Fix bug with merging configuration files

[jlowin]

There is a function in collections.py that merges two dictionaries, and is used to load a user configuration into an existing default configuration.

The basic logic is that it iterates over each key of the user config, and if that key has a non-dict value, it updates that key in the default config with the user value. However, if the key is a dict, then it recurses into that dict and performs a nested merge. The idea is that this allows merging of nested dictionaries without forcing the user dict to have every key in the default dict.

However, the merge function only recursed if isinstance(config, dict) was True... and Configs are not, in fact, dicts. This resulted in very bad merges whenever a user config was present that was at all different from the default config, since the merge function wouldn't treat the config as a dict and do a nested merge.

This PR adjusts the merge function to test for isinstance(config, MutableMapping), adds merge unit tests, and also adds a unit test to make sure user configs are loaded appropriately.

[jlowin]

Oh, and this also stops the eager generation of user configuration files, which was creating some issues with stale files in local testing and testing on prefect server (due to an unrelated issue).

[cicdw]

LGTM