Changed root call to not depend on file

Currently named "base", but need to DL and name from that.
Added directory tree structure for tracking paths
Refactored ScrapeUtility into Scrape

Needs general clean-up
Changed url path pair to use URI
Changed constructor queueing to generate URIs
Renamed pair to something more useful
Removed unnecessary try-catch. Fixed some spacing
Cleaned up a couple bits.

Removed pointless comment.
Added TODO placement.
Removed redundant system call.
Update methods that create URIs to use the already created ones
Refactored command line parsing into main with extra classes into seperate files
Added tree init and fixed startup to use correct dir (for scrape and non-scrape)
Added cleanup on cancelling the program