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[feature] Add an Agentic AI documentation section (guidance, MCP, shared context) for Gautschi - #275

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[feature] Add an Agentic AI documentation section (guidance, MCP, shared context) for Gautschi#275
glentner wants to merge 30 commits into
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feature/agentic-ai-docs

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Summary

Researchers already run agentic coding tools (Claude Code, Codex, Gemini CLI, opencode, Warp) on and against RCAC clusters, but the docs site had zero public guidance on it — no acceptable-use rules, no setup, no mention of our MCP servers, and no account of the context we inject into agents. This PR builds RCAC's documentation pillar for agentic AI, following the strategy of proactive engagement, not prohibition (verify, don't forbid).

It adds a new top-level Agentic AI section plus a cross-linked Using AI Agents chapter in the Gautschi user guide, and — as a shared construction exercise — authors the first real canonical shared-context and per-harness settings files for Gautschi (the source of truth Puppet copies to /etc/agents.d and the HPC MCP server injects over SSH).

Scope is Gautschi only (other clusters are an explicit follow-up). No MCP-server code, no Puppet pipeline, no theme/CSS/JS changes, no blog post.

Reader-facing outcome: stance + acceptable use + best-practices/limitations; a Running Agents guide organized by deployment mode (on-cluster login nodes vs. local via MCP + SSH) covering all five harnesses; an MCP-servers page (rcac-mcp, globus-mcp, rcac-docs-mcp); and the Gautschi /etc/agents.d context files + per-harness settings published verbatim with a feedback path.

Artifacts

Phases completed

Phase Name Satisfies
P1 Scaffold: section hub + top-level nav anchor R1
P2 Acceptable Use & Etiquette page R2
P3 Best Practices & Limitations page R3
P4 MCP Servers page (rcac-mcp / globus-mcp / rcac-docs-mcp) R7, R8, R9, R16
P5 Running Agents: overview + on-cluster (login nodes) R4, R5
P6 Running Agents: local, targeting the cluster (MCP + SSH) R4, R6
P7 Shared context: hub + the five /etc/agents.d files R10, R12, R16
P8 Per-harness settings & permissions (all five harnesses) R11, R12
P9 Gautschi "Using AI Agents" chapter R13, R16
P10 Integration: hub cards, cross-links, breadcrumbs, a11y + accuracy sweep R14, R15, R16

Verification

Blind adversarial review (fresh context, graded against GOAL.md + invariants, by rendering — see REVIEW.md). Verdict: approved (cycle 1), no CONFIRMED defects.

  • Build integrity (hammerable:false): mkdocs build --strict | strict_check.pyPASS, 0 warnings. All 11 new pages are in mkdocs.yml nav:; snippet --8<-- includes expand verbatim in the built HTML; macros render; content-level a11y (one H1/page, heading descent, table header rows, relative links / absolute assets) verified.
  • Requirements: every R-ID R1–R16 satisfied; all human-review refinements verified (paper cited as a footer note; "mostly harmless" 0×; "Tea, Earl Grey, hot" ×1; Warp rides a live SSH session, not the MCP bridge; cluster-side settings register the hosted docs MCP, never rcac-mcp; Apptainer-not-Docker with the auto-bind-mount caveat).
  • For maintainer eyes (PLAUSIBLE, non-blocking): (1) MCP tool names / uvx install commands couldn't be verified against the private repos from the review sandbox — a maintainer with repo access should confirm; (2) filesystem-technology labels (/home ZFS, /depot GPFS, /scratch Lustre) match the human-corrected facts in GOAL.md but aren't stated on the gold-standard storage page.
  • Post-rebase: branch was reintegrated onto the current origin/main (after PR [harness] Add the RCAC-Docs documentation factory (spec-driven authoring lifecycle) #273 merged) with zero conflicts; the --strict gate was re-verified and strict-baseline.txt trimmed to empty (origin's 4f3e3574 fixed all 7 prior warnings). Details in REVIEW.md → "Post-rebase integration".

Note — this branch also carries in-feature [harness] commits. Alongside the content, it includes documentation-factory self-improvement commits (.agents/**, AGENTS.md) developed during this job. They do not touch the published site. See the merge-method note in the PR discussion.

🔧 Harness feedback — 1 open finding (route later via /docs-harness)
  • F1 · low · docs-review's scope/branch-hygiene check is optional, so bundled non-content commits nearly slipped past review (target: .agents/skills/docs-review/SKILL.md).

Full detail in spec/agentic-ai-docs/META.md. Do not resolve here.

🤖 Generated with Claude Code

glentner added 28 commits July 15, 2026 14:54
Human review of the rendered section (pre /docs-review) requested four changes;
applied across the drafted pages and recorded in GOAL/PLAN/TECH:

1. Paper as a measured footer reference (GitHub replication package) on the hub,
   not the lead; DOI deferred until on the ACM DL.
2. Measured, professional tone: removed "mostly harmless" and pop-culture framing
   throughout; kept the single load-bearing "Tea, Earl Grey, hot" prompting example.
3. Distinguished the cluster MCP (rcac-mcp: background SSH bridge, pure tool-calling,
   for the CLI harnesses) from Warp (desktop terminal; user SSHs in and the agent
   rides the live session; does not use the cluster MCP; wire in /etc/agents.d once
   SSH'd). Neutralized the "MCP + SSH" umbrella label to "over SSH".
4. Framed per-harness settings as RCAC-deployed to system-managed paths and enforced
   (transparency), not user-installed; honest caveats for Codex (no managed path) and
   Warp (no settings file -> inline team-managed Agent Profile). Deleted the
   misleading warp/AGENTS.md snippet.

Verified via adversarial multi-lens review + --strict build (clean), HPC accuracy
preserved (a10/-A standby only in prohibitions), breadcrumbs regenerated.
…ot rcac-mcp

Follow-up to the human-review pass. The published per-harness settings are
cluster-side (for an agent running on the Gautschi nodes), so registering the
local-side rcac-mcp SSH bridge there was wrong: it needs uvx (not on the nodes'
PATH) and is pointless for an agent that already has direct shell/Slurm access.

- codex/gemini/opencode cluster-side configs now register the hosted, no-auth
  documentation MCP (https://docs.rcac.purdue.edu/mcp, doc_search/doc_load) over
  plain HTTP using each harness's remote-HTTP schema (httpUrl / url / type:remote);
  the rcac-mcp (uvx + --ssh-host) entries were removed.
- settings.md now states the cluster-side vs local-side split explicitly, adds the
  Claude .mcp.json HTTP docs server, and points local rcac-mcp users to the Local
  page. rcac-mcp remains the local-side registration on running_agents/local.md.
- GOAL/PLAN/TECH updated to record the refinement.
@glentner glentner added the harness-feedback PR carries open documentation-factory (.agents/) self-improvement findings label Jul 15, 2026
Comment thread mkdocs.yml
- File Storage and Transfer: userguides/gautschi/storage.md
- Gateway (Open OnDemand): userguides/gautschi/gateway.md
- Compiling Source Code: userguides/gautschi/compile.md
- Using AI Agents: userguides/gautschi/using_ai_agents.md

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We need this entry on index page of Gautschi as well.

@Guangzhen-Jin

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  1. Can you add your name in authors field for all md files under agentic-ai? Some of them are missing.
  2. Some files under agentic-ai are using {% set resource = "gautschi" %}. Is it because only Gautschi has the tools? If not, can we have a note there mentioning something like "we are using Gautschi as an example" to avoid confusion from other cluster users?

@glentner

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Ah, on (1) yes.

On (2) that's a great question and I'm not sure how to handle this. I'm starting with Gautschi for now. All of this is (will be) true of Gautschi. Other clusters will have slightly different context files but most of the content is the same.

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