Decouple Rego input and query options

The process to decouple the input and query compilation had already been
started. Aside from custom compilation stages which might live out of the tree
there are no usages of the input in the current QueryCompiler implementation,
all had been removed previously. This change removes the connection between
the two and more formally breaks the two apart.

The benefit here is that we can compile and cache queries independent from
the input.

Signed-off-by: Patrick East <east.patrick@gmail.com>