Add some missing subdirs to makefiles
Move Dim variable up into generic problem
Fix stupid bug in bem where I was always using equation index 0
Add option for simple multimeshes to choose separation of the meshes
Initialise Alt_eff_damp to avoid uninitialised memory spam in valgrind
Smarter handling of multiple meshes in some llg problem sub functions
Add self tests for multiple meshes (two spheres, close or far away)

* Close not working yet, need to do some calculations...
Fix fully implicit bem, test works but is very slow
Don't setup boundary info in generic problem build, do it in factories instead
Rename output_jac command line arg to output-jac (consistency)
Remove leftover debug outputs
Improvements to doc behaviour in generic problem

* Dump residuals as well as Jacobians

* If dump jacobians always then dump at each newton STEP
  (since this is how often they change in non-linear problems, which are
  typical)

* Fix some calls to MyProblem::actions_... not being called correctly

* Make doc intervals more intuitive: doc interval = 0 instead of "all"
  (since it's a time, "all" doesn't really make sense)

* Some other trivial things...

* Change Jacobians stored for checks in self_test/llg_jacobian
  (also store residuals)
Re-enable purely implicit llg with bem

Many changes including:

* Remove (not working) code for surface anisotropy

* Add get_jacobian functions which include bem contributions

* Fix fd-jac option in micromag elements being checked twice

* Add some comments for things to optimise/improve later

* Swap to adding identity block for bem purely on problem level
  (less hacky, works with fd-jacobian)
Fix validation directories for some tests that I moved around earlier