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Java package / class library convention?

I am a C# developer and I am messing around with Java. In C# I would normally have my front end project and then when I need to add another layer to the project (i.e service layer etc) I would add a class library in the solution and add a reference to it.
What is the convention in Java? Do you add another Java project to the workspace and then reference the project? Or do you add a package to the project which contains your front end?
UPDATE
Sorry, I am using eclipse...hence the reference to 'workspace'

There's no real convention. When you say "workspace" you're not referring to Java, but rather a development environment (sounds like Eclipse). There are a number of ways to do it; you could do it the way you're suggesting, you could include the dependency via Maven, you could combine them all together in one project, etc.
Which to choose depends on your needs, who else will be consuming either the individual libraries or the completed project, and so on.

How to divide your source code depends a lot on the structure of your project. It is important to pay attention to a good code organization. You should keep classes for a common task or for a distinct application layer in own packages. You should watch for inter-package dependencies.
Using different "projects" (be it Maven or Eclipse projects) helps ensuring that you (your developers) do not violate structural boundaries because the compiler checks the dependencies (one project references the other project, like in C#/VS). Maven generates a build artifact (e.g. a JAR file) for every project.
To summarize, I think it is a good idea to create new individual projects for each program module in order to be able to manage the dependencies between the projects explicitly.

You are assuming everyone works with eclipse, it seems (your references to "workspace").
You can do anything you want, but keep in mind others might not be able to include 'separate' projects for various components of the application.
You can easily address that issue by using some build tool (ant, maven) to build appropriate jars for the various app components, like data-model, persistence, API, etc.
If you front-end is an RIA, might make more sense to develop it as a separate project, although not necessary. If your app is some sort of Java driven UI, you can still do whatever you want, in both cases make sure the UI components have their own package hierarchy.

Yes, I guess I would create a separate package. So your UI code might be in com.mycompany.app.ui, your service code in com.mycompany.app.service, etc. However you want to organize your classes is up to you. Java itself doesn't care what packages the classes are in. The packages just help to make the code more manageable for the developers.

Unlike most things in Java, there's no real convention defined for how to split up project.
In my experience, it makes sense to include code that serves a particular business purpose in a single project, and to separate out code that you intend to share between multiple projects, or code that is not specific to a particular business purpose (e.g. database access, JMS libraries, etc.), into a separate project.

If the UI and the server layer are being developed in a single project, which means packaged and deployed in the same WAR file, I'd create a new package for the service and add classes and interfaces as needed.
If the service layer is deployed separately, I'd add dependencies as a JAR to the web project. All I should need are clients for the service.

If you're working in Eclipse follow these steps:
1) Right-click the project and choose "Build Path"-"Configure Build Path..."
2) Switch to Libraries tab and click Add External JARs (or just Add JARs if they're already in the workspace).
3) Now you can either manually add import of the corresponding class, or just hit Ctrl+Shift+O (Source-Organize Imports) and Eclipse will do the job for you.

I suggest you can use netbeans then you can create a java class library,when you deploy your project,netbeans will generate jar files for you,and place them at the right location.I'm also a ms developer,hope it helps

Extending/Inheriting Tomcat Projects

We are developing webapps with Eclipse + Tomcat plugin. We recently started a new app which will run on Facebook and StudiVZ (FB competitor in Germany). Since the functionality of the app will be 95% the same we split the code into separate Eclipse projects (app-core, app-facebook, app-vz). The -core project is source-linked into the -facebook and -vz projects in Eclipse. We are also using Hudson for CI and made ant scripts that import the code from the -core project before building. So basically we tried to inherit on a project level.
The described method has some flaws:
Versioning is complicated
The -core project does not run standalone, which makes automatic testing partly impossible
We need to modify some models where the -core projects classes depend on
Other problems that make me think this is not the best solution
Does anyone have suggestions for a better solution?

There are a wealth of build tools available for Java that address dependency management and versioning specifically. Many of these integrate with Hudson and Eclipse.
I'd suggest looking at Maven and how it does dependency management as a good starting point. Even if you don't use Maven itself, many of the solutions out there build on Maven's dependency management mechanism. Something like Apache Ivy allows you to use maven dependency management, but still use your own custom Ant scripts; whereas something like Gradle is wholesale replacement.

You should be able to split your project into 3 or more parts and then establish dependencies via Java Build Path. You need to clean up the dependencies between the projects. If you need to configure your core components depending on whether it is a -facebook or a -vz project, you might need to separate configuration, maybe even use Spring or similar dependency injection framework.
When trying to introduce reuse into web-based Java projects, usually the problems arise in the UI code. Not many frameworks were built with this approach in mind.

I don't use/hate Eclipse[1], but can point to how we deal with a similar problem.
We use Maven with IntelliJ. In particular, both of these support modules which have defined internal dependencies. In your case it could be -fb and -vz modules depending on core, or you can split core into smaller parts (such as DAO, business logic, etc.).
When compiling, deliverables of "upper" modules would be used to build "lower" modules.
Let's go over points/flaws you have raised:
versioning is no longer a problem as everything sits under the same root of Subversion/GIT/VCS of your choice
Why is that a problem? Certainly this shouldn't be an issue for unit tests as how I understand TDD, these should not require complex environments. For automated tests, you would have to test the core API (as this is the interface between core and everything else, right?) hence this shouldn't require any fronted stuff?
you need to explain your other points to tell why you don't like it
It is against Geneva convention to ask a developer to use anything other than IDE of his/her choice.

How to organize projects?

I've been working with Visual Studio for a long long time, but now I'm been requested to work on a Java web project. We've decide to use Spring MVC as framework, and we want to use Log4J (for logging obviously =P) and JUnit for unit testing. Now, in the "Microsoft way" I will create a Solution, and I'll add A web project and a Unit testing project; now that I'm usign Netbeans, is it possible to do like that? Or how should I organize my projects?
Thanks for sharing your experience!

Have you thought about using Maven as a way to manage your project? I've heard really good things about it.
You can find a list of what Maven is, exactly, here.
In short, it has the following goals (I took these from the web site):
Making the build process easy
Providing a uniform build system
Providing quality project information
Providing guidelines for best practices development
Allowing transparent migration to new features

Try to use maven, and there is a standard way for a project :)

In Netbeans you specify what type of project you want to create, say Java Web Application. Netbeans will then create the files and folders to support that project. Within the project view explorer, you can see the 'Test Packages' node, this is where you add java classes to support your unit testing. When you add a unit test, Netbeans will add a reference to the correct JUnit library to your project (you can see this on project properties > libraries > compile test).
For Spring MVC, the same goes. You add a dependency in Netbeans, either at project creation time, or from the properties dialog afterwards.
This is just tip of the iceberg. So I hope this information allows you to at least get started and you can return with more specific questions as you get further in.

How to modularize a (large) Java App?

I have a rather large (several MLOC) application at hand that I'd like to split up into more maintainable separate parts. Currently the product is comprised of about 40 Eclipse projects, many of them having inter-dependencies. This alone makes a continuous build system unfeasible, because it would have to rebuild very much with each checkin.
Is there a "best practice" way of how to
identify parts that can immediately be separated
document inter-dependencies visually
untangle the existing code
handle "patches" we need to apply to libraries (currently handled by putting them in the classpath before the actual library)
If there are (free/open) tools to support this, I'd appreciate pointers.
Even though I do not have any experience with Maven it seems like it forces a very modular design. I wonder now whether this is something that can be retrofitted iteratively or if a project that was to use it would have to be layouted with modularity in mind right from the start.
Edit 2009-07-10
We are in the process of splitting out some core modules using Apache Ant/Ivy. Really helpful and well designed tool, not imposing as much on you as maven does.
I wrote down some more general details and personal opinion about why we are doing that on my blog - too long to post here and maybe not interesting to everyone, so follow at your own discretion: www.danielschneller.com

Using OSGi could be a good fit for you. It would allow to create modules out of the application. You can also organize dependencies in a better way. If you define your interfaces between the different modules correctly, then you can use continuous integration as you only have to rebuild the module that you affected on check-in.
The mechanisms provided by OSGi will help you untangle the existing code. Because of the way the classloading works, it also helps you handle the patches in an easier way.
Some concepts of OSGi that seem to be a good match for you, as shown from wikipedia:
The framework is conceptually divided into the following areas:
Bundles - Bundles are normal jar components with extra manifest headers.
Services - The services layer connects bundles in a dynamic way by offering a publish-find-bind model for plain old Java objects(POJO).
Services Registry - The API for management services (ServiceRegistration, ServiceTracker and ServiceReference).
Life-Cycle - The API for life cycle management (install, start, stop, update, and uninstall bundles).
Modules - The layer that defines encapsulation and declaration of dependencies (how a bundle can import and export code).
Security - The layer that handles the security aspects by limiting bundle functionality to pre-defined capabilities.

First: good luck & good coffee. You'll need both.
I once had a similiar problem. Legacy code with awful circular dependencies, even between classes from different packages like org.example.pkg1.A depends on org.example.pk2.B and vice versa.
I started with maven2 and fresh eclipse projects. First I tried to identify the most common functionalities (logging layer, common interfaces, common services) and created maven projects. Each time I was happy with a part, I deployed the library to the central nexus repository so that it was almost immediately available for other projects.
So I slowly worked up through the layers. maven2 handled the dependencies and the m2eclipse plugin provided a helpful dependency view. BTW - it's usually not too difficult to convert an eclipse project into a maven project. m2eclipse can do it for you and you just have to create a few new folders (like src/main/java) and adjust the build path for source folders. Takes just a minute or two. But expect more difficulties, if your project is an eclipse plugin or rcp application and you want maven not only to manage artifacts but also to build and deploy the application.
To opinion, eclipse, maven and nexus (or any other maven repository manager) are a good basis to start. You're lucky, if you have a good documentation of the system architecture and this architecture is really implemented ;)

I had a similar experience in a small code base (40 kloc). There are no °rules":
compiled with and without a "module" in order to see it's usage
I started from "leaf modules", modules without other dependencies
I handled cyclic dependencies (this is a very error-prone task)
with maven there is a great deal with documentation (reports) that can be deployed
in your CI process
with maven you can always see what uses what both in the site both in netbeans (with a
very nice directed graph)
with maven you can import library code in your codebase, apply source patches and
compile with your products (sometimes this is very easy sometimes it is very
difficult)
Check also Dependency Analyzer:
(source: javalobby.org)
Netbeans:
(source: zimmer428.net)

Maven is painful to migrate to for an existing system. However it can cope with 100+ module projects without much difficulty.

The first thing you need to decide is what infra-structure you will move to. Should it be a lot of independently maintained modules (which translates to individual Eclipse projects) or will you consider it a single chunk of code which is versioned and deployed as a whole. The first is well suited for migrating to a Maven like build environment - the latter for having all the source code in at once.
In any case you WILL need a continuous integration system running. Your first task is to make the code base build automatically, so you can let your CI system watch over your source repository and rebuild it whenyou change things. I decided for a non-Maven approach here, and we focus on having an easy Eclipse environment so I created a build enviornment using ant4eclipse and Team ProjectSet files (which we use anyway).
The next step would be getting rid of the circular dependencies - this will make your build simpler, get rid of Eclipse warnings, and eventually allow you to get to the "checkout, compile once, run" stage. This might take a while :-( When you migrate methods and classes, do not MOVE them, but extract or delegate them and leave their old name lying around and mark them deprecated. This will separate your untangeling with your refactoring, and allow code "outside" your project to still work with the code inside your project.
You WILL benefit from a source repository which allows for moving files, and keeping history. CVS is very weak in this regard.

I wouldn't recommend Maven for a legacy source code base. It could give you many headaches just trying to adapt everything to work with it.
I suppose what you need is to do an architectural layout of your project. A tool might help, but the most important part is to organize a logical view of the modules.

It's not free but Structure101 will give you as good as you will get in terms of tool support for hitting all your bullet points. But for the record I'm biased, so you might want to check out SonarJ and Lattix too. ;-)

Multiple Java projects and refactoring

I have recently joined a project that is using multiple different projects. A lot of these projects are depending on each other, using JAR files of the other project included in a library, so anytime you change one project, you have to then know which other projest use it and update them too. I would like to make this much easier, and was thinking about merging all this java code into one project in seperate packages. Is it possible to do this and then deploy only some of the packages in a jar. I would like to not deploy only part of it but have been sassked if this is possible.
Is there a better way to handle this?

Approach 1: Using Hudson
If you use a continuous integration server like Hudson, then you can configure upstream/downstream projects (see Terminology).
A project can have one or several downstream projcets. The downstream projects are added to the build queue if the current project is built successfully. It is possible to setup that it should add the downstream project to the call queue even if the current project is unstable (default is off).
What this means is, if someone checks in some code into one project, at least you would get early warning if it broke other builds.
Approach 2: Using Maven
If the projects are not too complex, then perhaps you could create a main project, and make these sub-projects child modules of this project. However, mangling a project into a form that Maven likes can be quite tricky.

If you use Eclipse (or any decent IDE) you can just make one project depend on another, and supply that configuration aspect in your SVN, and assume checkouts in your build scripts.
Note that if one project depends on a certain version of another project, the Jar file is a far simpler way to manage this. A major refactoring could immediately means lots of work in all the other projects to fix things, whereas you could just drop the new jar in to each project as required and do the migration work then.

I guess it probably all depends on the specific project, but I think I would keep all the projects separate. This help keep the whole system loosely coupled. You can use a tool such as maven to help manage all the dependencies between the projects. Managing dependencies like this is one of maven's main strengths.

Using Ant as your build tool, you can package your project any way that you want. However, leaving parts of your code out of the distribution seems like it would be error prone; you might accidentally leave out necessary classes (presumably, all of your classes are necessary).
In relation to keeping your code in different projects, I have a loose guideline. Keep the code that changes together in the same project and package it in its own jar file. This works best when some of your code can be broken out into utility libraries that change less frequently than your main application.
For example, you might have an application where you've generated web service client classes from a web service WSDL (using something like the Axis library). The web service interface will likely change infrequently, so you don't want to have the regeneration step reoccurring all the time in your main application build. Create a separate project for this piece so that you only have to recreate the web service client classes when the WSDL changes. Create a separate jar and use it in your main application. This style also allows other projects to reuse these utility modules.
When following this style, you should place a version number in the jar manifest so that you can keep track of which applications are using which versions of your module. Depending on how far you want to take this, you could also keep a text file in the jar that details the changes that have occurred for each revision (much like an open source library).

It's all possible (we had the same situation some years ago). How hard or easy it'll be depends on your IDE (refactoring, merging, organizing new project) and you build tool (deploying). We used IDEA as IDE and Ant as build tool and it wasn't too hard. One sunday (nobody working+committing), 2 people on one computer.
I'm not sure what you mean by
"deploy only some of the packages in a jar"
I think you will need all of them at runtime, won't you? As I understood they depend on each other.