That's why you want to use volumes for mutable data such as your source code repo - you isolate the changing parts and keep the containers static.
It seems that by that point you've lost the advantage of using images; if parts of the system must be loaded outside of the container, it seems you might as well simply use a configuration manager to install the stuff and then run LXC/LXD containers instead of using images at all.
For me, mounting my local app files as a volume is useful during development since it keeps the workflow fast. I don't have to rebuild the image every time I want to try the app out, I get to use the new code without delay.
If I were deploying as a container, I presume my build process would check the app out of git and build the image based on that fresh checkout. I'm just using Docker as a convenient way of simulating my production environment (dev'ing on Ubuntu 15.04, but deploying to Debian 7), and still be able to iterate rapidly.