Warn about input file not existing when running hidden
Use correct path for experiment in simulation test
Clean up dead code, fix compile warnings
Dead code
Remove dead code
Remove more dead code
More cleanup, all warnings gone
Set default save/load extension to .xml
Upgrade doxygen config to 1.8.8 (requires doxygen 2014-10-11 e446e2e due to bug with annotations)
Disable file version and graphviz dot path

Version not very useful
dot path can come from PATH
Enable caller/calle graph for doxygen, limit depth to 1, use svg
Cleanup for consistency
Merge branch 'refactor'