Adds composer self-install

Changes dependencies to avoid un-necessary updates
Run phptools-init as dependancy

Required by all stages.
Also adds phptools.phpmd and phptools.phpcs for command line runners.
Merge pull request #1 from blongden/feature/composer-enhancements

Adds composer self-install
Merge pull request #2 from blongden/feature/various-fixes

Run phptools-init as dependancy