Feature/webapp adaptation

[reednel]

The bulk of the functional changes in this update are the addition of arguments for interfacing with the R Shiny app (in development). These arguments may provide utility for the average user, but they do not impact core functionality in any way.

New arguments:

• -Galias=: an alias for the G file.
• -Halias=: an alias for the H file.
• -Balias=: an alias for the B file.
• -p: passthrough; whether or not to write the input files into the output folder.
• -t: timestamp; the output folder's name includes the date and time of execution.
• -g: greekstamp; the output folder's name includes the values for alpha and beta.

In addition to the new arguments, slight refactoring was made across file_io.cpp, making naming conventions more uniform and select functions a bit more generic.