Run func commands from source or output directory based on configuration

In some languages, there is a required build step in order to run functions (ex: Java, TypeScript, C# that is not C# script).

If the current directory has configuration that gives source and output file paths for the function app, those should be honored as the locations to run func commands.

Note that `func host start` and commands around publishing should be run from the build output, while others around extensions and adding functions should be run from the source.