Improve further + JSON output

There's a bit of everything in this PR, but I've (tried to) made sure each separate commit message was clear enough for review.

JSON output with the -j CLI option
Improve parsing of options with getopt
Remove horrible macros that were creating the gates in gateLookup
Move some of the implementation code to .cc files instead of headers
Add a first unit test for gates using doctest
Re-write measure_all as a single iteration over all states, instead of calling the measure of a single qubit. Way more efficient.

QuTech-Delft / qx-simulator