#3536151 Prioritise all project values over defaults in expand_composer.php

In addition to prioritising all of the projects own elements, this MR adds three command-line options to the script

*   --input {string}   Name of the file to read.
*   --suffix {string}  Suffix to append to the output filename. Useful for
*                      avoiding overwriting the input during development.
*   -v --verbose       Show verbose output.

Closes #3536151