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Is there any software that will allow me to generate trouble tickets (for Trac, Team Foundation Server, etc.) from TODO or otherwise annotated comments in the source code?

quanticle
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For Trac, there is a plugin called 'codetags' which provides a summary of encoded/tagged source comments without creating an actual ticket for each item.

http://trac-hacks.org/wiki/CodeTagsPlugin

Perhaps with some adaption or further extension, this plugin could help you create a ticket, or a batch of tickets based on tagged comments.

JustinC
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I've created a package for Atom Editor called imdone-atom that can create, update and close GitHub issues from TODO comments in your code. I'll be adding more integrations like Waffle.io, Jira and Phabricator and also a stand alone (non-atom) version soon.

Trac could be easily added if there is an open API.