Update and fix issues with installation docs

[amoeba]

[Could use a taker on doing this work]

@ThomasThelen noted some weirdness in the installation docs (https://github.com/NCEAS/metacat/blob/dev-2.11/docs/user/metacat/source/install.rst#apache-httpd-server-highly-recommended):

  <Directory "/var/www/webapps/metacat/cgi-bin/">

Which should probably reference /var/lib/tomcat7/webapps/metacat/cgi-bin instead.

Then, when I looked at the rest of this section, it's a bit confusing. It starts out telling you to edit httpd.conf but then follows up by telling you to copy our example conf file into your sites-available. Is there any reason for this?

I also noted that our Tomcat instructions don't cover disabling 8080 which is someone I learned recently we do on our production deployments.

I think we should:

• Tidy up the flow and structure of the install docs and check for consistency
• Update our example configs (both in docs and in git) with more up to date examples