Fixed some compilation and build problems
First working version with c++11 compilation option. Output for yeast data was equal to pre-c++11 version
Some more boost replacements
Boost dependencies removed from percolator except filesystem (not everything from converters)
Tried adding XML compiler option, many errors
XML dependencies removed, not tested yet
First tests seem to work, but yeast xml example does not work with xmlsupport on
XML dependency is now optional (default is off)
Merged master into c++11
Compiles on all platforms now
Fixed some compiler warnings
Fixed compiler error with const declarations, take a closer look at this later
removed some unused variables and functions from SetHandler
Problems counting the number of features
Only exp_mass and calc_mass are not computed, otherwise seems to work fine
Removed SetHandler Iterator dependencies except in PercolatorCInterface
Removed C interface and cleaned up some code
Cleaned up some code in Scores.cpp
Tested profiler. CPack.txt needs to be configured not to strip
added scan number to tab delimited file format, results are similar but not identical to xml input