Docs cleanup/improvements

Based on the resent release of the beta00009 docs, there's still plenty more that needs to be done as the structure of the site had to change due to docfx and xrefs since you cannot have overlapping xrefs within the same docfx site build, they are unique. The changes are now consistent with how the Lucene api docs are structured which is per 'package'.

* [ ] Remove any hard coded values and have these values passed ot the build as part of automation, this means re-enabling some custom docfx plugins and investigating why they conflict with some default xref functionality.
* [ ] Fix parts of the site that don't load from correct relative (_rel) paths that were needed to be hard coded for now, this includes the index.json search document.
* [ ] Ensure the main docs site's links link through to the correct 'package' site, for example, Codecs is linking through to the 'Core' package Codecs but it should link through to the Codecs package just like the Lucene docs site does. There are probably others and this is an issue with xrefs.
* [ ] Investigate and correct xref links that aren't being processed correctly, these are mostly on individual package docs
* [ ] Investigate warnings during docfx build to try to remove them all
* [ ] Update site.ps1 build script to be consistent with the docs.ps1 script parameters
* [ ] Update the documentation for building the website/docs since some of this has changed with the new docfx build
* [ ] Update the documentation for adding new and 'overwrite' docs to the API documentation
* [ ] Automate more of the steps involved in creating and deploying the website/docs

Start by comparing site.ps1 with docs.ps1 and reviewing the beta00009 DocFX build output, including warnings and the index.json search document. Trace the relative paths, package links, and xref failures in the generated site. Done means the documentation builds without the listed warnings, links resolve to the correct package sites, build parameters are consistent, and the website and contribution documentation reflects the updated process.

Written by the indexing model from the issue text.