[WIP Proposal] Extract bootstrapping from index.php, handle all in bootstrap.php

There is currently no clear separation between index.php and bootstrap.php - both files have to be run to bootstrap a complete environment, but loading index.php then always attempts to run either a web request or a 
minion task.

This means the bit of bootstrapping that happens in index.php has to be partially duplicated in the unittest module and also in any end-user projects that want to make the kohana environment available to other CLI or web tools (eg PHPUnit, Behat, Doctrine, etc). This causes maintenance issues if the default path structure changes, or if you want to use a non-standard directory layout. It additionally makes it more tricky than it should be to move the index.php down to an explicit web document root for security. I explained the issue more in http://dev.kohanaframework.org/issues/4777 last year.

I'd appreciate feedback/agreement on this proposal before I finish off making the required changes to unittest and minion to support it.
The main issue I still have with this is when to include install.php. In the old version it was included by index.php immediately after directories were defined but before any other bootstrapping. It can't really happen there now, because that would prevent unit tests running amongst other things.

There's a few options:
* Duplicate the path constants in install.php (or remove reference to them) so that it can be included right at the top of index.php.
* Leave it here, so it runs after bootstrapping - but this might mean that kohana fails with errors related to some of the things the install.php is supposed to check (writable directories, for eg).
* Run it from the old location (now in bootstrap.php) but only if a new constant - say KOHANA_RUN_INSTALL_CHECKS - is defined. That constant would be set in index.php.