Jira (and Confluence)

Jira is a very powerful tool, by Atlassian, that manages software development tickets (or instructions). This software is designed to let the project team work iteratively, taking on small development tasks, estimating them, and assigning them, allowing the team to work through tasks within a particular timebox. Jira provides extensive workflow building, Kanban boarding, and integrates with the development environment to create releases.

Notably, Atlassian also delivers Confluence which can be plugged into Jira to provide a wiki. The wiki can house all documentation about the requirements for the project and individual tickets can be linked providing an easy way to navigate between high level specifications and specific development tickets. 

https://www.atlassian.com/software/jira