Move config-file-diffs path to analyze/config_file_diffs

Store analyzed data in analyze directory and store config files diffs
in config_file_diffs subdirectory.
This way the files in the config_files scope are the definitive
reference of what is in the description.

Fixes #363
This is a repetitive and error-prone way to set the format version. Isn't there a better way to do this? What is the goal here?