49 sort out data

[jwestw]

There were a few problems with the data files and folders.

• put more settings of data files and folders in the config file
• debugging: corrected the res_dict so it had all the keys it needed in it
• created a "make path" function
• put the h5 writing behind a try statement
• moved h5 write to output folder

[jwestw]

Closes #49