Make all necessary changes for v1.0.0

[nir0s]

This commit contains the following:

• Change CLI command names repl and iter to in-path and from-config respectively
• Changed the logging to be much less verbose and formatted much much better
• path and config-file in in-path and from-config have been changed to positional arguments respectively
• Reorganize the code, remove unnecessary logger configuration and make repex a single module
• Introduced better error handling
• Standardize error messages
• sys.exit is now only used in the CLI and instead exceptions are raised for each error so that tracebacks are exposed to anyone using the Python API directly
• handle_file is not longer exposed as a function in the API
• Some breaking API changes were introduced, in, for instance, the iterate and get_all_files functions.
• 99% test coverage!

[nir0s]

This will provides solutions for both #34 and #35