We use Jira to create bugs that should be fixed, Svn to get all the code and roll it all together and Trac to see who did what and messed everything up and view all previous versions.
Typically some one finds a bug or thinks of a good idea to add. They will go into Jira and create a new issue with a great description of what happens that will get assigned to someone to fix it. Jira will create a new page for this issue and give it a bug number. The bug number [TL-XXXX] where X's are a number is then used to create a branch from the trunk where all work to implement this change will take place. In Jira you can make comments on what was changed and specifically why.
Trac merges all of this together in a great way. When ever you commit changes to a branch and give it a message, that message will show up on the bug page in "SVN commits" to let everyone know what you did and list all modified/added/deleted files. Jira does this automatically.
When you are ready for it to be integrated into the trunk on the bug page you have to change its status to "Fixed" and wait for some one to verify it to be correct. Then you can commit this branch to the trunk and fix any conflicts. And then you can change its status to "Integrated" and the bug is then taken off of the list of work in progess list. Then delete your branch and Jira will track that message you give it.
Trac keeps track of all the changes and you can run diffs on multiple versions and see any conflicts or what was changed. You can also view the files online as well. Trac is a pretty good GUI system.
While Subversion is nice by itself, integrating it with Trac and Jira is great. It makes it more complete. It is a great combination for large scale projects that makes dealing with things much easier.
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