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Lots of tools available in different configs - loosly hobbled together, loosly coupled, tightly coupled. I guess you're looking for more of the latter - a tool (or tool set) that tightly integrates the work planning and the work products. Maybe with good traceability amongst all the pieces. Maybe also including test plans, operational plans, product management, to name a few others.
Many of the tools to-date have been created for discrete purposes - planning and execution, managing requirements, etc. Quite understandable as the discrete problems are more obvious in the early days; integrated functions, though obvious at this time, become essential after resolving the initial problems. It's iteration/agile in action.
So going forward, what would a well integrated tool (or tool set) look like? What characteristics would it have?
Some that come to mind:
1. As noted in the posts above, ability to store, track, and link into project work products - internally created work products as well as deliverables.
2. As noted above, ability to identify, plan, and track work activities, assign work, team can see assigned work, perhaps integration with timecontrol/timereporting systems, ability to support backlogs, etc. Ideally, an ability to track all levels of work - large multi day tasks as well as small hourly tasks.
3. Integration with an org's resource mgt systems.
4. Integration with other project timelines, resources, dependencies, deliverables.
5. Integration with an Org's standard processes, procedures, templates, etc.
6. Organization-oriented reporting and metrics
7. Ability to manage risks, issues, communications, etc., etc.
I've gone off on a tangent and not answered your question, I know. But fleshing out what you're looking for will help you find it.