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

[tyson-swetnam]

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