Warn on missing variables

[aparlato]

Closes #13

We already had some validation checking for undefined values, but it happened after we ran mergeOverrides which was unintentionally cleaning up these values by cloning layers using JSON.parse(JSON.stringify()).

Since we still want to validate the fully built layer, this PR:

• switches to using lodash's cloneDeep method for cloning the object to maintain undefined values
• adds an example scenario where we expect a warning for a missing property value
• adds a test to confirm mergeOverrides does not remove undefined values

Noting here that we are not explicitly warning that a variable is missing, but that a property value is undefined (which would usually be due to a missing variable). This can be easily inferred from the message to get to the root of the problem.

[ebrelsford]

Looks great, mind updating the CHANGELOG while you're at it?