Set up boiler plate for sequential rejection implementation.
Removed obsolete conditional SMC code that hasn't been maintained.
Removed separate resample() methods from Resampler classes that are no
longer used by AuxiliaryParticleFilter.
Removed some more obsolete conditional SMC code.
Removed Resampler concept, moved documentation into Resampler class.
Removed references in docs to old concept::Resampler.
Removed block size from Stopper interface (can use the length of each
vector of weights passed in).
Added initial Adapter interface.
Fixed criterion in Stopper.
Updated names of filters, samplers and NetCDF schemas to be shorter and
more consistent in usage.
Some cleanup of Doxygen docs, creating separate sampler and filter
subgroups under the method group.
Added some to-dos.
Created hierarchy of State classes for filters so that interface is
common up to these types. Allows samplers to use the lower-level step()
methods of filters, not just the higher-level filter() method.
Merge remote-tracking branch 'origin/master' into scalable_smc
Moved high-level filter() functions, reimplemented identically for each
filter type, into a new Filter wrapper class that inherits from any
other and buckles on these functions. Created new FilterFactory class
that creates filter objects using this new wrapper class. Removed
existing *FilterFactory classes that were specific to each filter type.
Removed output buffers from filter object state, now passed in as
argument.

Removed use of nvcc_wrapper.pl wrapper for nvcc compiler. Was need when
using libtool, but this is no longer used, and using nvcc directly seems
to work.
Merge branch 'master' into scalable_smc

Conflicts:
	share/src/bi/bugs.hpp
Consolidated pf and ekf client programs into one filter client program
that does both. Fixed EKF with ODE models. Fixed some segfaults
introduced by recent refactoring.
Consolidated mh and simulate client programs into new sample program,
sir and srs to be merged in yet. Removed cache factories. Removed use of
pointers for I/O types in favour of references, with null buffers
introduced that essentially just ignore output. Working through
refactoring of samplers.
Merge remote-tracking branch 'origin/master' into scalable_smc

Conflicts:
	share/src/bi/buffer/SparseInputNetCDFBuffer.cpp
	share/src/bi/host/math/vector.hpp
	share/tt/build/Makefile.am.tt
Refactoring I/O classes.
Refactoring of buffer and cache classes complete.