... and use sstreams instead of sprintf

This commit fixes the formatting warning in the Mutation classes.

- For mut_type() and sense() calls, we changed the PRId8 format specification
  to PRId32
- For the -1 constants, we explicitly cast them to the right size
  (int8_t or int16_t) to reflect the format specification

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

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

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.

Current state of the work, it's kind of functional but there's still a lot to be done...

* 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