This commit re-adds some modifications from the aevol_6 branch that
had not been kept by the large merge between the aevol_6 and aevol_7
branches.

This commit removes the handwritten destructor of the
DnaReplicationReport class, since it the same thing as the default
destructor would.

Magic command for reference:
find ! -path '*test*' ! -path './libaevol/SFMT-src-1.4/*' \( -name '*.cpp' -o -name '*.h' \) -print0 | xargs -0 sed -i -r 's/\bget_(\w+)\b/\1/g'

Functions with empty argument list should be declared f() rather than f(void).

Took aevol_run.cpp's header as reference header and set it for all Aevol source files.

* Find member variables that could clash

: grep -rEo --no-filename '\w+' --include '*.cpp' --include '*.h' | sort -u | grep '^_' > _litigious_tokens.txt
: grep -rEo --no-filename '\w+' --include '*.cpp' --include '*.h' | sort -u | grep '_$' > litigious_tokens_.txt
: grep -Fx -f <(sed -e 's/_$//' litigious_tokens_.txt) <(sed -e 's/^_//' _litigious_tokens.txt)
: cat clashes.txt
: | xargs -n 1 -I% sh -c "echo --- % --- ; grep -rlE --include '*.cpp' --include '*.h' '\W_%'
: | xargs grep -l '%_\W'"

From the resulting list,
files of interest, trimmed:
ExpManager.h | t_end
GeneticUnit.cpp | dna rna_list

False positives removed (needed no action)
Dna.cpp | indiv
ExpManager_X11.cpp | win
GeneticUnit.cpp | non_coding_computed
GeneticUnit.cpp | transcribed
Individual.cpp | modularity
OutputManager.cpp | tree
PhenotypicTargetHandler.cpp | var_sigma var_tau
Protein.cpp | gen_unit height mean width
ReplicationReport.cpp | indiv
Rna.cpp | gen_unit
StatRecord.cpp
Stats.cpp | exp_m

* Manual fixes
[x] ExpManager.h | t_end
[x] GeneticUnit.cpp | dna rna_list (almost false positive, would have caused no harm)

* Automatic fix all other symbols
: find ! -path '*test*' ! -path './libaevol/SFMT-src-1.4/*' \( -name '*.cpp' -o -name '*.h' \) -print0
: | xargs -0 sed -i -r -e 's/([^a-zA-Z0-9_])_([a-zA-Z0-9][a-zA-Z0-9_]+)/\1\2_/g'

* Minor afterhand fixes
fix OPENMP_ and changed_ with similar `find | xargs sed`s

* Check there are no more _members
: grep -rEo --no-filename '[^a-zA-Z0-9_]_[a-zA-Z0-9][a-zA-Z0-9_]+' --include '*.cpp' --include '*.h' --exclude-dir tests
: | sed -e 's/^.//' | sort -u

Instead of a single class with switches everywhere, mutations are now
handled through a proper polymorphism.

Here is the class hierarchy:
Mutation
  <-- LocalMutation
        <-- PointMutation
        <-- SmallInsertion
        <-- SmallDeletion
  <-- Rearrangement
        <-- Duplication
        <-- Deletion
        <-- Translocation
        <-- Inversion
  <-- HT
        <-- InsertionHT
        <-- ReplacementHT

It used to be done from ReplicationReport, bad !

The responsability of the creation of the tree was shared between
different entities (the tree of course, but also the individuals
and their dna).
This made it really difficult to deal with.

The solution presented here isn't optimal (yet ?). In particular,
trees had to be temporarily disabled for experiments with plasmids.
The tree now handles itself more independently. It is filled with
naive ReplicationReports which will have to be :
  - initialized at the beginning of a replication
  - filled in at the end of a replication
  - finalized at the end of a generation

In the future, it would be nice to implement that as an Observer
pattern to decouple the involved classes

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, 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...

The name convention ae_* for aevol-related classes and functions comes
from C language lacking namespaces. It was meant to prevent name
clashes. Since C++ provides namespaces, this commit wraps everything
inside an "aevol" namespace.

This means that there is no need anylonger to name classes according to
ae_*. But any new class needs to be within the aevol namespace if it is
part of aevol or to start with a "using" clause if it relies on aevol.

 - They are managed in ae_dna and ae_mutation and no more in ae_selection
 - They are saved in ae_dna_replic_report with the transferred sequence (to simplify the post-treatments)

Updated all the file headers

  ae_list and ae_list_node are now template classes. This should not influence execution time as template instanciation occurs as comilation time.

  Changes for developers:
    * It is no longer possible to declare a plain ae_list variable, you must declare an ae_list<whatever_you_want> variable. Things are clearer this way since one knows what type of object the list will contain.
    * It is no longer necessary to cast an object to the correct type:

    example:
      before: ae_list_node* rna_node;
              // ...
              ((ae_rna*) rna_node->get_obj())->rna_method()

      now:    ae_list_node<ae_rna*>* rna_node;
              // ...
              rna_node->get_obj()->rna_method()

I'm pretty sure Dule will like that ;)

Modified compilation chain:

  --with-regul changed to --with-raevol
  --without-xlib changed to the (standard) without-x

  lib-aevol was changed to libaevol for a more intuitive use with -laevol.
  Libraries generated with different compilation options are no longer differentiated by postfixes (save for the RAEVOL option) => if --with-raevol is used, the generated lib will be called libraevol (whether X and/or DEBUG are used or not). if --without-raevol (default), the generated lib will be called libaevol.
  make clean is called automatically at the end of ./configure to avoid compatibility issues.

Ported feature TRANSFER

Log overview (see previous logs for more details)
------------------------------------------------------------------------
NEW
  * Added 2 parameters TRANSFER_INS_RATE and TRANSFER_REPL_RATE to set the rate of insertion (resp. replacement) transfer.
    Default: 0.0 => No transfer.
    Both rates are per replication rates and trigger a transfer attempt (the actual occurrence of a transfer event will depend on whether an alignment is found). There can be at most one transfer of each type per replication.
  * Every possible ae_mutation now has a _length
  * Added method ae_dna::copy_into_new_GU( int32_t pos_1, int32_t pos_2 ) const
  * Added method inline void ae_genetic_unit::copy_promoters_included_in( int32_t pos_1, int32_t pos_2, ae_list** new_promoter_lists )
  * An ae_vis_a_vis now contains its score
  * Added a header for R in the output file of fixed_mutations
  * Added a new post-treatment "mutagenesis"
  * Added checking options (NO_CHECK / LIGHT_CHECK / FULL_CHECK) to the "fixed_mutations" post-treatment
  * Added a log file for transfer. Keyword TRANSFER, file name log_transfer.out
  * Added a test case for transfer.
  * New file ae_enums.h
  
MODIFIED
  * Moved the replication procedure to ae_population.
  * Deported the genome size barrier checks one level up ( e.g. from do_deletion( pos_1, pos_2 ) to do_deletion() and do_rearrangements_with_align() ).
  * Method void ae_genetic_unit::copy_lagging_promoters_starting_between( int32_t pos_1, int32_t pos_2, ae_list* new_promoter_list ) no longer has the ( pos_1 > pos_2 ) prerequisite
  * Renamed class utils to ae_utils
  
BUGFIX
  * Replaying a translocation when alignments are on could cause an error
  * The -c (or --fullcheck) option in lineage was not declared hence didn't work...
  * ae_individual::reevaluate( ae_environment* envir ) didn't reset the (new) attributes _transcribed, _translated and _folded yielding a flat fitness.
  * In post-treatments that deleted ae_common::sim, ae_dna::undergo_this_mutation( ae_mutation * mut ) could check whether it had to write in the BARRIER log. It hence tried to access a member of ae_common::sim that was NULL.
  * LOADS and BARRIER logs now work correctly
  * There were some inconsistencies with Whole Genome Events (i.e. Whole Genome Duplications)
------------------------------------------------------------------------

* Organized the repository to manage branches. *
************************************************

Everything you already know has been moved to "trunk"
Added a "branches" directory with 2 subdirectories "releases" and "features"
  * "releases" will be used for branches related to a given release, e.g. when a change to post-treatments are needed for the analysis of data generated using that release.
    For example: I am analysing data that I generated using versions 2.1.2 of the code. I hence created the branch "releases/aevol-2.1.2" so that I can code my post-treatments in a properly versionned way. These development may (depending on the level of specificity) be added to the trunk eventually (using svn merge)
  * "features" is meant to be used when developing a new feature that takes time developing. This will enable us to use svn feature more thouroughly, e.g. commit more often (even "unstable" versions) in a personal branch of the svn.

If you don't want to use branches or if you just want to be able to update regularly, you need not change your habits, just add "/trunk" when you check out
=> "svn checkout svn+ssh://username@svn.gforge.liris.cnrs.fr/svnroot/aevol/trunk"

Questions/remarks are welcome!
David