Merge from ReForm

See merge request !10

Move Debug/DebFileOut.hh/cc to Utils/FileOutput.hh/cc and allow the functionality to be used outside of Debug

* Add functionality to store index mesh in OBJ and OFF formats; Add DEB_index_mesh_out[_if]
* Switch DEB_index_mesh_out to obj format
* Add TEST_if()

* Adds optional pre-call and post-call events in the journal to implement reference count abridgement.
* Adds new documentation for many functions, and improves existing.
* Removes "JOURNAL_FUNCTION" from the created macros when journal is turned off, because there is no such macro when journal is turned on.
* Adds the ability to unlink names in the journal manually. This was already being done by destructors, but there wasn't a way to do it for names managed in other ways.
* Add HandleT<> to support handle tracking
* Generalize the key<> function to handles and make key a pair of size_t 
* Simplify ReturnLink and make it work for HandleT<>
* Adds an operator< to the HandleT class so that it can be used as a key in associative containers (T-Splines uses it this way for ref-count collapsing).

Add JOURNAL_ADD_TYPE_INTERNAL_TRACKED,  ab internal type that is tracked by the name book at all time

* Move type_name<> to JournalCppDefs.hh and namespace Cpp and enable automatic handling on *, & and const types

* Add JOURNAL_ADD_TYPE, JOURNAL_ADD_TYPE_INTERNAL, JOURNAL_TYPE_EXTERNAL 

* Leverage argument<> for CArrayT<> elements

* Add Journal::to_lower() and improve object naming when the class name is all capitals

* Prevent de-referencing of possibly invalid argument pointers

* Add define_consrtuct[_default] to simplify for non-opaque data constructors, e.g., vectors, planes, matrices, transforms, etc.

* Fix a bug where references to a pointer could inadvertently dereference an invalid pointer

* Disable automatic includes by default; enable them by defining JOURNAL_AUTO_INCLUDE.

* Add JOURNAL_MAIN_VOID to prevent return from the main() function in C++ journals.

* Add extract_directory() and replace_filename() in JournalFileSystem.hh/cc

* Add support for output arguments accessed by * and **
* Add ArgT and ArgQ, the macro JT (journal traits) to provide a generic approach to disambiguate definitions for value, reference and pointer arguments
* Add support for linked arguments
* Recursive Cpp::define() for ArgLinkT<> and ArgT<>
* Reference to pointer arguments now defer processing to the pointer argument implementation, rendering define overloads for pointer to custom types redundant
* Journal non-linked pointers to opaque data now using their actual addresses cast with reinterpret_cast<>
* Remove links to this pointers when emitting object destructor calls
* Remove Data::key
* Add Data::type to allow different types of initialization
* Simplify ArgLinkT
* Add ReturnLinkT and JOURNAL_[METHOD|FUNCTION]_RETURN_LINK
* Remove OutputT
* Add JOURNAL_TYPE_NAME macro
* Add Journal::Cpp casts
* Fix a bug where define(..., float) was outputting invalid float constants
* Improve the comment on Journal::Filename

* Refactor Journal::Stream::Impl
* Add Scheme journal implementation
* Apply SMI class naming conventions for Scheme
* Remove Base::Command as this is breaking ENDL output during static initialization
* Clang reformat for JournalStream.cc
* Improve the naming API
* Various fixes for the Scheme journal
* Replace define() overloads with template<> define() specializations

MTBR-691 refactor C++-related code from Journal::Stream::Impl to allow journals in other languages (#3)

Fix a bug where the Journal can be turned on before the stream pointer is initialized, resulting in a failure to output and memory leaks

Ensure Journal stream is always flushed when `\n` is printed

* Add the Journal sources
* Remove ReForm specific code in Journal and allow various configuration options
* Fix a macro that was incorrect if JOURNAL_ON was undefined
* Journal can work either with Boost or the std::experimental filesystem implementations
* OStringStream using std::ostringstream now and sets the locale to "C"
* Debug::FIle now uses OStringStream
* Add IOutputStream:Base::print(float)
* Fix initialization bugs
* Allow comment streaming, allow existing journal entries to be output as comments, improve code consistency
* Document the Journal functions
* Add Journal::output_path()

Flush the test stream after each result output to make sure results are not lost in the event of a crash