Changed random number generators to std::random because they are sure to compile with clang 3.4 and boost 1.55. annoying that the two don't play well together. -Wno-deprecate-register is necessary too. Brownion now compiles.
The SIR example is fixed. Now has recovery and reads parameters from the command line. It's much clearer with the new GSPN construction method. Also adding install-sh because moved to a new machine and configure fails without it, so it must be one of the necessary temporaries in order not to have to do autoreconf.
ExplicitTransitions now rigorously hides its members once it is built. There are also comments and tidying before committing to the main repository. Need to check this on gcc before the rebase.