Fixed the libc++ issue.

Also it seems that on libc++ end is a reserved keyword from the std namespace,
so I renamed the time_t end structure to endt. Also updated the Rakefile to make
it compatible with the new SimKernel version.
Fixed the remaining libc++ incompatibilities.

Also updated the binless methods to be compatible with the latest FLANN (1.8.4).
Merge branch 'yaml-cpp-v0.5' of https://github.com/dherkova/te-causality into new_simkernel

Since the libc++ changes happened in the context of the SimKernel update, I merge them here to have everything in one place.
Simplified compile process with SimKernel library.

Once SimKernel is installed properly, the compilation (and the Rakefile) are much simpler.
Minor changes: Removed comments and redundancies.
Merge branch 'new_simkernel'

This closes issue #8.