Fix periodicity in theory-box HOD code

[lgarrison]

From @boryanah in #28 (comment), there appears to be at least one place where we use non-periodic KDTree where we should be using periodic KDTree. Let's fix that and double-check all the KDTree usage.

[boryanah]

Yep, will work on that -- KDTree should be non-periodic for the LCs and periodic for the box.

[boryanah]

merged into fix-origin branch