... and use sstreams instead of sprintf

This commit removes the explicitly deleted move constructor, and
move and copy operators, in Mutation classes, as they are deleted
in the base class Mutation.h.

This commit gets rid of the -Wdefaulted-function-deleted warning
that popped up in Mutation-derived classes.

It came from the fact that Mutation.h had these definitions:

               |     copy      |      move
----------------------------------------------------
constructor    |   default     |    default
----------------------------------------------------
operator       |   delete      |    delete

whereas the derived classes had the following:

               |     copy      |      move
----------------------------------------------------
constructor    |   default     |    delete
----------------------------------------------------
operator       |   default     |    delete

This meant that the move operator was defaulted in the base class
but deleted in the derived classes, producing the warning (the
discrepancy was introduced in 6615dbb4).

This commit deletes all copy operators, leaving only copy constructors,
which are used in the Clone() method shared by Mutation classes.

Note that in *HT classes, the copy constructor is defaulted but
the classes contain pointers, so there might be a memory issue when
calling the constructor.

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'

Looking forward to honour Google Style guide, the purpose is to rename getters
from get_var() to var(). Many of such renames cause conflicts, though. In this
commit, only the safe names were changed.

grep -rEo '\bget_\w+\(' --include '*.h' --no-filename --exclude-dir tests \
 | sed -e 's/get_//' -e 's/($//' \
 | sort -u \
 | xargs -n 1 -I% sh -c "grep -roq '\b%\b' --include '*.cpp' --include '*.h' --exclude-dir tests || echo %" \
 | xargs -n1 -I% sh -c "find ! -path '*test*' ! -path './libaevol/SFMT-src-1.4/*' \( -name '*.cpp' -o -name '*.h' \) -print0 \
 | xargs -0 sed -i -r 's/\bget_%\(/%\(/g'"

Yes. I know...

http://google-styleguide.googlecode.com/svn/trunk/cppguide.html#Function_Names

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

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

In a classical aevol experiment it will only mean that generation
number is now called time.

In a different setup where individuals actually have a life span,
this means that a generation may correspond to several time steps.
This means that we can e.g. let molecules of public good diffuse/degrade
through several time steps btw each generation and of course makes the
whole thing more R-Aevol compliant.

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

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.

Updated all the file headers

When DUMP_STEP is given, the probes of each individual are written 
in stat/dump/individual_probes_numgener.out every DUMP_STEP generations

Experiment creation, backup and load from backup are now functional on the new architecture

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.

* 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