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Eclipse: how to properly integrate a Maven/Ant project into a larger one?

I have a Java project that depends on a 3-rd party component. This component is available both as a jar and as a Maven/Ant project. One option for me is to simply add the jar as a library. However, I prefer to add the source code into my project since I may need to slightly modify their source code to better suit my needs.
What's the right way to do it in Eclipse?
My main project has a simple structure: src/ and lib/. The external component also has a standard structure: src/, test/, build/, target/, pom.xml, build.xml. So do I need to copy piece by piece (like contents of one src/ into the other src/), in which case what goes where? Or do I somehow copy it all at once? Or smth else?

The best way would be if you use maven on your projet for dependency management. This way, if you have the other projects open in eclipse, your project will resolve them as local projects, but if you don't, maven will try to fetch the jars from the configured nexus repository.
This way, you avoid having to manually configure your Eclipse projects. Maven will be able to configure your project anywhere you want to build it, not having to manually configure dependency resolution.

Import both the projects into eclipse. Add the reference of 3pp jar project to your project as a reference by clicking on Add on build path option. While delivering it as output there will be a dependency to the 3pp jar project. So either deliver it as separate jar and add it to classpath while executing your project else you have to copy the entire source files into your project and deliver it test complete jar.
Making a jar will be handled by eclipse itself.

Adding plain Java project as a classpath to an eclipse plugin

I have a plain Java project (not a plugin project) which I want to add to a classpath of a eclipse plugin which I am developing. But in web projects I can add that project as a build path and it works fine. But I tried same thing in eclipse plugin, I am able to compile successfully, but at run time I am getting java.lang.ClassNotFoundException.
I know OSGi quite well and I know how to add OSGi into an classpath (using export-packages) but what I want is to add Standard, non-osgi project into an classpath, so that I wont' get runtime errors. Is there anyway I can achieve this?
I can export project as a jar file or make it as a plugin project and it would work fine. But that's not my option currently because, still that API is in pre-alpha stage, and there would be lot of changes going on. So I am trying to avoid pain of exporting it as jar file everytime. Is there any option for me other than this?

I have a similar situation: I want non-OSGi Maven dependencies integrated into the classpath of my plugin. I succeeded with a roundabout solution, which I think is the best I could get.
I have a build step outside of Eclipse where I copy the class files of the dependency into the plugin's lib folder. The lib folder is specified in MANIFEST.MF as an entry in Bundle-ClassPath and (here comes the hack) as a source folder in build.properties. That was the only way to make the plugin work both when launched from within Eclipse and when exported.

Project Build classes do not include external project imports

I have a project which imports another projects to its build path. When I clean the project to compile classes, the classes imported from external projects are not showing up as part of the compiled classes directory.
Do anyone know how to make sure these external import classes gets compile and included into my build classes?
Thanks

I don't think it's possible. But when you deploy your project, you'll certainly want to create a jar file to hold all your classes. And Eclipse has a wizard to export a jar file and choose to embed dependencies in the jar.
The usual way, however, is to have each project generate its own jar, and to use all the jar of the project + the jars of the dependencies as the classpath of the deployed project.

#Bitmap,
is this a WAR or EAR project?
In EAR project you have to specify clearly the "JAVA EE Module dependency" to include the referenced projects.
If you include a project as a build dependency, it will be for compile-time only.
If these are simple java projects you may want to look at "JAR JAR" enter link description here
to achieve this.
HTH

Runtime issues during developing an Eclipse Plugin

Right now, I am trying to create a plug-in of Eclipse which depends on other jar; therefore, I created a plug-in base on the jar and deployed it under my Eclipses' plugin foler. It works well when I start it from my working environment via an Eclipse. However, as soon as I have exported it into a jar and have deployed into Eclipse, it not work any more as it couldn't find out the dependent jar. What happened and how to solve the issue? Does anyone know that? please save me.

The MANIFEST.MF has a Tab called "Dependencies" in which alle plugins should placed the current plugin depends on.
At runtime you have to place the "dependencies" plugins in the same folder as the one you want to start or you want to work with.
When a plugin has jars it should use, you have to put the jars to the "Runtime" Classpath Entry and you should add the jar to the "Build" Binary Build entry.

Also, does the plugin.xml associated with your 'external jar' plugin does export the right packages ?
Did you check this article describing all steps necessary to packaging 3rd party jars as plug-ins ?
Other very important points are described in the article PDE and 3rdParty Bundles in OSGI Enterprise apps with rules such as:
Always put dependent JAR Files in separate bundles and describe the dependencies in your Manifest file. Don't hide those JARs in your own bundle.
If possible use Import-Package to resolve your dependencies.
Export only your "public" packages - no internal.
Use Require-Bundle only to resolve dependencies inside your own „universe“, not against common bundles.
Always version Require-Bundle, Import-Package und Export-Package.
Require-Bundle always has a dependency to a bundle with a specific name.
Import-Package isn't dependent from the name of the bundle, so its more flexible. Of course its more work to look at your packages and decide which you need to import or to export compared to a one-liner with Require-Bundle
If a bundle itself contains packages inside the bundle and exports them, never put these packages also into the Manifest as imported packages.
Before deploying of a bundle as plug-in be sure the Package-Uses are re-calculated. Wrong Package-Use entries for exported packages can stop PDE to export your Plug-In.

The working behavior out of Eclipse is normal, since the dependent jar is in the classpath of the project.
Have you had a look at the plugin folder you deployed? I suspect, that the dependency isn't contained in the plugin folder.

I just had a similar problem. I fixed it using the plugin view:
Add jar using the Classpath section of the Runtime tab
Use the Organise Manifest Wizard from the Overview tab to do all the required manifest changes
Use the Export Wizard from the Overview tab to export the finished plugin.
Note I am using Eclipse 3.3 so your milage may vary.

Eclipse debug-time classpath problem: How do you include a dependent project's output into a web project's runtime classpath?

So I started with a web services project (just a dynamic web project) that builds and debugs correctly from eclipse. We've pulled a chunk of common code out that we want to put into a shared library so now those classes are going into a separate jar project that the web project references.
On the web project, I did Project->Properties->Java Build Path->Projects->Add and added the jar project. And this correctly solved all the compile-time classpath problems and everything builds fine. But at runtime, when the tomcat server fires up, spring attempts to inject some of the classes contained in the jar file and I get a NoClassDefFoundError.
My .class and properties files and the contents of my META-INF directory are showing up in the ./build directory, but my WEB-INF/lib directory seems to be referenced in-place, and the jar dependency doesn't get copied in to it to show up as part of the Web App Library.
What is the magical incantation to tell eclipse that the other jar project needs to be available to tomcat at runtime? From our ant build script, we first just build the other project into WEB-INF/lib and everything works fine, but not for eclipse debugging.

I figured this out after spending some time on it. If you are in Eclipse Helios , go to properties > deployment assembly > add > project and select the dependent project you wish to add.

Java EE module dependencies would solve this problem.
You have already done the task of extracting your common classes into its own project, possibly because other projects depend on these classes. Either way, you'll have to ensure that this is a Utility project (appears under Java EE in the project wizards), and not just a plain Java project.
One that is done, you can proceed to add the Utility project to your build path (compile-time path) as you have figured out.
The additional (final) step is to establish a Java EE module dependency between your Dynamic Web project and the shared library, which causes the utility's classes to be placed in WEB-INF\lib during deployment, and even during export of the WAR. To do so, visit the dynamic web project's properties, and browse to the Java EE module dependencies. Ensure that your utility project is selected here. Redeploy/publish your application and you should be good to go.