# Directory Update Log ## 2026-10-08 * **Update**: Rewrote [Formation](https://idss-mesa.github.io/docs/servers/formation-mcp/) (formerly formation-mcp) for CyVerse's hosted Formation MCP server at : 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](https://idss-mesa.github.io/docs/claude-ai/), 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](https://idss-mesa.github.io/docs/quickstart/) and [Credentials](https://idss-mesa.github.io/docs/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](https://idss-mesa.github.io/docs/opencode/), [Servers](https://idss-mesa.github.io/docs/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](https://idss-mesa.github.io/docs/install/), [Quickstart](https://idss-mesa.github.io/docs/quickstart/) (new "Sign in to Formation" step), [Credentials](https://idss-mesa.github.io/docs/credentials/), the four client pages, [Troubleshooting](https://idss-mesa.github.io/docs/troubleshooting/), the [home page](https://idss-mesa.github.io/docs/), and `README.md` match. * **Update**: [Claude Code](https://idss-mesa.github.io/docs/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](https://idss-mesa.github.io/docs/apps/agents/) 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](https://idss-mesa.github.io/docs/portal/) section, end-user guides for : [Overview](https://idss-mesa.github.io/docs/portal/overview/) (signing in, navigation, dashboard, themes), [Managing data](https://idss-mesa.github.io/docs/portal/data/) (Data Browser views, upload, move, trash, sharing, AVU metadata, search), [Starting applications](https://idss-mesa.github.io/docs/portal/applications/) (catalog sections, filters, Instant Launch, Launch with Options, CPU or GPU builds), and [Managing analyses](https://idss-mesa.github.io/docs/portal/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](https://idss-mesa.github.io/docs/apps/) section with a page for each MESA VICE app — [MESA CLI (Cloud Shell)](https://idss-mesa.github.io/docs/apps/cli/), [MESA JupyterLab](https://idss-mesa.github.io/docs/apps/jupyterlab/), [MESA RStudio Geospatial](https://idss-mesa.github.io/docs/apps/rstudio/), [MESA VS Code](https://idss-mesa.github.io/docs/apps/vscode/), and [MESA KASM Ubuntu Desktop](https://idss-mesa.github.io/docs/apps/kasm/) — and [AI agents in the MESA apps](https://idss-mesa.github.io/docs/apps/agents/) for the agent CLIs, `cyverse-login`, AI Verde, and local Ollama models they share. * **Update**: The [home page](https://idss-mesa.github.io/docs/), the site description, and [llms.txt](https://idss-mesa.github.io/docs/llms.txt) now cover the portal and the featured apps alongside the MCP stack; [For AI agents](https://idss-mesa.github.io/docs/about/ai-agents/) points to the new sections. ## 2026-09-12 * **Update**: Made the Markdown easier for agents to find, following [DUST 2026](https://unm-carc.github.io/dust-2026/about/ai-agents/). Every rendered page now carries two *visible* pointers, because text-extracting fetchers and URL allowlists never see ``: 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](https://idss-mesa.github.io/docs/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](https://idss-mesa.github.io/docs/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](https://idss-mesa.github.io/docs/about/ai-agents/) documents the raw-source convention, adds an "If you cannot fetch this site" section, and warns that the `` signals are invisible to most fetch tools. The [home page](https://idss-mesa.github.io/docs/) 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](https://github.com/GoogleCloudPlatform/knowledge-catalog/blob/main/okf/SPEC.md). 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](https://idss-mesa.github.io/docs/) now declares `okf_version: "0.2"`. * **Creation**: Added the [About](https://idss-mesa.github.io/docs/about/) section with [For AI agents](https://idss-mesa.github.io/docs/about/ai-agents/) — how agents should consume this site and why they should call the MESA servers for data — and a [Servers](https://idss-mesa.github.io/docs/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 `.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](https://idss-mesa.github.io/docs/codex/), [Antigravity](https://idss-mesa.github.io/docs/antigravity/), and [OpenCode](https://idss-mesa.github.io/docs/opencode/) integration pages alongside [Claude Code](https://idss-mesa.github.io/docs/claude-code/), documented the new `--for` installer flag and client auto-detection, and added per-client tabs to the [Quickstart](https://idss-mesa.github.io/docs/quickstart/) and [Install reference](https://idss-mesa.github.io/docs/install/). * **Update**: Adopted the [Open Knowledge Format v0.1](https://github.com/GoogleCloudPlatform/knowledge-catalog) across `docs/` — frontmatter (`type`, `title`, `description`, `tags`, `timestamp`) on every content page, plus this update log. [index.md](https://idss-mesa.github.io/docs/) 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](https://github.com/idss-mesa/docs/commit/bba04fd)). * **Creation**: Initial MESA umbrella repo — one-liner `install.sh` plus Zensical docs ([27360b8](https://github.com/idss-mesa/docs/commit/27360b8)).