The time will be universal, accessible via Time::get_time()
A time step goes by when someone (anyone) invoques Time::plusplus()

Remains of forgotten attemps at STL-izing ae_population.

And move them to ae_population.cpp.

R-Aevol files were in the tree but not even compiled. Moved them to
raevol sub-directory so that it is clear they are not maintained in the
same way. (Actually, they are kept as they are for reference when
importing current R-Aevol code.)

Get ae_individual::get_protein_list and ae_individual::get_rna_list to
return std::lists.

Forgot to reserve memory for vector. Accessing elements with operator[]
doesn't create them!

Taken from ae_stat_record.cpp:
ae_stat_record::ae_stat_record(..., ae_individual * indiv,...)

Nice. Except that the constness of indiv is abused. Later on:
ae_genetic_unit& gen_unit = **indiv->get_genetic_unit_list_std().begin();
...
_nb_bases_in_0_CDS = gen_unit.get_nb_bases_in_0_CDS()

Where get_nb_bases_in_0_CDS() is NOT const and cannot (yet) be, because
it calls compute_non_coding which alters ae_genetic_unit's state.

Hence, a bit sad, I feel allowed to remove the `const` qualifier.

Besides being unused, this function was a duplicate of get_nb_genetic_units.

Deleted functions can't be called.

http://en.cppreference.com/w/cpp/language/function#Deleted_functions

And fix #includes and libaevol/Makefile.am.

Renamed ae_dna_replic_report to DnaReplicReport.
Renamed member variables with no prefix _ and with a trailing _.

Variable names should not start with and underscore as these names are
reserved to the compiler implementation. (C++03 standard:
§17.4.3.1.2/1). But class member variables can END with a trailing
underscore.

In the process of simplifying ae_dna_replic_report::get_nb_etc(),
symbols were needed to describe composite mutations. Would have been
nice to create a separate type extending ae_mutation_type but it's not
supported by C++ as of C++11 or 14. Alternatives like encapsulating the
enums in classes felt too heavy for this task.

In the process, got to add constness to functions in many other
files. Could have dropped constness from declarations, but since I was
at it...

Has to be tested thoroughly, still...

And a bit of other ae_lists removal.