Fixing issues rmcantin#16 and rmcantin#19 on github

Fixing issue in saving state

Fixed bug in initial values not being rescaled properly

Cleaning source tree and improving docs

--HG--
rename : system_calls_examples/branin_system_calls.cpp => examples/branin_system_calls.cpp
rename : system_calls_examples/branin_xml.cpp => examples/branin_xml.cpp
rename : system_calls_examples/eval_branin.py => examples/standalone_calls/eval_branin.py
rename : system_calls_examples/eval_branin_xml.py => examples/standalone_calls/eval_branin_xml.py
rename : system_calls_examples/problem_template.xml => examples/standalone_calls/problem_template.xml
rename : wrappers/bayesopt.h => include/bayesopt/bayesopt.h
rename : include/bayesopt.hpp => include/bayesopt/bayesopt.hpp
rename : include/bayesoptbase.hpp => include/bayesopt/bayesoptbase.hpp
rename : include/boparameters.h => include/bayesopt/parameters.h
rename : include/boparameters.hpp => include/bayesopt/parameters.hpp
rename : wrappers/bayesoptwpr.cpp => src/wrappers/bayesoptwpr.cpp

Fixing typo

Adding new changes to the docs.

Merged rmcantin/bayesopt into default

Bug in Python interface. Matlab linking issues doc moved to install.

Error handling in kernel, mean and criterion functions

Improved documentation.