Confluence/Jira/Fisheye/Crucible/Subversion permissions setup, best practice

My development team currently uses a combination of Confluence/Jira/Fisheye/Crucible/Subversion to manage our software products.

We recently brought on a new developer, but he will not have access to all of the source code. We use a single svn repo with multiple folders to track several modules and apps that are built from the modules. With svn permissions, it's trivial to restrict his access. However, I don't see a folder-level permissions capability within JIRA/Fisheye/Crucible when connecting to a repo. I want him to have the full power of the dev tools. So I'm asking 1) is there a way to do this and I'm missing it, and 2) what are the best practices for this sort of situation?

I'm willing to change my repo layout if that's what everyone recommends. However, the organization that would make the most sense to me would likely require a JIRA/Crucible project to point to more than one repo. Is that possible?

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Yes -- it's possible to point JIRA and Crucible to multiple repos. On Crucible side you'd add those repos as 'additional Fisheye content' -- https://confluence.atlassian.com/x/QRemEQ

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