HHVM: simplify logging options

* native_stack_trace is true by default; so remove.
* error_reporting_level is set to HPHP_ALL by default.

Additional fixes:
* Remove unneeded dir (/usr/share/pear) from include path.
* Make runtime dirs run before the service

Change-Id: I05dd12a8cc141eba05448c8d6226462048d04cf9