* Address issue #74: missing json configuration options.
* Allow parameters from input file to be overriden on command line.
* Missing parameters in json input will defer to defaults.
* Add option for saving current options to json file (allowing
  for json parameter file format discovery.)
* Fix annoying command line argument reordering from TCLAP.
* Fix bug in assignment of `nothing` to a util::optional<T>
  variable.

Command-line support for limitting trace output.

New options:
 * -p, --probe-ratio      Attach probes to this proportion of cells
 * -X, --probe-soma-only  Don't probe dendrites
 * -P, --trace-prefix     Specify where to write traces
                          (default: 'trace_')
 * -T, --trace-max-gid    Don't trace cells with a larger gid than this.

Fixes issue #40

The resulting trees are not equivalent to the initial ones. All
offending branches were split and their non-contiguous part was moved
directly below the root.

asynchronous communication and compute 

Feature/model refactor

* fixed const interface to the serial proxy for thread private storage
* added a serial proxy for tbb task group and moved the tbb task group
  behind the threading interface.
* added comments to the communicator to better document each method

- moved spike source storage to its own file
- added unit tests for spike storage

Merging for PR#64 review.

Address PR#64 review comments.

- communicator no longer accepts or stores thread-local spike buffers
- buffers and queues are stored and managed outside communicator
- a new type thread_private_spike_store that manages the thread
  private spike buffers

Feature/model+recipe

Regression test for bugfix in commit #712c00a7

Incorrect source ids were being given to detectors;
targets were then rightly ignoring the generated spikes.

Also: small coding style compliance edits.

fix compiler warnings and tests with ASSERTIONS on

- update modparser external repo to a version that fixes some compiler
  warnings with clang
- fix a handful of compiler warnings for signed-unsigned comparison in
  tests and when ASSERTIONS are on
- comment out EXPECTS(has_contiguous_segments) where they fail in the
  tests so that we can run all the tests with full debug flags

Bugfix: build fail without TBB.

Plus: coding guidelines compliance.

Address code review pre-merge.

- add double buffering of spikes and events to communicator
- communicator::exchange() generates buffered events from buffered spikes
- this allows communication alongside cell update methods accessing spike
  and event lists

* coding convention adherence
* cell_local_index_type -> cell_lid_type
* time-type parameterized spikes and events
* communicator reset() clears events in flight
* communicator uses routine for gid->group index mapping
* event_queue 'Event' types to follow specified convention/concept.

Not sure how this compiled in the other dev environment...
nonetheless, should be fixed.

Turns out this helps when trying to deliver spikes.

* Makes model.hpp part of library interface; genericize
  value, time types.
* Clarify separation of concerns between model and miniapp.
* Model keeps a record of (local) probe ids for sampler
  attachment by caller.

* Merges upstream master
* Completes abstraction of recipe from model from miniapp
* Adds little stream masking utility to ioutil.hpp
* Unit tests for new functionality still absent