I am looking for an issue tracker/bug tracker where I can decide access control on a per-issue basis. Issue trackers I've seen (trac, redmine, JIRA) each do that on a level of project, so I'd have to make a project for every subset of people allowed to see given issue--and this is prohibitive in my usecase.
Could could try out fogbugz http://www.fogcreek.com/fogbugz/ however it isnt free but it is really good.
Persmissions info can be found here
Guide on managing them - https://developers.fogbugz.com/default.asp?W119
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Bugzilla allows the bug submitter to designate individual bugs as security bugs or otherwise confidential. In that case they will only be seen by a previously designated list of staff, and will not be public.