Doc running App from anywhere & CreateApp refactor

Conflicts:

	omero/developers/Web/CreateApp.txt
Add app settings to docs from PR #1788
Update default nginx config
Document custom OMERO.web url subdirectory
Add note about conflicting mod_fastcgi options
Fix indentation
Make apache/nginx configs into subsections, rearrange text
Remove os x specific reference, add missing :
Add section about tag plugin in users CLI documentation

This commit adds some basic user documentation for the tag plugin written by
by @criswell. The main functionalities of the CLI tag plugin (create, list
and link) are listed as subsections.
11802 fix - whatsnew updates
Removing beta2 & adding tag CL plugin docs
Mark's suggestion - has enabled -> enables
Removing reference to beta2
tagsets -> tag sets
Fix tag set spelling
Add warning for import changes in upgraded Apps
Fix section title and tagsets output
Merge pull request #591 from hflynn/remove_beta2

Removing reference to beta2
Fix ticks
Merge pull request #581 from will-moore/web_app_docs_11730_develop

Doc running App from anywhere & CreateApp refactor