be more forging of user provided file names

be more forging of user provided file names
ticket:192
It turned out my use of boost::filesystem::path could toss an exception
if there were spaces in the file name on OS X. I needed to do a bit more
work to construct a safe filename for saving analyses and motifs.

Also I discovered that runtime_error was not the root exception class,
std::exception was. So I adjusted my try/catch to catch that exception
in the hope that I can provide more meaningful error messages.