Merge pull request #585 from hflynn/rebased/develop/va_password

Removing swordfish as root password for VA (rebased onto develop)
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
merge develop -D org -I include -E exclude: PR 533 (Removing BF anchor until it exists)
merge develop -D org -I include -E exclude: PR 581 (Doc running App from anywhere & CreateApp refactor)
merge develop -D org -I include -E exclude: PR 584 (Web config docs 11723 11724)
merge develop -D org -I include -E exclude: PR 586 (adding two more issues to the Homebrew installation)
merge develop -D org -I include -E exclude: PR 589 (Add section about tag plugin in users CLI documentation)
merge develop -D org -I include -E exclude: PR 590 (11802 fix - updating what's new for OMERO 5 docs)
merge develop -D org -I include -E exclude: PR 591 (Removing reference to beta2)