Resolving deprecation warnings using Default Logstash config to allow us to upgrade

I am currently going through the Elasticsearch deprecation logs to check what we may need to resolve prior to upgrading our ELK Stack from v6.0.0 where I have found the following but have no clue how to resolve. We have Logstash created Daily indices using the default settings is there a way in logstash to resolve the below errors?

[o.e.d.a.a.i.t.p.PutIndexTemplateRequest] Deprecated field [template] used, replaced by [index_patterns]
Deprecated field [inline] used, expected [source] instead
[_default_] mapping is deprecated since it is not useful anymore now that indexes cannot have more than one type
Fielddata access on the _uid field is deprecated, use _id instead

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