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Directory Update Log

2026-10-08

  • Update: Rewrote Formation (formerly formation-mcp) for CyVerse's hosted Formation MCP server at https://de.cyverse.org/formation/mcp: per-client setup (claude.ai and Claude Desktop, Claude Code, Codex, OpenCode, Antigravity), browser sign-in with a CyVerse account, the 12 tools and their limits, and how to move off the local formation-mcp. CyVerse has since removed the REST API that server called (Formation source change of 2026-06-11, first released in Formation v2026.07.07), so it no longer works.
  • Creation: Added claude.ai and Claude Desktop, adding Formation as a custom connector (Free, Pro and Max; Team and Enterprise owners and members), the optional public Data Store connector, using it in chats and in Claude Code.
  • Update: install.sh keeps the permissions of the client configs it rewrites (a new one is created readable by you only) and writes through a symlinked config; leaves an identical Claude Code formation entry alone so a re-run keeps the sign-in; skips formation for Codex older than 0.77; signs Codex and OpenCode out of Formation on --uninstall; and its summary matches --no-go and CODEX_HOME. The pages now note that Codex's --no-browser needs 0.156, Codex's default tool timeout by version, that codex mcp add sets no timeout, that Codex, OpenCode, and Antigravity sign-in to Formation is not yet confirmed by CyVerse, and that OpenCode and Goose cannot sign in inside the MESA apps. The authenticated-install one-liner in Quickstart and Credentials now passes the credentials to bash, not curl.
  • Update: install.sh finds a Claude Code local-scope formation entry under the key Claude uses (the git root, or the physical directory), removes an old Codex formation entry even when Codex is too old for the hosted one, treats a Codex source build (0.0.0) as current, and says per client when formation was not registered. OpenCode, Servers, and README.md carry the same sign-in caveats; Claude Code is the stated fallback where OpenCode and Goose cannot sign in.
  • Update: install.sh now registers formation by URL with every client (Claude Code --transport http, Codex url with tool_timeout_sec = 600, OpenCode remote, Antigravity serverUrl) instead of building formation-mcp, even with --no-go; a re-run replaces the old local entry and deletes ~/.mesa/bin/formation-mcp. New override MESA_FORMATION_URL. Install reference, Quickstart (new "Sign in to Formation" step), Credentials, the four client pages, Troubleshooting, the home page, and README.md match.
  • Update: Claude Code has a new "Hosted servers and connectors" section; its hosted iRODS commands now match the MESA app images (public mcp-public.cyverse.ai, authenticated mcp.cyverse.ai with the mcp-client OAuth client).
  • Update: AI agents in the MESA apps no longer says cyverse-login signs agents in to Formation; it adds a "Sign in to Formation" step for each agent, and the five app pages point to it.
  • Creation: Added the MESA Portal section, end-user guides for https://mesa.cyverse.org: Overview (signing in, navigation, dashboard, themes), Managing data (Data Browser views, upload, move, trash, sharing, AVU metadata, search), Starting applications (catalog sections, filters, Instant Launch, Launch with Options, CPU or GPU builds), and Managing analyses (statuses, Open App, Extend Time, Monitor, Save & Exit, Terminate, results). Adapted from the portal's own user guides, with 21 screenshots in assets/portal/ rendered from the portal's sample data.
  • Creation: Added the Featured apps section with a page for each MESA VICE app — MESA CLI (Cloud Shell), MESA JupyterLab, MESA RStudio Geospatial, MESA VS Code, and MESA KASM Ubuntu Desktop — and AI agents in the MESA apps for the agent CLIs, cyverse-login, AI Verde, and local Ollama models they share.
  • Update: The home page, the site description, and llms.txt now cover the portal and the featured apps alongside the MCP stack; For AI agents points to the new sections.

2026-09-12

  • Update: Made the Markdown easier for agents to find, following DUST 2026. Every rendered page now carries two visible pointers, because text-extracting fetchers and URL allowlists never see <head>: a "View this page as Markdown" button beside Edit and View source, and a "Machine-readable versions" line at the end of the article linking the Markdown twin, the raw GitHub source, llms.txt, and llms-full.txt. The site footer carries the same three links on every page.
  • Update: llms.txt now lists three addresses per page — rendered page, Markdown twin, and raw source on raw.githubusercontent.com — because sandboxed agents often reach github.com when they cannot reach *.github.io, and its Meta section states the corpus size and token estimate. llms-full.txt and the per-page Markdown mirror now rewrite relative links to absolute URLs, so links survive being read away from their source directory.
  • Update: For AI agents documents the raw-source convention, adds an "If you cannot fetch this site" section, and warns that the <head> signals are invisible to most fetch tools. The home page lists the same addresses.
  • Update: The three scripts now share scripts/okf_common.py (config, frontmatter, URL, and link-rewriting helpers, ported from UNM-CARC/dust-2026) and read site_url, repo_url, edit_uri, and nav from zensical.toml instead of hard-coding them.

2026-09-10

  • Update: Migrated the bundle to Open Knowledge Format v0.2. Every content page replaces v0.1's timestamp with generated: { by, at } and gains sources (the MESA repositories and install.sh, and each client vendor's MCP documentation), status, and stale_after. The root index now declares okf_version: "0.2".
  • Creation: Added the About section with For AI agents — how agents should consume this site and why they should call the MESA servers for data — and a Servers section listing.
  • Update: Replaced scripts/agent_markdown.py with the UNM-CARC/neon-mcp agent surface: scripts/okf_validate.py (CI-enforced conformance), scripts/gen_llms_txt.py (committed llms.txt and llms-full.txt grouped by the site nav, CI drift-checked), and scripts/postbuild_agent_surface.py (page URL + index.md Markdown mirror alongside the legacy <path>.md copies, okf:* head metadata, and robots.txt). Added AGENTS.md and CLAUDE.md for coding agents.

2026-07-19

  • Update: Changed the copyright holder to The Regents of the University of New Mexico (site footer, LICENSE, and README).

2026-07-18

  • Update: Generalized MESA from a Claude-Code-only installer to four agent clients — added Codex CLI, Antigravity, and OpenCode integration pages alongside Claude Code, documented the new --for installer flag and client auto-detection, and added per-client tabs to the Quickstart and Install reference.
  • Update: Adopted the Open Knowledge Format v0.1 across docs/ — frontmatter (type, title, description, tags, timestamp) on every content page, plus this update log. index.md intentionally deviates from the reserved-index rule because Zensical requires it as the site homepage.

2026-06-18

  • Update: Defaulted mesa-mcp to main now that the DataCite tools are merged (bba04fd).
  • Creation: Initial MESA umbrella repo — one-liner install.sh plus Zensical docs (27360b8).

Machine-readable versions of this page: Markdown twin · raw source on GitHub · llms.txt · llms-full.txt (whole site). See For AI agents.