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How does Maven manage duplicate artifactIds when they belong to a different group?

I'm building some different web projects with Maven and thinking about how to name their artifacts. For the REST API layer, it's convenient to share some classes, so I want to create exchange-api.jar files which will be shared among different projects.
Let's suppose I've got a web application which has it's own exchange-api module. The groupId would be com.mycompany.app1 so the whole maven id for the artifact should be com.mycompany.app1:exchange-api:1.0. Now let's suppose I want to access other app's API from this application. I have to include the dependency com.mycompany.app2:exchange-api:1.0. artifactIds are the same, but the groupId is different. However, both should end up as exchange-api-1.0.jar in the classpath.
How does Maven take care of this? Should I use a unique artifactId for each of them?

Maven manages this problem allowing you to customize the file name mapping, this can be done both for WAR and EAR applications. However I think that your naming convention is poor. Suppose that your projects are publicly downloadable and people not using Maven download them manually and add them to their projects: do you think that a generic "exchange-api" would be clear enough? I think no. Good names are app1-exchange-api and app2-exchange-api. Or simply app1-api and app2-api. There are several examples of this rule: Spring, Hibernate and so on.

Eclipse project layout classpath issues

I have a large scale project I am working on at the moment using Eclipse. Normally, as a one man team, these problems would not be an issue, but as our team is not one person we need to be able to break up pieces of the project to be worked on by certain team members.
In simplicity, let's say I have two layers to be separated apart:
1. Each DAO is a separate Java project, to be worked upon individually
2. The web-tier service layer contains all of our service endpoints and must be able to reference all of the DAOs. This layer runs on Tomcat as a dynamic web project, and utilizes Adobe LiveCycle Data Services as the piece that handles creation and management of endpoints.
Now, the issue we are running into is that when we create a DAO and unit test it individually it runs great. But when we reference it into our service project and try to run it we begin to get all kinds of issues related to the fact that we have two different versions of certain jars referenced in and as such we begin to have errors when running the server.
As a result, we know we can solve the issue by pulling the problem jars and ensuring that this is not an issue again in the future, but as I said before this is a large scale project with multiple people working on it and we don't want to be spending our time weeding out dependency issues when under the gun.
We are looking for recommendations on where to proceed for alternative solutions? Our team is new to JavaEE and as such we don't have much of a bearing on what we can use to tie everything together in it, or if it is a viable solution. Should we be looking at turning our DAOs into EJBs and deploying them in an EAR library? If so, where would our service layer lie, and would the service layer be able to reference the DAO classes since the EJB maintains it's own classpath (from what we have read?) Are we looking down the wrong path, or are we completely wrong in our current understanding of JavaEE?
Any assistance is greatly appreciated. We are still in the framework stage of this project and we want to be sure that we will be able to maintain it in the long run.

I second the Maven recommendation. That can add all sorts of sanity to your project structure.
Maven can even generate Eclipse workspaces via mvn eclipse:eclipse
An important clarification on the EJBs note. As of ava EE 6 is you no longer need to separate EJBs from Servlets and can use them together in the very same jar in the war file.
So understand from that that using EJBs or not no longer has any impact on packaging or classloaders as it once did. These are now separate decisions. EARs and classloader separation should now be viewed as a feature you might want to use should you want classloader separation and the complexity it brings. Most applications simply do not need that and are more than fine with just a war file containing servlets, ejbs, jpa entities, cdi beans, jaxrs services and whatever else you need. You are free to decide how you want to separate them or if you want to bother separating them at all.
EJBs do make great DAOs due to transaction management, something you don't get from plain Tomcat but can be made available in Tomcat via TomEE and works fine in Eclipse. You should consider EJBs for that reason, not for dependency reasons.
Side note, as you're new to Java EE, you might find this helpful:
http://openejb.apache.org/examples-trunk/index.html

In order to have things organized when working with Java EE in teams of 1+ people I could suggest:
Use Maven to manage your build process and library dependencies.
Maven has a small learning curve, but once you grasp it you will be grateful. By using Maven you no longer depends on Eclipse to manage your classpath.
A thing about it that I think is really helpful when working in teams is the install feature. Suppose you are woking on the version 1.0 of an EJB module, say core-ejb-module-1.0, and you've got it to a stable state and want everyone working in the project to refer to it from now on.
You then run a maven command like this on it: mvn clean package install
Maven will clean this module, compile it, run tests, create the jar and then install it to a repository that you define. Could be any computer in your company.
Now you may tell the guys working on other projects to update this dependency version on their .pom file and in the next build they run, before compiling, maven will download this library and then use it. Really neat. No more classpath hell.
(There are other ways to always automatically refer to the latest library as stated in this post, but there are some caveats. Anyway it's just an example.)
Use JPA/EJB instead of DAO Pattern.
Some people say DAO meaning any sort of data access, others really mean that they use the DAO Pattern to access objects. If that is your case, you no longer need to use it when using JPA. (At least for most common scenarios).
In my case, I have a generic EntityService which is capable of doing CRUD operations on any Entity and has a centralized query management. Then every EJB's that should perform database related operations may inject this guy and do its job.
As a suggestion, with Maven, you project could be organized as such:
core project structure
core (The pom root)
core-ejb-module (Includes all generic EJB's, like the EntityService for instance.)
core-jpa-module (Includes all JPA generic definitions, like Interfaces, MappedSuperclasses and such.)
core-jsf-module (Includes all JSF generic definitions, like abstract controllers, generic converters and wrappers for FacesContext, etc..)
Now that you have a core generic module setup, you could create:
an application structure
app (The pom root)
app-ear-module (Includes all other modules in this application. Shared jars goes in the ear /lib folder, so all other modules could reference to them.)
app-ejb-module-a (Includes EJB's for the business layer of your application. It uses the core-ejb-module)
app-ejb-module-b (You may have lots of ejb modules. You may even have a project that contains only ejb modules. Other apps will declare their dependency on them via Maven.)
app-jpa-module (Contains definitions for JPA Entities that represents you database tables. Depends on the core-jpa-module)
app-web-module (Holds the pages, Controllers and Converters for this application.)
I think you got the idea. Things tend to be loosely coupled and you may organize your projects as you like.
This is just a simple example to illustrate. I didn't explained a lot about Maven but if you're interested I think it will help you indeed.
I hope it gives you some ideas and may help you in any way.
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If you can run all the sub-components using the same set of dependencies, you may find it helpful to migrate to a Maven build.
With Maven, you can define a top-level project that manages all the 3rd party dependency versions in one place, so all modules are built, tested and deployed against the same library versions. You are also likely to find Maven a good fit for the multi-module approach you have adopted, as it ensures that a project is rebuilt correctly if one of its dependencies changes.
You would still be able to use dynamic web projects as before; Eclipse will automatically deploy the DAOs as part of the service project (IIRC you need to characterise the DAOs as utility modules).
If you do go down the EJB root, you are correct that each EAR will get its own class-loader, and can therefore use a varying set of dependencies. However, in your position I would tend to look at improving your dependency management first - it'll probably be cheaper and easier.

Build classes in same package into separate jars

I have a server application and two Swing-based client applications. We're developing them in eclipse and there's a separate project for each.
Many classes are shared. For example, the my.server package has some classes for both the server and the clients while others are for the server only. Although I prefer to put them in the same package because they are closely related and some of them rely on package visibility, I don't want to distribute classes that an application does not need as not only would it bloat the file size, but also it would be a security risk.
At the moment, each of the server and the clients has the same jars, which is a mess. Ideally, I'd like to automatically create jars based on dependency as following.
Server:
server.jar: classes used by Server only
server-client1-common.jar: classes shared by Server and Client 1
server-client2-common.jar: classes shared by Server and Client 2
Client 1:
client1.jar: classes used by Client 1 only
server-client1-common.jar: classes shared by Server and Client 1
client-common.jar: classes shared by Client 1 and Client 2, but not Server
Client 2:
client2.jar: classes used by Client 2 only
server-client2-common.jar: classes shared by Server and Client 2
client-common.jar: classes shared by Client 1 and Client 2, but not Server
I realize that you can do this manually using ant, but it would be a maintenance disaster. Is there a tool that takes care of such dependency automatically?

What do you mean by "maintenance disaster"? If you create an ANT script, just run it and it will compile and pack the jars for you.
As a more robust alternative, you might use maven. For something more lightweight, the built-in eclipse export tool might work.

I cannot present you with a ready-to-go solution. Here's an idea though: create an annotation or a set of annotations like this:
#jarselector(types='server')
class ServerOnly {
...
}
#jarselector(types='server,client1')
class ServerAndClient {
...
}
Then create your own ant task by extending the jar task (or maven plugin) or write your own task, that takes this annotation and packages classes according to the annotation, which you would then be using as a filter.
You would only have to create the task once - I've done it in the past, it is less complicated than it sounds and the problem sounds big enough to warrant the effort.
Afterwards you have to annotate all your classes once (or depending on your implementation only those classes the clients need, or only those that are not shared by every jar etc.). Whoever sees a class can see immediately what it is used for. When creating a new class you can easily add the annotation.
I really don't think there is a ready made ant task or maven plugin that does this.
Alternatively - if you really cannot change your package structure - you could also use multiple source directories to keep the packages but split the files in different directories. Eclipse doesn't care how many source directories you use. You would then need to adapt your build tool just once for the source directories and could then sort the files that way.

One of the best practices regarding building applications is to have one jar per project.
Maven, for example, uses this as default. You can trick it to do otherwise, but it is better to join them instead of "fight" them.
http://maven.apache.org/guides/mini/guide-using-one-source-directory.html
http://www.sonatype.com/people/2010/01/how-to-create-two-jars-from-one-project-and-why-you-shouldnt/
So, in your case you should create 6 projects:
Server, Client1, Client2, ServerClient1Common, ServerClient2Common, ClientCommon
In order to select the classes needed, I don't think there is a tool, and probably you should know better what is the common functionality.
Create the Common projects, and add them to the build path - dependencies. Then start moving your classes into the Common project, leaving them in the same package.
For example, create ServerClient1Common project.
For Client1, go to Configure Build Path -> Projects. Add ServerClient1Common. Remove all references to Server Project.
For Server, go to Configure Build Path -> Projects. Add ServerClient1Common. Remove all references to Client1 Project.
You should now have a lot of missing classes/imports. Try to solve them one by one.
At the end, you should be able compile the 3 projects and to obtain the jars you mentioned.
PS: Other strategies (like one uber-project with different build targets, or 3 projects with entwined ant/maven builders) are messier. There is maybe one exception - another way of splitting the classes, but I do not know if it applies to you: client1.jar, client1-interface.jar, client2.jar, client2-interface.jar, server.jar, server-interface.jar. This way you could use 3 projects with each having two target jars. To run client2.jar you will need server-interface.jar

Have a separate Eclipse project for each JAR that you're going to create. Then set up the dependencies on the "Projects" tab of the Build Path, for each of the top level projects. So, the "server" project will have "server-client1-common" and "server-client2-common" listed as required projects. And so on.
I've seen this model used by a number of different organisations, and I've always thought that this was the "industry accepted" way of doing it. It just works!

Is there any benefit in using Maven Multimodule when working in a small application?

We are building a small application using different architectural layers such as domain, interface, infrastructure and application. This follows the Onion DDD model. Now I am wondering if there is any benefit in splitting the application into a multimodule maven project. As far as I can see now it seems to make things more difficult than needed. The entire application will be deployed as a single WAR file into a Tomcat container.

Splitting your application makes sense for the following:
When a certain part of the project needs to have new functionality or bug fixes, you can simply focus on that module and run just the tests for it. Compiling a fraction of all the code and running just the related tests speeds up your work.
You can re-use the code from the modules across different projects. Let's assume your project contains some well-written generic-enough code for mail sending. If you later have another project that need mail sending functionality, you can simply re-use your existing module or build upon it (in another module by adding it as a dependency).
Easier maintainability on the long run. Maybe now it seems like a small project. In a few months things might look different and then you'll need to do more refactoring to split things into logical units (modules).
Conceptual clarity (as added by Adriaan Koster).
Concerning the WAR: You can have an assembly module which puts things together and produces a final WAR file from all the related modules.
Initially, this may seem as more work, but in the long-run, modularized projects are easier to work with and to maintain. Most sane developers would prefer this approach.

Using multiple modules forces you to have a hierarchy of dependencies. You have one module which is standalone and doesn't depend on any other of your modules. You have another which only depends on that. It might appear harder than allowing anything to depend on anything else but this approach results in a mess of dependencies which is hard to fix later.
If you are trying to follow a layered model I suggest you place each layer in a different module. This will ensure you are not tempted to break the model.

Short answer: today it is small, tomorrow it will bigger and more complicated to maintain, reuse, extend, integrate with other system and so on

As far as I know, Maven do little help for WAR dependencies. As you are talking about single WAR, this should never be a problem.
You can separate java classes into several "jar" submodules, but if you split the WAR project into several smaller WARs, using some kind of "overlapped" packaging things get complicated.
Just information, one of our projects, it contains too many web pages, so we decided to split it into several WAR submodules, however, the session is not shared between different WARs deployed, and we are not going to use Kerberos stuff. At last, we modified a lot sources of Glassfish, Jetty, MyFaces, etc. To make them resolve web.xml stuff inside JARs. And converted the whole project to Facelets 2.0 (to avoid the dependency of JDK tools.jar and custom resource handler), the only reason is to change the WAR submodules to JAR submodules, and move all webapp/pages into class resources. So the conclusion, Maven does great job for JAR dependencies, but no WAR or single WAR.
EDIT You can put applicationContext.xml in one of the base submodule, and import it by classpath:com/example/applicationContext.xml. Also Spring 3.0 do have annotation supports, you can make spring auto scan them instead of declaring them all in the xml.

Spliting your project into multiple maven projects is useful if you want to reuse your classes in another project or if your projects are deployed in different configurations.
Maybe think of a webservice - if you are hosting the server, you could build a project for your domain classes (models) and your endpoint interfaces that could be used by server and client. The server would be another project that is build to a WAR.
To develop further clients the first project could be used, too.
Use a parent project for dependency management on common projects (like logging) and different profiles and build configurations.

Using one Java source file in two different projects, both under development

I am developing a Spring (Java framework for server-side web-development)web application, which will respond to another client-side Java application(which uses socket communication) by a JSON object. At the same time, I'm working on both server-side and client-side Java applications.
The problem is that I have a bunch of files(say, a Json variable interfaces) that are being used at both projects. For now, I have duplicate copies of that interface, in different packages in the two projects. But this causes inconsistency, because I have to update the both files whenever I need to make a change in the interface.
Does anyone have a neat solution for this?
Thanks

You should treat your shared code at the package level and not the file level.
You should create a package of interface definitions that are used by both the client and server side of your architecture and whenever that package changes, both sides will have to change accordingly.
EDIT:
I wasn't explicit about it but zellus' suggestion about importing the common code as a jar is a good one.

You might create a separate project for your common JSON code. Using subversion, svn:externals allow a neat integration on the source level. Importing the common code as jar file is another approach.

If you're using maven, you could create a local maven project containing all the classes you might need in different projects and add this dependency to your pom.xml which requires these classes.