Continuing to clean up InitialiseSettings.php

- Reorder $wgLogo by project family (more logical ordering,
  allowing to maintain logos across families more easily)
- Move extension stuff (Math, Score) out of core settings
  section
- Also miscellaneous cleanup (indents, comments, etc)

Once again, I have double-checked this to ensure nothing
has actually been changed. Code has been moved around but
not actually functionally modified (diff engines, of
course, hate this kind of stuff).

Bug: 29902
Change-Id: I34d1f29d2c7f5c3977b63523c83a2e80d39a7edb