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