+1 for GitHub/GitLab or whatever for issue tracking. Code, version control and all tasks, bug reports in one place.
I also don’t understand people using Jira, it’s so overcomplicated, bad from UX point of view, big learning curve and you don’t need most of it features.
People keep confusing “Agile” with it’s real meaning — flexibility and adaptation to your situation and your team.
waffle.io looks amazing, will check it.
However, you need to store and organize somewhere ideas, user stories from managers/shareholders and I found trello.com is much better and easier then Jira. You can use it also to organize your own time and projects, it also has drag and drop function and mobile app. Have you tried trello Eric Elliott? What’s your experience with it?