rename halmd.utility.numeric to halmd.numeric

This corresponds to the tree structure of the C++ part. Further, numeric
routines are not typical utility tasks.
lua: remove hard-coded defaults from add_options()

So far, add_options() is present only in the modules
halmd.observables.utility.{semilog_grid,wavevector}.

Hard-coded numbers are not generic and are almost never a good idea. The
values are easily provided as kwargs in the user script.

Further changes:

* use utility.assert_* functions to test parameter presence

* fix typo for default parameter "tolerance"