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Documentation update log

2026-09-11

  • Fix: The interactive apps overview now matches Data Store in interactive apps: the CSI driver mounts the Data Store at /data-store (~/data-store is a link to it), your home folder is /data-store/iplant/home/<username>, and Git work belongs on the container's local disk rather than the mount.
  • Creation: Migrated the CyVerse Learning Center user guide (CyVerse-learning-materials/learning-materials-home, commit b7392d2) from MkDocs Material to Zensical, structured as an Open Knowledge Format (OKF) v0.2 bundle and styled after the CARC documentation. Every adapted page carries generated and sources frontmatter (with the upstream file's last git modification) and a provenance footer; all adapted pages are unverified pending review.
  • Creation: Reorganized the tree into kebab-case sections: Getting started (from home/), Data Store (from ds/, with Discovery Environment, GoCommands, iCommands, SFTP, and WebDAV subsections), Discovery Environment (from de/, with the VICE interactive apps subsection), Cloud, AI (now including the three MCP server configuration pages), Education (from edu/), and Developers (from dev/). Section index.md files that held content moved to sibling overview.md (or descriptively named) pages, and every section gained an OKF §8 listing. The metadata, DOI, data-usage, and Teams pages that the old navigation listed twice now live only under Data Store › Discovery Environment; the Discovery Environment listing links to them. MIGRATION.md in the repository maps every old URL to its new one.
  • Creation: Wrote the landing page, section listings, Credits, Contributing, and For AI agents pages, and gave the previously empty CACAO page real content based on the CyVerse developer documentation. Rewrote Getting help around current CyVerse support channels (the Intercom chat widget it described is gone) and added the previously unlisted Self-guided course page to the navigation.
  • Update: Added "Under the hood" notes linking to the CyVerse Developer Documentation on the Data Store, access-method, Discovery Environment, VICE, app-integration, DOI, sharing, metadata, account, subscription, and cloud pages, plus UNM CARC tips on GoCommands data transfer and HPC apps. Corrected outdated details against those docs: Jetstream2 access now goes through ACCESS-CI (not XSEDE), Atmosphere is marked deprecated, stale docs.cyverse.org/services/... links point at the current developer-doc pages, the subscription portal is subscribe.cyverse.org, and the retired CyVerse wiki link on Create apps points at its Confluence successor.
  • Update: Normalized admonitions to lowercase standard types and fixed over-indented admonition bodies (notably throughout DNA Subway, where they rendered as code blocks); converted 31 leftover reStructuredText guilabel roles in DNA Subway to bold UI labels (plus a stray title-ref), added missing blank lines that kept eight DNA Subway admonitions from rendering, and its three YouTube embeds, plus the DataHog video on Checking your data storage quotas, to privacy-enhanced responsive players; fixed every relative link the migration could not resolve, empty links, {target_blank} typos, and reStructuredText remnants in the glossary; converted self-links to learning.cyverse.org into relative links; and made page H1s match their titles (demoting DataWatch's extra H1s).
  • Deletion: Dropped the outdated FAQ (dozens of links into the retired CyVerse wiki, Atmosphere- and Condor-era answers, and Intercom chat references), the legacy BisQue page, the unpublished ds/old/ drafts, the chatbot widget and its assets, the Intercom script, MkDocs theme overrides, the CNAME file, the MkDocs configuration and requirements, the tracked .cache/, other_docs/, and drafts/ folders, and images no page referenced. All originals remain in the CyVerse repository at commit b7392d2.