The code for all of the functions in a given function app lives in a root folder that contains a host configuration file and one or more subfolders, each of which contain the code for a separate function, as in the following example:
wwwroot
| - host.json
| - mynodefunction
| | - function.json
| | - index.js
| | - node_modules
| | | - ... packages ...
| | - package.json
| - mycsharpfunction
| | - function.json
| | - run.csx
The host.json file contains some runtime-specific configuration and sits in the root folder of the function app. For information on settings that are available, see host.json in the WebJobs.Script repository wiki.
Each function has a folder that contains one or more code files, the function.json configuration and other dependencies.