Update multilayer 1d examples to new 5.0 packages

This commit addresses the following changes:
 - Renaming of the Riemann solvers in the Riemann repository
 - Changing of the data module from `clawdata` to `data`
Some other fixups are also included.
Add more info on method comparison
Add info text for shelf contour plots
Updated from clawdata to data
Add bathy download script for atlantic
Add bathy download script for Gulf
Modify old Irene setrun to Sandy
Makefile path corrections, small setrun adjustment
Corrections to square basin example

This example is not working yet!
Removing Stommel surge example
Remove inlet surge example
Add surge gitignore for bathy files
Switch partially over to contourf plots
Merge pull request #17 from mandli/switch-clawdata-data

Update Paths and `data` modules for multilayer and surge app examples