That is a very good question!
You can build integrations to make JIRA and Confluence do ANYTHING your imagination may dream of doing. (Disclaimer: Some ideas are not always good ideas. ) If you want to build a connect plugin to interface JIRA or Confluence with a particular third-party tool, there are docs to do just that:
The Connect plugins are a really awesome thing that Atlassian released after I joined. It allows you to work in languages other than JAVA to rapidly develop really neat plugins that you could even put on the Atlassian Marketplace once you are done!
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