Changes to APLCore:run and Additions to APLQuery

Most of the final implementations have been added to switch over to the
new code.

In APLCore:run most of the lines of code were removed to be implemented
in APLQuery function for handling page dynamics. Also changed the loop
function according to WP's version of using WP_Query class.

In APLQuery, most of the old code was commented out for new code. The
constructor was changed to rely more on class functions rather than
nested code, and currently no longer queries posts on construct, but
will still set the 'multiple' query strings according to APL and WP.
Until inheritance becomes more of a possibility with class variables, it
now requires the APLQuery:query_wp function to be called after
constructing a new class to preserve the WP_Class format. Also added the
$_query_str_array class variable as a result to be used when querying
with WP_Query. Added APLQuery:post__not_in() to exclude posts after
querying posts since post__in conflicts.

Some new bugs fixed. Added post_type to Page Parents without
taxonomies/terms to fix child pages not being queried. Added an extra if
check for empty page_ids to fix adding a null value to _postParents.