Sometime before the acquisition, we decided on JIRA as the issue tracker and started evaluating it, including history migration, a bit of customization, and trying to understand what processes need to be in place in order to be effective and deal with the complexities we were seeing regarding real world software development and maintenance.
This was an easy decision, as we really really like JIRA the more we look at it. The main advance in the JIRA space this year was in my view the plethora of plugins that became available, and provide functionality we needed, as well as convince us of the strategicness of the JIRA/Atlassian ecosystem.
Another easy decision was migrating to Confluence, the atlassian enterprise Wiki, for our knowledge base and documentation platform.

Another thing we are seeing is commercial vendors in the development tools space (SCM, Build management, etc.) integrating with atlassian. This is very positive and not surprising, considering the openness of the platform, the reach into many customers, and I guess the BizDev efforts of the atlassian guys, which I think try to be Best of Breed for issue tracking and wiki, while relying on very strong partnerships with every sexy major player/community in the space (not necessarily the heavy-weight guys like Mercury/CA) to provide other functionality people expect.

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