Improve mesh factories

* Refinement is always 5 * 2^n per unit length

* Change cubeoid meshes to be closer to unit size

* Update llg_jacobian test data accordingly

* Add warnings to ut meshes (Corners may not be correct)

* Move semi implicit meshes into llg_problem.h
  (ready for joining problems)
In parameter sweep, handle boolean args better
In parameter-sweep.py relabel driver->binary

Because now the problem type (driver) is usually determined by another
argument to ./driver/driver
Output hms in micromagnetics element even for decoupled ms problems
Initial commit of merging semi implicit problems into llg driver

* Mostly just moved code from semi implicit problem into llg problem
  (inside conitionals)

* Building the problem is still somewhat messy

* Add relevant command line flags

* Also modified self tests to use driver.cc
In parse.py label decoupled ms problems in legend
Add error for pinning single phi in parallel since it won't work
Make phi*_index() functions in LLGProblem simpler

* Fixes bug where phi1 wasn't pinned because the index was wrong
  in decoupled problems

* Needed to change some bem setup code to get the correct indices
In llg residual test use structured mesh instead of unstructured
Add boundary markers to unstructured square mesh

* This allows bem to automatically detect edge nodes

* Also translated mesh to match location of structured square mesh
Add boundary markers for unstructured cubeoid

* Allows bem to auto detect corner angles
Shrink unstructured cubeoid to match structured cubeoid size

* Needed to update cubeoid energies test data
Remove two_sphere/close energy test because nothing to test it against
Add option to fail if error norm exceeds a specified value
Add output of minimum element size to trace file
Initial commit of experiment script for intermag Dresden results
Add option to disable explicit solver optimisations for debugging
Move some code out of parse.py into a general python header
Initial commit of self test for odes

* Doesn't test that time step sizes chosen by adaptivity yet..
Fix bug in ode problems where initial condition was not set