ES 2+ Configuration yaml

I am afraid I was unable to find the answer by looking through the documentation.

The new elasticsearch.yaml is much briefer and it is not clear whether previous entries are supported, such as number_of_replicas.

Where can I get documentation on all entries supported in the yaml?

Thanks

Have a look at https://www.elastic.co/guide/en/elasticsearch/reference/current/index-modules.html for index level settings. Might help.

That said, it's better to set index settings when creating the index (through create index API) instead of doing that in node settings.

Thank you. This is obviously just the default.
Surprising that the template has been changed, removing many commented defaults, any reason for that?

Because in 90% if not 99% of the time, you should not change default settings.
You should consider them as very advanced settings so you should touch them only if you read the documentation and understand what changing them implies.