Adjust bundles scanner to work with arrays.

StdClass objects deep in autoloader array configs were making it difficult to work
with prebootup processing.
Update tests
First draft at bootstrapping kernel dynamically.
Add create schema argument.
Refactor for reusability.
Wire in bootstrap installer, module and theme regeneration.

This is all temporary wiring before things can become more elegant.
Refactor installer for new boot process.

There are no more old style system modules so removed logic to handle both for installation of
system modules.

No need to scan 'system/' directory because these are core and hard wired into application kernel.
Removed reliance of Doctrine 1 and DBUtil during install
Merge branch 'boot' into 1.3