Emanote’s layer system allows you to “merge” multiple notebooks and treat them as if they were a single notebook. The -L option in the command line accepts layers, and you can specify multiple of them with the right most taking the most precedence.
“Default” layer
Emanote implicitly includes what is known as the “default” layer. Its contents can be seen here. This layer contains HTML Templates, index.yaml and other default assets, like the logo, favicon and fonts. When you run emanote -L /your/notebook run, your notebook is overlaid on top of this default layer. What this means, in effect, is that you override just about any file in the default layer, such the HTML content of HTML Templates, in your own notebook directory. As an example, see template/hooks of this documentation notbook.
Merge semantics
The default merge semantic is to replace with the file on the right layer. For some file types, special merge semantic applies. For example, YAML files are merged by deep merge, not file-level replacement. This is what allows you to create index.yaml that overrides only a subset of the default configuration.