Fix/Unused Variables

Going through some of the warnings my IDE is throwing up so I'll probably end up doing a couple of these tiny pull requests.

• cal_tools/cal_tools/agipdlib.py: corr_bools={} setting keyword arguments to mutables isn't a great idea since the state can persist across function calls, maybe in this case that was the intention but it usually isn't. Changed it to None and then set it to a dict if no argument is given.
• cal_tools/cal_tools/lpdlib.py: self.cnl = True was set, but it looks like that should have taken its value from the correct_non_linear argument, set it to that.
• cal_tools/cal_tools/metrology.py an offset is defined but never applied to the coordinates. Similar code appears throughout the file so I just did the same thing there as well, think it should be correct.

@danilevc I noticed, and remember you mentioning, that there's a template used for merge requests, but can't remember where to find it. Can you point me to it and then I'll update this text to fit the template?