Restructure docs in deployment order and migrate to OKF v0.2

Convert the documentation bundle to the Open Knowledge Format v0.2 and
reorganize it to follow the order in which CyVerse is actually deployed.

Format (OKF v0.2)
- Every concept document carries YAML frontmatter: type, title,
  description, tags, status, generated, and sources where the content is
  derived from something.
- Every directory carries an index.md listing, with the bundle-root
  index declaring okf_version.
- Bundle history is recorded in docs/log.md.
- references/ holds provenance notes for derived material.

Structure
- architecture/  what the system is, what it needs, what depends on what
- platform/      the products and services offered to users
- deployment/    phases 1-7, ordered by dependency
- operations/    running a deployed system
- api/, development/, references/
- deployments/, database/, guides/, and services/ are retired; their
  content moved into the tree above.

New content
- deployment/from-scratch.md: end-to-end runbook for a two-node
  deployment, written from an anonymized pilot deployment record. All
  hostnames, zone names, DNs, realm and client names, and credentials
  are placeholders; secrets are generated per install.
- Previously undocumented steps: HAProxy, iRODS provider and DE
  integration, iCAT, database migrations, cert-manager, Harbor, Argo,
  OpenLDAP, OpenSearch, NATS, bootstrap, verification, troubleshooting.
- architecture/component-inventory.md and network-requirements.md.

Editorial
- Deduplicated: mail (exim4 + local-exim), the golang-migrate procedure
  repeated in every database document, the deployment-order list that
  appeared in three places, the database list that appeared twice, and
  two retired overview pages now covered by directory indexes.
- Corrected: databases ordered before the services that need them; the
  rsyslog path; dirname vs basename for the kubeconfig directory; the
  helm uninstall invocation; VRRP as IP protocol 112 rather than a TCP
  port; QMS extensions created in the qms database; recomputed sizing
  totals with the source's 100/110 TB discrepancy noted.
- Fixed the docs build: zensical.toml named a theme that is not
  installable, so the published build was failing, and extra_css named a
  stylesheet that does not exist.
- Marked Elasticsearch deprecated in favor of OpenSearch, and
  ingress-nginx transitional in favor of Traefik.
- Replaced site-specific hostnames, DNs, and sample credentials with
  placeholders; replaced XXX placeholders in the system overview.
- Fixed 13 broken anchors and links; the build now reports no issues.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01UKieNHmYbysTvGDK2SC1YM

Author: claude

docs/about.md

@@ -0,0 +1,132 @@
+---
+type: Reference
+title: "About this documentation"
+description: "What CyVerse is, who this documentation is for, and where each audience should start."
+tags: [about, orientation]
+status: stable
+generated: { by: process:okf-migration, at: 2026-07-29T00:00:00Z }
+sources:
+  - id: okf-spec
+    resource: https://github.com/GoogleCloudPlatform/knowledge-catalog/blob/main/okf/SPEC.md
+    title: Open Knowledge Format v0.2 specification
+    author: team:google-cloud-platform
+    last_modified: 2026-07-29
+---
+
+![](assets/cyverse_logo_2022.svg)
+
+# What CyVerse is
+
+CyVerse is a computational infrastructure for data-intensive science, and the
+people who operate it. It is fully open source and funded by the
+[United States National Science Foundation](https://www.nsf.gov/){target=_blank}.
+
+It is both a Software as a Service platform and the Infrastructure as Code needed
+to run one: the same stack that serves the public US deployment can be deployed by
+another institution on its own hardware or in the cloud. That is what this
+documentation is for.
+
+<figure markdown>
+  ![layercake](assets/layerCake.svg){width=800}
+  <figcaption>Hardware at the bottom, services in the middle, products on top</figcaption>
+</figure>
+
+# Who this is for
+
+## Deploying CyVerse
+
+Start with [prerequisites](deployment/planning/prerequisites.md), then read
+[deploying from scratch](deployment/from-scratch.md) end to end before running
+anything. Work the phases in [deployment](deployment/) in order, and check each one
+against [verification](deployment/07-post-install/verification.md).
+
+Before provisioning: [component inventory and
+sizing](architecture/component-inventory.md) and [network
+requirements](architecture/network-requirements.md).
+
+## Operating a deployment
+
+[operations/](operations/) covers day-to-day administration: users and VICE access
+in [DE administration](operations/discovery-environment.md), data and curation in
+[Data Store administration](operations/data-store.md), accounts in [User Portal
+administration](operations/user-portal.md), and the recurring questions in the
+[FAQ](operations/faq.md).
+
+## Integrating with the APIs
+
+[Terrain](api/terrain.md) is the API behind every CyVerse product. The
+[endpoint index](api/endpoint-index.md) lists everything documented here, and the
+live [Swagger reference](https://de.cyverse.org/terrain/docs/){target=_blank} is
+the most current source. Authentication is [OAuth 2.0 through
+Keycloak](platform/authentication.md).
+
+## Contributing code
+
+[development/](development/) covers the development environment and contribution
+workflow. Source lives in the
+[CyVerse](https://github.com/cyverse){target=_blank} and
+[CyVerse DE](https://github.com/cyverse-de){target=_blank} GitHub organizations.
+
+# What CyVerse offers its users
+
+| Product | What it does |
+|---------|--------------|
+| [Discovery Environment](platform/discovery-environment.md) | Web-based data science workbench with hundreds of integrated tools |
+| [Data Store](platform/data-store.md) | Multi-petabyte iRODS storage with HTTPS, WebDAV, SFTP, and API access |
+| [Data Commons](platform/data-commons.md) | Publishing curated and community-released datasets, with DataCite DOIs |
+| VICE | Interactive computing — JupyterLab, RStudio, Shiny — inside the DE |
+| [Cloud services (CACAO)](platform/cloud.md) | Infrastructure as code for multi-cloud deployments |
+| [BisQue](platform/bisque.md) | Bio-image semantic query and analysis |
+| [DNA Subway](platform/dna-subway.md) | Educational genomics workflows |
+
+# How this documentation is organized
+
+This bundle follows the [Open Knowledge Format](https://github.com/GoogleCloudPlatform/knowledge-catalog/blob/main/okf/SPEC.md)
+v0.2.[^okf-spec] In practice that means three things you can rely on:
+
+* **Every document declares itself.** Frontmatter carries its `type`, a one-line
+  `description`, `tags`, and a `status` of `draft`, `stable`, or `deprecated`. A
+  `draft` document is incomplete and says so rather than pretending otherwise.
+* **Every directory has an index.** `index.md` lists what is in a directory with a
+  line of description each, so you can see what exists before opening anything.
+* **Derived documents cite their sources.** Where a document was written from
+  something else, `sources` in its frontmatter says what, including material
+  mirrored under [references/](references/).
+
+Changes to the bundle are recorded in [the log](log.md).
+
+# Links
+
+* :material-web: [CyVerse website](https://cyverse.org){target=_blank}
+* :material-frequently-asked-questions: [FAQ](operations/faq.md)
+* :simple-github: [GitHub organization](https://github.com/cyverse-de){target=_blank}
+* :material-api: [Live Terrain API](https://de.cyverse.org/terrain/docs/){target=_blank}
+* :simple-docker: [Harbor registry](https://harbor.cyverse.org/){target=_blank}
+* :material-school: [User-facing learning materials](https://learning.cyverse.org/){target=_blank}
+
+# Funding
+
+[![nsf](assets/NSF.svg){width=100}](https://www.nsf.gov/){target=_blank}
+
+CyVerse has been funded by the National Science Foundation from 2008 to the
+present.
+
+[![NSF-0735191](https://img.shields.io/badge/NSF-0735191-blue.svg)](https://www.nsf.gov/awardsearch/showAward?AWD_ID=0735191) [![NSF-1265383](https://img.shields.io/badge/NSF-1265383-blue.svg)](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1265383) [![NSF-1743442](https://img.shields.io/badge/NSF-1743442-blue.svg)](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1743442)
+
+!!! Info ":fontawesome-brands-creative-commons-by: SOFTWARE LICENSE"
+
+    Copyright (c) 2010-2026, The Arizona Board of Regents on behalf of The University of Arizona
+
+    All rights reserved.
+
+    Developed by: CyVerse as a collaboration between participants at BIO5 at The University of Arizona (the primary hosting institution), Cold Spring Harbor Laboratory, The University of Texas at Austin, and individual contributors. Find out more at http://www.cyverse.org/.
+
+    Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+    * Neither the name of CyVerse, BIO5, The University of Arizona, Cold Spring Harbor Laboratory, The University of Texas at Austin, nor the names of other contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+[^okf-spec]: Open Knowledge Format v0.2 specification