Add missing config options to Logstash section of reference.yml

[dedemorton]

Closes #3062

A couple of open issues:

• So do we want to remove the deprecation statement under port in the reference docs? (NO)
• The reference docs say that the default setting for port is 10200, but the code here says 5044. I'll change it in the reference docs (assuming I'm reading the code correctly...let me know). (Fixed docs.)

[urso]

So do we want to remove the deprecation statement under port in the reference docs?

No. We should add the deprecation notice to the config file. Setting will be removed in 7.0

The reference docs say that the default setting for port is 10200, but the code here says 5044. I'll change it in the reference docs (assuming I'm reading the code correctly...let me know).

10200 is actually correct. It's the one used in code. But for some reason we started documenting 5044 about everywhere. We will change the default to 5044 in beats.

See #7881

[urso]

Let's mark port as deprecated.

[urso]

Checking the code we did change the default to 5044 at some point.

[dedemorton]

Actually, since port is deprecated, we should not add it to the reference.yml since we say the following at the top of that file:

# This file is a full configuration example documenting all non-deprecated
# options in comments. For a shorter configuration example, that contains only
# the most common options, please see filebeat.yml in the same directory.

[dedemorton]

@urso This should be ready for a final review.