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What is the best way to share the new version of Java source code between a group of programmers?

I started to work with a group of five new programmers on a large project. I'm looking for the best way to share the source code between all the members. Each person is modifying different parts but all parts are related. I'm looking for a platform or way that when I change any parts of code they can see it on-line or as soon as possible.
Currently we conflicted with each other. For instance I worked on the parts of the source code and when I finish my job and I went back to our subversion repository which is google code to upload the new version. Then I realize someone else has been edited the code! What can I do in this situation?
We are using netbeans and everyone is working far away from each other so we can not have a face to face meeting.

You write about your subversion repository: well, that's good, because version control software is exactly what you need.
Conflicts can appear when people work on same parts of the code, but usually this doesn't happen too often. If it does, you should talk with your team members and set up a policy to update their local working copies more often. Another idea would be to set up subversion to send out e-mail notifications whenever someone commits changes.
When a conflict appears, the one who updates his local working copy has to resolve the conflict. Resolving doesn't mean to overwrite other people's work but to adjust local changes so that they work well together with the code which has already been committed to the repository by someone else.

If a lot of people are working on the same classes Subversion does a poor job of merging and as a result conflicts occur all too frequently. When conflicts do occur, the only solution is to resolve them - most IDEs have tools for this, as does Tortoise.
There's a few things you can do as a team to minimize conflicts:
change the minimum amount of code (avoiding formatting changes)
check in small changes
check in often
sync often
This does mean you have to be careful with your changes, so like everything in development there's trade-offs.
An alternative is switch to a distributed version control such at Git. DVCS is based on the need to merge and so do a far better job of it.

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I have an application written in Java. In is stored in several files. It uses different classes with different methods. The code is big and complicated. I think it would be easier to understand the code if I have a graphical model of the code (some kind of directed graph). Are there some standard methods for visualization of code. I am thinking about usage of UML (not sure it is a correct choice). Can anybody recommend me something?
ADDED:
I consider two possibilities:
Creating the graph by hands (explicitly).
Creating graph in an automatic way. For example to use some tools that read the available code and generate some graph describing the structure of the code.
ADDED 2:
It would be nice to have something for free.

I tried using a number of UML tools and found that the reverse-engineering capabilities in most UML tools were not helpful for understanding code. They focus on designing needs and reverse-engineering capabilities often just ends up showing huge pictures of lots of useless information. When I was working on the Microsoft Office codebase, I found using a pen-and-paper more helpful that the typical design/modelling tools.
You typically want to think about doing this in a number of ways:
Use your brain: Someone else mentioned it - there is no substitute to actually trying to understand a code base. You might need to take notes down and refer back to it later. Can tools help? Definitely. But don't expect them to do most of the work for you.
Find documentation and talk to co-workers: There is no better way than having some source describe the main concepts in a codebase. If you can find someone to help you, take a pen and paper, go to him and take lots of notes. How much to bug the other person? In the beginning - as much as is practical for your work, but no amount is too little.
Think about tools: If you are new to a part of a project - you are going to be spending a significant amount of time understanding the code, so see how much help you can get automatically. There are good tools and bad tools. Try to figure out which tools have capabilities that might be helpful for you first. As I mentioned above, the average UML tool focuses more on modeling and does not seem to not be the right fit for you.
Time vs Cost: Sure, free is great. But if a free tool is not being used by many people - it might be that the tool does not work. There are many tools that were create just as an exploration of what could be done, but are not really helpful and therefore just made available for free in hopes that someone else will adopt it. Another way to think about it, decide how much your time is worth - it might make sense to spend a day or two to get a tool to work for you.
Once there, keep these in mind when going trying to understand the project:
The Mile High View: A layered architectural diagram can be really helpful to know how the main concepts in a project are related to one another. Tools like Lattix and Architexa can be really helpful here.
The Core: Try to figure out how the code works with regards to the main concepts. Class diagrams are exceptionally useful here. Pen-and-paper works often enough here, but tools can not only speed up the process but also help you save and share such diagrams. I think AgileJ and Architexa are your best bets here, but your average UML tool can often be good enough.
Key Use Cases: I would suggest tracing atleast one key use case for your app. You likely can get the most important use cases from anyone on your team, and stepping through it will be really helpful. Most IDE's are really helpful here. If you try drawing them, then sequence diagrams arethe most appropriate. For tools here I think MaintainJ, JDeveloper and Architexa are your best bets here.
Note: I am the founder of Architexa - we build tools to help you understand and document Java code, but I have tried to be unbiased above. My intention is to suggest tools and options given that this is what I focused on as part of my PhD.

The most important tool you should use is your brain, and it's free.
There's no reason why you have to use any sort of standard method of visualization, and you can use whatever media you like. Paper, whiteboard, photoshop, visio, powerpoint, notepad: all of these can be effective. Draw a diagram of classes, objects, methods, properties, variables - whatever you think is useful to see in order to understand the application. The audience is not only other members of your team, but also yourself. Create diagrams that are useful for you to look at and quickly understand. Post them around your workspace and look at them regularly to remind yourself of the overall system architecture as you build it.
UML and other code documentation standards are good guidelines for the types of diagrams you can do and the information you should consider including. However, it is overkill for most applications and basically exists for people who can't take personal responsibility for documenting without standards. If you follow UML to the letter, you'll end up spending way too much time on your documentation instead of creating your application.

It is stored in several files. It uses different classes with different methods. The code is big and complicated.
All Java code written outside the school is like that, particularly for a new developer starting on a project.
This is an old question, but as this is coming up in Google searches, I am adding my response here so that it could be useful to the future visitors. Let me also disclose that I am the author of MaintainJ.
Don't try to understand the whole application
Let me ask you this - why do you want to understand the code? Most probably you are fixing a bug or enhancing a feature of the application. The first thing you should not try to do is to understand the whole application. Trying to understand the entire architecture while starting afresh on a project will just overwhelm you.
Believe me when I say this - developers with 10+ years of solid coding experience may not understand how certain parts of the application work even after working on the same project for more than a year (assuming they are not the original developers). They may not understand how the authentication works or how the transaction management works in the application. I am talking about typical enterprise applications with 1000 to 2000 classes and using different frameworks.
Two important skills required to maintain large applications
Then how do they survive and are paid big bucks? Experienced developers usually understand what they are doing; meaning, if they are to fix a bug, they will find the location of the bug, then fix it and make sure that it does not break the rest of the app. If they need to enhance a feature or add a new feature, most of the time, they just have to imitate an existing feature that does a similar thing.
There are two important skills that help them to do this.
They are able to analyze the impact of the change(s) they do while fixing a bug. First they locate the problem, change the code and test it to make sure that it works. Then, because they know the Java language well and the frameworks 'well enough', they can tell if it will break any other parts of the app. If not, they are done.
I said that they simply need to imitate to enhance the application. To imitate effectively, one needs to know Java well and understand the frameworks 'well enough'. For example, when they are adding a new Struts Action class and adding to the configuration xml, they will first find a similar feature, try to follow the flow of that feature and understand how it works. They may have to tweak a bit of the configuration (like the 'form' data being in 'request' than in 'session' scope). But if they know the frameworks 'well enough', they can easily do this.
The bottom line is, you don't need to understand what all the 2000 classes are doing to fix a bug or enhance the app. Just understand what's needed.
Focus on delivering immediate value
So am I discouraging you from understanding the architecture? No, not at all. All I am asking you is to deliver. Once you start on a project and once you have set up the development environment on your PC, you should not take more than a week to deliver something, however small it may be. If you are an experienced programmer and don't deliver anything after 2 weeks, how can a manager know if you really working or reading sports news?
So, to make life easier for everyone, deliver something. Don't go with the attitude that you need to understand the whole application to deliver something valuable. It's completely false. Adding a small and localized Javascript validation may be very valuable to the business and when you deliver it, the manager feels relieved that he has got some value for his money. Moreover, it gives you the time to read the sports news.
As time passes by and after you deliver 5 small fixes, you would start to slowly understand the architecture. Do not underestimate the time needed to understand each aspect of the app. Give 3-4 days to understand the authentication. May be 2-3 days to understand the transaction management. It really depends on the application and your prior experience on similar applications, but I am just giving the ballpark estimates. Steal the time in between fixing the defects. Do not ask for that time.
When you understand something, write notes or draw the class/sequence/data model diagram.
Diagrams
Haaa...it took me so long to mention diagrams :). I started with the disclosure that I am the author of MaintainJ, the tool that generates runtime sequence diagrams. Let me tell you how it can help you.
The big part of maintenance is to locate the source of a problem or to understand how a feature works.
MaintainJ generated sequence diagrams show the call flow and data flow for a single use case. So, in a simple sequence diagram, you can see which methods are called for a use case. So, if you are fixing a bug, the bug is most probably in one of those methods. Just fix it, ensure that it does not break anything else and get out.
If you need to enhance a feature, understand the call flow of that feature using the sequence diagram and then enhance it. The enhancement may be like adding an extra field or adding a new validation, etc. Usually, adding new code is less risky.
If you need to add a new feature, find some other feature similar to what you need to develop, understand the call flow of that feature using MaintainJ and then imitate it.
Sounds simple? It is actually simple, but there will be cases where you will be doing larger enhancements like building an entirely new feature or something that affects the fundamental design of the application. By the time you are attempting something like that, you should be familiar with the application and understand the architecture of the app reasonably well.
Two caveats to my argument above
I mentioned that adding code is less risky than changing existing code. Because you want to avoid changing, you may be tempted to simply copy an existing method and add to it rather than changing the existing code. Resist this temptation. All applications have certain structure or 'uniformity'. Do not ruin it by bad practices like code duplication. You should know when you are deviating from the 'uniformity'. Ask a senior developer on the project to review the changes. If you must do something that does not follow the conventions, at least make sure that it's local to a small class (a private method in a 200 line class would not ruin the application's esthetics).
If you follow the approach outlined above, though you can survive for years in the industry, you run the risk of not understanding the application architectures, which is not good in the long run. This can be avoided by working on bigger changes or by just less Facebook time. Spend time to understand the architecture when you are a little free and document it for other developers.
Conclusion
Focus on immediate value and use the tools that deliver that, but don't be lazy. Tools and diagrams help, but you can do without them too. You can follow my advice by just taking some time of a senior developer on the project.

Some plugins I know for Eclipse:
Architexa
http://www.architexa.com/
nWire
http://www.nwiresoftware.com/
If you want to reverse engineer the code, you should try Enterprise Architect

have you tried Google CodePro Analytix ?
it can for example display dependencies and is free (screenshot from cod.google.com):

Here is a non UML Tool which has very nice visualization features.
You can mapping the lines of code per class / method to colors / side lenght of rectangles.
You can also show the dependencies between the classes.
http://www.moosetechnology.org/
The nice thing is, you can use Smalltalk scripting for displaying what you need:
http://www.moosetechnology.org/docs/faq/JavaModelManipulation
Here you can see how such a visualization looks like:
http://www.moosetechnology.org/tools/moosejee/casestudy

JUDE Community UML used to be able to import Java, but it is no longer the case. It is a good, free tool.
If your app is really complex I think that diagrams won't carry you very far. When diagrams become very complex they become hard to read and lose their power. Some well chosen diagrams, even if generated by hand, might be enough.
You don't need every method, parameter, and return value spelled out. Usually it's just the relationships and interactions between objects or packages that you need.

Here is a another tool that could do the trick:
http://xplrarc.massey.ac.nz/

You can use JArchitect tool, a pretty complete tool to visualize your code structure using the dependency graph, and browse you source code like a database using CQlinq.
JArchitect is free for open source contributors

Some great tools I use -
StarUML (allows code to diagram conversion)
MS Visio
XMind (very very useful for overview of the system)
Pen and Paper!

Understanding and modifying large projects

I am a novice programmer and as a part of my project I have to modify a open source tool (written in java) which has hundreds of classes. I have to modify a significant part of it to suit the needs of the project. I have been struggling with it for the last one month trying to read code, trying to find out the functionalities of each class and trying to figure out the pipeline from start to end.
80% of the classes have incomplete/missing documentation. The remaining 20% are those that form the general purpose API for the tool.
One month of code reading has just helped me understand the basic architecture. But I have not been able to figure out the exact changes I need to make for my project. One time, I started modifying a part of the code and soon made so many changes that I could no longer remember.
A friend suggested that I try to write down the class hierarchy. Is there a better(standard?) way to do this?

check in the code in some source code repository (Subversion, CVS, Git, Mercurial...)
make sure that you can build the project from the source and run it
if you already have an application that uses this open source tool try removing the binary dependency and introduce project dependency in eclipse or any other IDE. run your code and step through the code that you want to understand
after every small change commit
if you have different ideas branch the code

There's a great book called Working Effectively with Legacy Code, by Michael Feathers. There's a shorter article version here.
One of his points is that the best thing you can do is write unit tests for the existing code. This helps you understand where the entry points are and how the code should work. Then it lets you refactor it without worrying that you're going to break it.
From the article linked, the summary of his strategy:
1. Identify change points
2. Find an inflection point
3. Cover the inflection point
a. Break external dependencies
b. Break internal dependencies
c. Write tests
4. Make changes
5. Refactor the covered code.

Two things that Eclipse (and other IDEs as well) offer to 'fight' this. I've used them on very large projects:
Call hierarchy - right-click a method and choose "call hierarchy", or use CTRL + ALT + H. This gives you all methods that call the selected method, with option to check further down the tree. This feature is really very useful.
Type hierarchy - see the inheritance hierarchy of classes. In eclipse it's F4 or CTRL + T.
Also:
find a way to make so that changes take effect on-save, and you don't have to redeploy
use a debugger - run in debug mode, within the IDE, so that you see how the flow proceeds

My friend, you are in deep doodoo. Modifying large, badly documented legacy code is one of those projects that makes experienced programmers seriously contemplate the joys of selling insurance, or some other alternative career. However it isn't impossible, and here are some tips that I hope will help.
Your first task is to understand the code as much as possible. You are at least on the right track there. Getting a good idea of the class structure is absolutely important, and a diagram is probably the best way. The other thing I would suggest is that when you find out what a class does, add the missing documentation yourself. That way when you come back to it you wont' have forgotten what you found out.
Don't forget the debugger. If you want to find out what is really going on, stepping through the relevant code, or simply finding out what a call stack really looks like at a certain point can be very helpful.

The only way to understand code is to read it. Keep working that is my advice.
There are projects with better documentation than others. Here is a couple of projects that I know are well organized:
Tomcat ,
Jetty,
Hudson,
You should check java-source for more open source projects.

Personally I think it is very difficult to try to understand an entire application all at once. Instead, try to focus only on certain modules. For example, if you can identify a module that you need to change (e.g. based on a screen, or certain input/output point), then start by making one small change and testing it. Go from there, making a small change, testing, and moving on.
Additionally, if your project has unit tests (consider yourself lucky) and review the unit tests of the module you are focusing on. That will help you get an idea of what the module is expected to do.

In my opinion there is no standard approach to understand a project. It depends on many factors, from the understandability of the code/architecture you're analyzing to your previous experience on large projects.
I suggest you to reverse-engineer the code by using a modeling tool, so that you can generate some UML models from the existing source code. These diagrams can be helpful as a graphic guideline during your anaysis of the code.
Don't be afraid to use debugging to grab the logic of the most complex functionalities of the project. Running the most complex code instruction by instruction, seeing the exact values of the variables and the interactions between the objects can be helpful.
Before you refactor to change the project to suit your needs, be sure to write some test cases, so that you can verify that your modifications don't break the code in unexpected ways.

Here are a couple recommendations
Get the code into some form of CVS.
This way if you start making changes
you can always look back at previous
versions.
Take the time to document what you
have already learned/gone through. Javadoc is fine
for this.
Create a UML structure for you code.
There are lots of plugins out there and wil give you a nice representation of your code layout.

Trying to remember name of a code visualization tool

I recall a while back seeing an experimental code visualization tool, with the intention being to enable a user to manually track interconnectivity between different parts of their code for the purposes of implementing specific features. In particular, a user could pull out a window into their code and associate it with a completely different part of their code, seeing lots of independently controllable code snippets (and any relevant notes) linked together. The purpose of this tool was to enable someone working on a chunk of code that crossed multiple functions (or separate modules) to be able to more cleanly figure out what was going on and to see more of the relevant code at once. This is kind of similar to just opening boatloads of small windows at once, drawing lines between them, and having each window be a view of a file (some windows could be looking at different parts of the same file, some windows might just be notes).
I think the experimenters made an Eclipse plugin for the concept using Java.
Anyone have any idea what I'm talking about?

Maybe CodeBubble?
The essential goal of this project is to make it easier for developers to see many fragments of code (or other information) at once without having to navigate back and forth.
Each of these fragments is shown in a bubble.
(although Mylyn is kind of similar in its approach, but with less diagrams ;) )

Setting up a new Java development shop

I'm setting up a Java development shop, currently just for myself as the only developer, but with hopes of needing to hire others as the business grows. Obviously I'm hoping to set it up right so that as more people come in, they can be productive right away. Please help suggest things I want to do, and tools to do them.
Here's what I think I need:
Distributed source code/revision control (Subversion?)
Bug tracking (does Trac do this?)
documentation (both internal and customer facing)
team communication
frequent automated building
maybe something to make sure automatic tests pass as part of the check-in process?

I like Hudson for Continuous Integration builds, and I like JIRA for issue tracking. Eclipse has plugins for both.
Hudson can watch software repositories and rebuild those projects that use the changed resources.
If you need more documentation than javadoc can cover (which is quite a lot) then consider a Wiki. Easy to use, and with a bit of structure you can massage it into a PDF.
Source control is a bugger. Too many to choose from. For a small development team start with either subversion or CVS (which is old but has supreme IDE support) and when you outgrow that and know your needs, then migrate to a better one. Most have migration tools from svn or cvs. It is harder to move from e.g. git to Mercurial, and you defintively want one with more than one implementation. Remember to have good backups of the source control repository - it IS your business. Frequent rsyncs, often tapes.
EDIT: You also want decent hardware. For the Continuous Integration server, the fastest build machine you can afford. For yourself the largest monitor you can afford (not in size, in resolution) for your primary monitor and as many extra monitors as you can afford to have (including adapters to your computer). I have found that Mac's use the pixels better than Windows, so that might also be a point.
My primary monitor is pivoted 90 degrees. This allows me to see many lines at once instead of a few long lines. (For some reason tradition says that editing areas should be wide and short, which may work in word but not in code where lines should not be wider than 72 characters)
Note on Eclipse: Use the source repository to have a single workspace per project! Use the Java Editor Save Function to reformat your code everytime you save - this makes it more readable up front, and goes better with the source repository as changes are marked in the correct version.
Edit: The reason for the CI server needing to be better than your development machine is because it will run all your tests every time you check stuff into your source repository. After a while, that WILL take time.
Personally I have found tests working well for library routines. They specify what works and what doesn't. It is harder to write good tests for whole applications, but you may want to look into that from the beginning, as it allows you to ensure that everything works for every check in. Write a comment if you are not familiar with the concept.
Whatever you choose for the individual parts, you will be glad if they can work together. Hudson knows how to talk to JIRA for instance. JIRA knows how to look in CVS.

To see what a big amount of people thinks to make a good software development environment read this article on the 12 points of joels test
This list does not include the things more important for you. Getting clients getting them to pay and manage legal stuff and taxes.

Most important, the right staff:
get great people who find work and handle customers (aka sales)
get software engineers who are smart and get things done (http://www.joelonsoftware.com/items/2007/06/05.html)
get someone who knows about accounting and the local legal and tax regulations, so you don't get any surprises
Tools / Processes:
use a distributed version control system like git or mercurial
jira or the like for bug/issue tracking
continuous integration with hudson or cruisecontrol
wiki system to share the teams tangible knowledge
unit tests, clover, checkstyle, findbugs, ...
From a managerial point of view i would try
daily standup meetings (checkout scrum) to keep the team updated members to commit by saying what the did, do, and will do
timeboxed meetings, everything else sucks.
plan iterations/sprints
let team do task time estimations
pair programming (gets you better code)
code reviews (builds trust)
weekly in house "techtalks" to build a strong sense for the team
twitter like communication tool to keep all insync and informed with minimal distraction
develop team towards dynamic languages (groovy, scala, ...)
yourself, listen to what the guys at http://manager-tools.com/ have to say...
good luck!

We have been using:
version control:
subversion - Its not distributed but it is accessible over a few different protocols if firewalls are an issue. I'm not sure if distributed version control is necessary for us and reading Eric Sink's take is entertaining at least
issue tracking :
Fogbugz - You get some team discussion and communication for free with it because of the built-in wiki and discussion boards.
continuous integration:
CruiseControl - we had been talking about switching to Hudson, but Cruise is working really well right now - it runs our unit tests.
dev environment:
Netbeans and Eclipse - There is really no reason to pay for a Java IDE. An import point for getting going fast is that Netbeans and Eclipse both store all of their project data as text files which version control nicely. See this question. We had giant headaches when using an IDE which used binary project files.
profiler:
JDK VisualVM - Its free and it works. I used to really like YourKit, but VisualVM does so much now.
documention:
Combination of javadoc and fogbugz wiki pages plus the cruise dashboard for internal. For external we are using RoboHelp and we dislike it.
other tools:
Findbugs - huge help in catching things that are sometimes really stupid and sometimes amazing quirks that you'd have never realized. PMD is good for some of this as well.
We find chat tools to be really helpful for communication. We used to have access to Sametime and it had a giant conferencing feature that was really great. That was taken away for an unknown reason by the overlords though.

Here is what development stack our team of five developers is using over a year now:
Eclipse IDE (worked better for us than NetBeans)
Maven as a project comprehension and build tool -- simply a must tool!
Nexus: The Maven Repository Manager -- serves as a local Maven repo for proxying, and for managing internal and 3rd party libs; simple in use and is really necessary if you're going to use Maven
Subversion for source versioning -- was chosen mainly due to very good IDE support (Subclipse for Eclipse IDE)
Trac as a bug tracking and requirement management tool -- it nicely integrates with Subversion, has very useful plugins including blog and discussion plugins; also it can be integrated with Eclipse Mylyn.
Hudson as continuous integration, which nicely integrates with Subversion, Maven and Trac -- very valuable even for a small team.
Sonar code quality management platform -- a tool which integrates a large number of code quality matrix with intuitive web interface supporting code review and drill-down facility for analysis of the problems; integrates with Maven.
In our case this development stack is running under Ubuntu (workstation components: Eclipse IDE, Maven) and CentOS (server components: Maven, Nexus, Subversion, Trac, Hudson, Sonar).
As for the documentation, LaTeX (TexLive and Kile under Ubuntu) works just great supporting high quality PDF generation. The documentation source can be managed by Subversion the same way as the application source. Allows making of simple several page document and large multi-chapter books.
Hope this helps.

Distributed source code/revision control (Subversion?)
Subversion is good enough unless you want to use this as an opportunity to learn Git or Mercurial.
Bug tracking (does Trac do this?)
Trac works fine if you don't mind CamelCaseTurningIntoWikiWords. JIRA is fancier but (as noted) not free, and I find its data-ink ratio annoyingly low. Good once you learn which parts of the UI to ignore, though.
documentation (both internal and customer facing)
Internally, I would prefer communication over documentation unless you're really willing to commit to spending time keeping internal documentation updated. Javadoc your integration points (internal/external APIs), but try to keep your code and build scripts as self-documenting as you can.
That said, requirements docs are useful. I'd suggest using one tracking system for bugs and requirements. JIRA lets you create hierarchical issues, but I wouldn't bother with that till you need it.
Trac includes a Wiki, which can be handy although too much content will get stale.
Customer-facing docs are all over the map -- depends a lot on what you're doing. If you need big fat manuals (either printed or HTML or on-line help) FrameMaker + the DITA Open Toolkit is a nice combo, but a FrameMaker license is going to set you back $1000.
At a certain point this shades into corporate communications (marcom and PR), which are kind of a different animal.
team communication
Google Talk (or the instant messaging framework of your choice), email, and the occasional Skype teleconference are probably all you need.
An internal wiki and/or internal blogs might be nice but you probably don't need them right away, even once you've added a few more developers. Trac includes a wiki.
frequent automated building
Switching from CruiseControl to Hudson has made everyone here much happier -- two teams made the same decision independently and both are pleased with it. Hudson's flexible, easy to configure, and shiny.
I have yet to be convinced by Maven. I suspect its value depends on how much you want automated downloads of the latest versions of all your open-source libraries.
Edited (Feb. 2010) to add: Several months of Maven 2 experience now and I'm still not convinced. I think (like many frameworks, e.g. Rails) it may work well if you're starting from scratch and structuring your project according to its conventions, but if you already have your own structure in place it's a lot less advantageous.
maybe something to make sure automatic tests pass as part of the check-in process?
I'd advise against it. Most of the time the tests will be passing (or should be, anyway) As long as continuous integration notifies you quickly of failures, and you also have stable automated builds (a couple of days' worth of nightly builds, tagged iteration builds, etc.), you want more and faster checkins, not fewer and slower.

Subversion is not a distributed approach -- go for Mercurial, Bazaar or git instead!
Yes, Trac does do bug tracking (among other things -- check it out!).
Documentation is indeed a must but I'm not sure what you're asking -- tools for it? Why not just javadoc?
For communication you can have many tools, such as skype, email, IM of many kinds, and so forth -- you need to express your specific issues better to get specific advice, I think. Google Wave once it matures may be just great, but it's not production-ready yet.
For continuous build check out CruiseControl -- of course it also run tests &c.
You can write "triggers" for any of the build systems I've mentioned (and even good old svn;-) to run some test suite and reject the commit if it fails.

A few more items:
IDE
Billing Software - will you be charging by the
hour? If so you might want to track
what your time is going towards.
offsite backup of some kind.
Each one of your bullet points is probably worthy of a community wiki by themselves. Though in the end you might not care so much about best of breed in each area, but care more about how well they all integrate with your IDE or with each other.
Also, if you really want to get new teammates up and running quickly, consider putting as much of your dev environment into source control as you can, so you can just checkout your "dev-env" project onto a new computer and be up and running instantly!

One of your specs (in your question) says:
maybe something to make sure automatic
tests pass as part of the check-in
process?
I would suggest this is essential. Check out this matrix of continuous integration servers to see which one fits your requirements.

If you're starting off with just yourself as the only developer but scaling up at some point, depending on what it is you're developing, it might be worth to check out a Platform as a Service (PaaS) offering, like https://www.openshift.com or https://www.heroku.com/, both which offer developer accounts, but you can scale up to paid accounts as and when needed.
OpenShift have CI cartridges for Jenkins so you can spin up DVCS (git), CI using Jenkins, and an app server like JBoss AS or WildFly all in one go in a matter of minutes... depending on your needs and how much time you want to dedicate to setting this up yourself locally, I'd be more inclined to look at using a PaaS.

Rather than use Trac, consider Redmine. It allows you to have multiple projects stored in the one issue tracking system. You can then use the same setup for each project, rather than having to have N instances of Trac.

For starters, SVN will be enough for you. Definitely get a bugtracker. JIRA is good but isn't free. Enforce a rule "No commits without a bugtrecker ticket". This way you will be able to track the development. Do a cruise control and run a build + unit tests after every checkin into the main branch. Bigger changes should be made on a separate branch and then merged into the main branch.
Invest in a good IDE (I recommend intelliJ IDEA) and a good profiler (I recommend JProfiler). They're not free, but they are definitely worth their price.