Changing section separators for options

Colons now used rather than underscores. Previously command-line options
were specified e.g.

solver_type=rk4

but this caused problems with options containing underscores e.g. "max_timestep".
Now sections are separated by colons, this becomes

solver:type=rk4

and

solver:max_timestep=1.0

Sections can now be nested to an arbitrary number of sub-sections. Colons
are also used in BOUT.inp, so

[section:subsection]

or

[section:subsection:subsubsection]

etc. This is currently used in the test-laplace2 and test-petsc-laplace examples.

User manual updated
Bug-fixes for R-T example and Laplacian

o Putting filtering back into Laplacian inversion by default.
  Change broke some examples.

o Fixed R-T example to use Laplace() rather than Laplacian()
Merge branch 'master' of git://github.com/bendudson/BOUT

Conflicts:
	examples/test-laplace2/test_laplace.cxx
	src/invert/laplace/impls/petsc/petsc_laplace.cxx