source attachment -- simply browse to your jar with the sources -- and also javadoc location (point it to the jar with javadoc if you want the javadoc to appear as a tooltip when you hover the mouse over one of the classes/methods/etc in that library).