each version of the project gets a directory and contains everything the project needs. put all of those into a parent directory. use a symlink to point to the currently active version. E.g.:
/usr/local/thing/versions/thing-v1.3.7
/usr/local/thing/versions/thing-v1.4.2
/usr/local/thing/current -> /usr/local/thing/versions/thing-v1.3.7