You'll probably need to amend the core of Jira to do this, although if you are just adding new items, https://developer.atlassian.com/display/JIRADEV/Adding+Menu+Items+to+JIRA should be enough. It's worth starting there if you really want changes as well - once you've read that page, you'll be well equipped to look at amending the existing bar (also, if you just want to turn items off, you might be able to do it by disabling modules in the plugins that provide it)
If you do decide to proceed, please remember that Jira does not always have a project context. The user's dashboards, the issue navigator, reports, admin, etc - there is no "current project" when you're looking at those because they can, and do, refer to many projects at once.
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