Allow user to arbitrarily nest `templates/layers`

[aparlato]

As of now, the --layer-dir is expected to be flat. We should allow arbitrary levels of nesting there for organizational reasons as many styles are operating with a large amount of layers than become unmanageable.

The caveat here is that it would be prudent to make this backwards compatible and open to alternative use cases.

For example, if a user has a template/layers dir with directories in it that are not layer templates (eg scripts), we should allow them to skip this. We should also consider how to avoid issues around redundant file names since with nesting being treated as flat this is a possibility.