My current proposal is that there are two distinct sets of files needed by the application
There are build_scripts that must be copied into the container and executed to build the container at docker-compose build time. These should be placed in /docker/build_scripts.
There are runtime_scripts that are needed at runtime to perform operations like starting up the application and critical services. These should be placed in a directory called docker/runtime_scripts
Finally there are various configuration files that are not scripts but that need to be present at either runtime or other times, these should be placed in /docker/files and then copied out by the scripts in /docker/build_scripts to reach their final resting places on the file system.