Multiple AVR Projects Sharing Code - Managing Large Projects
Your option b is probably the most reasonable. Every environment should be able to set library paths. Another option is to decouple the build from the IDE with makefiles and set the library path there. I know AVR studio supports makefile-based projects. I presume eclipse does as well. This could be a good option to look at if you have different people on the team using different IDEs.

As for a github repo for libraries, I recommend using git subtree. This will include the entire history of the library inside the project repos and allows commits to be pulled into the project repos from the library repo or sectioned off in the project repo and pushed back to the library repo. I use this setup for a bunch of my projects; take a look at my github and look for repos with a lib folder in the root, such as verilog-ethernet.