So... by "manage projects" you mean all the metadata related to tasks, bugs, todos, features, deadlines and milestones? (I've heard some people use "manage projects" to mean "how do I build the source? make? cmake? etc.")

To be honest, I just save all that stuff in text files in the same repo as the code (though usually in a specific directory at the root of the project.) I have some tools that pull meta-data out of text files so I can query them for things like "give me a list of open items" or "give me a list of items tagged with a specific release target."

It takes some getting used to if you like HTML interfaces, but I grew up on the command line so it works for me.