Move general purpose phake/functions.php

Remove phake/functions.php:

* is_tty() moved to term_colors.php
* resolve_runfile() and load_runfile() moved to phake/Builder.php
* fatal() moved to phake/Bin.php

This code does not change any of the existing logic, it merely improves its structure.
PR #20 introduced a minor bug in that the "--trace" option is ignored, this PR also fixes this.

Among others, this also simplifies #11 by making it easier to embed the `Builder` into another project (e.g. https://github.com/clue/graph-phake)