Various YAML updates

[ageorgou]

Includes:

• Addressing recent warning for PyYAML safety (fixes #369)
• Fixing the error of accidentally erasing the config files when running from source, when a local configuration did not exist (fixes #347)
• Various small fixes and improvements to the configuration loading

Still to do:

• [x] Test line endings work well on Windows (when running from the jar), after changing from binary to text mode
• [ ] Remove the double version-checking and patching, assuming it is not necessary (now in #403)
• [x] Add a test to check that we don't overwrite the user's exusting configuration
• [ ] Double check that we do not update the local configuration files somewhere else (#344) - nothing found so far
• [ ] Display a message box if the settings file is corrupt, and log it (#345)

[ageorgou]

Will test the first point (that it works fine on Windows), and then leave the other points (particularly the logging and message box in case of error) for a different PR.

[ageorgou]

Seems to work OK on Windows - line endings don't show up correctly on Notepad but do on other tools, and that seems to be the same before these changes too. Will merge and open other issues for remaining changes, unless you have any other comments @giordano?