Follow the upstream skills/ vs dev-skills/ split

.agents/plugins/marketplace.json

@@ -28,6 +28,18 @@
       },
       "category": "Developer Tools"
     },
+    {
+      "name": "galaxy-dev-skills",
+      "source": {
+        "source": "local",
+        "path": "./plugins/galaxy-dev-skills"
+      },
+      "policy": {
+        "installation": "AVAILABLE",
+        "authentication": "ON_INSTALL"
+      },
+      "category": "Developer Tools"
+    },
     {
       "name": "foundry-skills",
       "source": {

.claude-plugin/marketplace.json

@@ -22,13 +22,27 @@
     {
       "name": "galaxy-skills",
       "source": "./plugins/galaxy-skills",
-      "description": "Curated Galaxy skills (tool development, Nextflow conversion, collections, hub posts, ...) mirrored from galaxyproject/galaxy-skills.",
+      "description": "Curated Galaxy skills for running analyses -- connection, MCP tool surface, collections, user-defined tools, reports, reproducibility. Mirrors the skills/ tree of galaxyproject/galaxy-skills.",
       "version": "2026.9.16",
       "category": "development",
       "keywords": [
         "galaxy",
         "bioinformatics",
-        "skills"
+        "skills",
+        "analysis"
+      ]
+    },
+    {
+      "name": "galaxy-dev-skills",
+      "source": "./plugins/galaxy-dev-skills",
+      "description": "Galaxy development skills -- tool wrappers, Nextflow conversion, ToolShed revisions, track hubs, Hub posts. Mirrors the dev-skills/ tree of galaxyproject/galaxy-skills.",
+      "version": "2026.9.16",
+      "category": "development",
+      "keywords": [
+        "galaxy",
+        "bioinformatics",
+        "skills",
+        "tool-development"
       ]
     },
     {

.cursor-plugin/marketplace.json

@@ -23,7 +23,7 @@
     {
       "name": "galaxy-skills",
       "source": "plugins/galaxy-skills",
-      "description": "Curated Galaxy developer skills mirrored from galaxyproject/galaxy-skills.",
+      "description": "Curated Galaxy skills for running analyses -- connection, MCP tool surface, collections, user-defined tools, reports, reproducibility. Mirrors the skills/ tree of galaxyproject/galaxy-skills.",
       "version": "2026.9.16",
       "category": "Developer Tools",
       "keywords": [
@@ -33,6 +33,20 @@
       ],
       "logo": "assets/logo.svg"
     },
+    {
+      "name": "galaxy-dev-skills",
+      "source": "plugins/galaxy-dev-skills",
+      "description": "Galaxy development skills -- tool wrappers, Nextflow conversion, ToolShed revisions, track hubs, Hub posts. Mirrors the dev-skills/ tree of galaxyproject/galaxy-skills.",
+      "version": "2026.9.16",
+      "category": "Developer Tools",
+      "keywords": [
+        "galaxy",
+        "bioinformatics",
+        "skills",
+        "tool-development"
+      ],
+      "logo": "assets/logo.svg"
+    },
     {
       "name": "foundry-skills",
       "source": "plugins/foundry-skills",

.github/ci-tools/check-pi-skills.mjs

@@ -23,7 +23,7 @@ for (const dir of pkg.pi.skills) {
   }
 }
 console.log(`${seen.size} skills loaded by Pi from ${pkg.pi.skills.length} roots`);
-for (const must of ["galaxy-connect", "tool-dev", "nf-process-to-galaxy-tool", "jupyterlite-galaxy", "discover-shed-tool"]) {
+for (const must of ["galaxy-connect", "collection-manipulation", "udt-authoring", "tool-dev", "nf-process-to-galaxy-tool", "jupyterlite-galaxy", "discover-shed-tool"]) {
   if (!seen.has(must)) { console.log(`MISSING expected skill ${must}`); problems++; }
 }
 if (seen.size < MIN_SKILLS) { console.log(`too few skills (${seen.size} < ${MIN_SKILLS})`); problems++; }

.github/workflows/validate.yml

@@ -49,21 +49,18 @@ jobs:
         with:
           python-version: "3.12"
       - run: npm install -g @openai/codex && codex --version
-      - name: Codex plugin-creator validator (galaxy-mcp, foundry-skills)
+      - name: Codex plugin-creator validator (all plugins)
         run: |
           pip install pyyaml
           base=https://raw.githubusercontent.com/openai/codex/main/codex-rs/skills/src/assets/samples/plugin-creator/scripts
           mkdir -p /tmp/codex-validator
           for f in validate_plugin.py identifier_validation.py; do curl -fsSL -o /tmp/codex-validator/$f "$base/$f"; done
-          python3 /tmp/codex-validator/validate_plugin.py plugins/galaxy-mcp
-          python3 /tmp/codex-validator/validate_plugin.py plugins/foundry-skills
-          # galaxy-skills fails only on an upstream frontmatter bug (galaxyproject/galaxy-skills#36); report, don't fail
-          python3 /tmp/codex-validator/validate_plugin.py plugins/galaxy-skills || echo "::warning::galaxy-skills: Codex validator reports upstream frontmatter issue"
+          for p in plugins/*/; do python3 /tmp/codex-validator/validate_plugin.py "$p"; done
       - name: Install from this checkout as a local marketplace
         run: |
           mkdir -p "$CODEX_HOME"
           codex plugin marketplace add "$GITHUB_WORKSPACE"
-          for p in galaxy-mcp galaxy-skills foundry-skills; do codex plugin add "$p@galaxyproject"; done
+          for p in galaxy-mcp galaxy-skills galaxy-dev-skills foundry-skills; do codex plugin add "$p@galaxyproject"; done
       - name: MCP server registered with forwarded env
         run: |
           codex mcp list | tee /tmp/mcp.txt
@@ -72,10 +69,10 @@ jobs:
         run: |
           git init -q /tmp/ws && cd /tmp/ws
           codex debug prompt-input "hello" > /tmp/prompt.json
-          n=$(grep -oE '(galaxy-skills|foundry-skills|galaxy-mcp):[a-z0-9-]+' /tmp/prompt.json | sort -u | wc -l)
+          n=$(grep -oE '(galaxy-skills|galaxy-dev-skills|foundry-skills|galaxy-mcp):[a-z0-9-]+' /tmp/prompt.json | sort -u | wc -l)
           echo "skills in prompt: $n"
           test "$n" -ge 70
-          for s in galaxy-mcp:galaxy-connect galaxy-skills:tool-dev galaxy-skills:nf-process-to-galaxy-tool foundry-skills:discover-shed-tool; do
+          for s in galaxy-mcp:galaxy-connect galaxy-skills:udt-authoring galaxy-skills:collection-manipulation galaxy-dev-skills:tool-dev galaxy-dev-skills:nf-process-to-galaxy-tool foundry-skills:discover-shed-tool; do
             grep -q "$s" /tmp/prompt.json || { echo "missing $s"; exit 1; }
           done
 

README.md

@@ -5,9 +5,11 @@ Plugins and setup guides that connect AI coding agents to
 
 1. **A Galaxy connection** through the [galaxy-mcp](https://github.com/galaxyproject/galaxy-mcp)
    MCP server, authenticated with your Galaxy API key.
-2. **Curated Galaxy skills** from [galaxyproject/galaxy-skills](https://github.com/galaxyproject/galaxy-skills)
-   (tool development, user-defined tools, Nextflow conversion, collections,
-   workflow reports, track hubs, hub posts, MCP usage).
+2. **Curated Galaxy skills** from [galaxyproject/galaxy-skills](https://github.com/galaxyproject/galaxy-skills),
+   split the way upstream splits them: skills for *using* Galaxy (MCP tool
+   surface, collections, user-defined tools, workflow reports,
+   reproducibility) and, separately, skills for *building* it (tool wrappers,
+   Nextflow conversion, ToolShed revisions, track hubs, hub posts).
 3. **Galaxy Workflow Foundry skills** from [galaxyproject/foundry](https://github.com/galaxyproject/foundry)
    (papers, Nextflow and CWL to validated Galaxy workflows).
 
@@ -26,7 +28,7 @@ Every guide starts with [getting a Galaxy API key](docs/galaxy-api-key.md).
 
 ## What is in the box
 
-Three plugins live under `plugins/`. Each directory is simultaneously a Claude
+Four plugins live under `plugins/`. Each directory is simultaneously a Claude
 Code plugin (`.claude-plugin/plugin.json`), a Codex plugin
 (`.codex-plugin/plugin.json`), a Cursor plugin (`.cursor-plugin/plugin.json`)
 and an Antigravity plugin (`plugin.json`); the root `package.json` exposes the
@@ -36,12 +38,14 @@ one-click installer for Claude Desktop (MCP server only).
 | Plugin | Contents | Origin |
 |--------|----------|--------|
 | `galaxy-mcp` | MCP server config for `uvx galaxy-mcp` (`mcp/claude.json`, `mcp/pi.json`, `mcp.json` for Cursor, `mcp_config.json` for Antigravity, inline in the Codex manifest) and the `galaxy-connect` skill: set up, verify and troubleshoot the connection | this repo |
-| `galaxy-skills` | 16 skills: `tool-dev`, `udt-authoring`, `nf-to-galaxy` (+3 sub-skills), `collection-manipulation`, `galaxy-integration` (+2 sub-skills), `reproduciblify`, `workflow-reports`, `trackhubs`, `update-usegalaxy-tool`, `hub-news-posts`, `tool-selection-diagram` | mirror of galaxyproject/galaxy-skills |
+| `galaxy-skills` | 7 skills for *using* Galaxy: `galaxy-integration` (+`jupyterlite`), `galaxy-mcp-reference`, `collection-manipulation`, `udt-authoring`, `workflow-reports`, `reproduciblify` | mirror of galaxyproject/galaxy-skills `skills/` |
+| `galaxy-dev-skills` | 9 skills for *building* Galaxy: `tool-dev` (+`tool-selection-diagram`), `nf-to-galaxy` (+3 sub-skills), `update-usegalaxy-tool`, `trackhubs`, `hub-news-posts` | mirror of galaxyproject/galaxy-skills `dev-skills/` |
 | `foundry-skills` | 59 cast skills, e.g. `pipeline-nextflow-to-galaxy`, `discover-shed-tool`, `validate-galaxy-workflow`, `author-galaxy-tool-wrapper` | mirror of galaxyproject/foundry `casts/claude/skills` |
 
-Install only the plugins you need. The two skill plugins add many skill
-descriptions to the agent's context; `foundry-skills` in particular is only
-worth it if you build Galaxy workflows.
+Install only the plugins you need. Every skill plugin adds its descriptions to
+the agent's context on every session: `galaxy-skills` is the one an analyst
+wants, `galaxy-dev-skills` is for people who write tool wrappers, and
+`foundry-skills` is only worth it if you build Galaxy workflows.
 
 ### How credentials reach the MCP server
 
@@ -67,7 +71,8 @@ is why the plugin ships one MCP file per harness:
 package.json                      Pi package manifest (pi.skills, pi.mcp)
 plugins/
   galaxy-mcp/                     MCP config + galaxy-connect skill (hand-written)
-  galaxy-skills/                  vendored copy of galaxyproject/galaxy-skills
+  galaxy-skills/                  vendored copy of galaxy-skills skills/ (using Galaxy)
+  galaxy-dev-skills/              vendored copy of galaxy-skills dev-skills/ (building Galaxy)
   foundry-skills/                 vendored copy of galaxyproject/foundry casts/claude/skills
 bundles/claude-desktop/           Claude Desktop .mcpb source (uv runtime, no bundled code)
 docs/                             per-harness guides (source for the Galaxy Hub pages)
@@ -92,7 +97,9 @@ them is documented to follow git submodules (Pi runs a plain `git clone`),
 Claude Code discovers plugin skills only one level deep, Pi stops recursing at a skill root, and Pi can
 only install packages that carry a manifest. Vendoring a plain copy is the one
 layout that works everywhere; `scripts/gen-manifests.py` lists nested skills
-explicitly where a harness needs it. The Antigravity `plugin.json` at each
+explicitly where a harness needs it. Each upstream tree is vendored into its own
+plugin rather than copying the repo root, which keeps upstream's using-vs-building
+split intact instead of registering both trees as one bundle. The Antigravity `plugin.json` at each
 plugin root must never carry an agent-plugins.org `$schema`: Codex and Cursor
 would then read it as an Agent Plugins manifest instead of their own
 (`validate.py` enforces this). The pinned upstream commit is recorded in

docs/antigravity.md

@@ -65,9 +65,9 @@ diagnosing the connection.
 ## Use the skills
 
 Run `/skills` to list them, or type `/` followed by the skill name, for example
-`/tool-dev`, `/udt-authoring`, `/nf-to-galaxy`, `/galaxy-transform-collection`,
-`/galaxy-integration`, `/reproduciblify`, `/pipeline-nextflow-to-galaxy`,
-`/discover-shed-tool`. The agent also picks skills up on its own from your
+`/galaxy-integration`, `/galaxy-mcp-reference`, `/collection-manipulation`,
+`/udt-authoring`, `/reproduciblify`, `/tool-dev`, `/nf-to-galaxy`,
+`/pipeline-nextflow-to-galaxy`, `/discover-shed-tool`. The agent also picks skills up on its own from your
 request.
 
 Antigravity lists only top-level skills. The `nf-to-galaxy` and

docs/claude-code.md

@@ -58,16 +58,17 @@ Type `/` to see them. Plugin skills are namespaced, for example:
 | Invocation | What it does |
 |------------|--------------|
 | `/galaxy-mcp:galaxy-connect` | Set up / verify / troubleshoot the Galaxy connection |
-| `/galaxy-skills:tool-dev` | Create, test and update Galaxy tool wrappers |
-| `/galaxy-skills:udt-authoring` | Author user-defined tools (`GalaxyUserTool` YAML) |
-| `/galaxy-skills:nf-to-galaxy` | Convert Nextflow processes and workflows |
+| `/galaxy-skills:galaxy-integration` | Connect to an instance and choose how to drive it |
+| `/galaxy-skills:galaxy-mcp-reference` | The Galaxy MCP tool surface and its pitfalls |
 | `/galaxy-skills:collection-manipulation` | Filter, sort and restructure dataset collections |
-| `/galaxy-skills:galaxy-integration` | Use the Galaxy MCP tools, JupyterLite and BioBlend well |
-| `/galaxy-skills:reproduciblify` | Rebuild a messy history as a clean, extractable analysis |
+| `/galaxy-skills:udt-authoring` | Author user-defined tools (`GalaxyUserTool` YAML) |
 | `/galaxy-skills:workflow-reports` | Draft workflow report templates |
-| `/galaxy-skills:trackhubs` | Publish UCSC track hubs and assembly hubs |
-| `/galaxy-skills:update-usegalaxy-tool` | Add or bump ToolShed revisions in usegalaxy-tools |
-| `/galaxy-skills:hub-news-posts` | Write Galaxy Hub news posts |
+| `/galaxy-skills:reproduciblify` | Rebuild a messy history as a clean, extractable analysis |
+| `/galaxy-dev-skills:tool-dev` | Create, test and update Galaxy tool wrappers |
+| `/galaxy-dev-skills:nf-to-galaxy` | Convert Nextflow processes and workflows |
+| `/galaxy-dev-skills:update-usegalaxy-tool` | Add or bump ToolShed revisions in usegalaxy-tools |
+| `/galaxy-dev-skills:trackhubs` | Publish UCSC track hubs and assembly hubs |
+| `/galaxy-dev-skills:hub-news-posts` | Write Galaxy Hub news posts |
 | `/foundry-skills:pipeline-nextflow-to-galaxy` | End-to-end Nextflow to Galaxy workflow conversion |
 | `/foundry-skills:discover-shed-tool` | Find and pin a Tool Shed wrapper |
 

docs/codex.md

@@ -56,11 +56,10 @@ have Codex diagnose the connection.
 
 ## Use the skills
 
-Type `$` or run `/skills` to pick a skill, for example `$tool-dev`,
-`$udt-authoring`, `$nf-to-galaxy`, `$collection-manipulation`,
-`$galaxy-integration`, `$reproduciblify`, `$pipeline-nextflow-to-galaxy`,
-`$discover-shed-tool`. Codex also selects skills implicitly from their
-descriptions.
+Type `$` or run `/skills` to pick a skill, for example `$galaxy-integration`,
+`$galaxy-mcp-reference`, `$collection-manipulation`, `$udt-authoring`,
+`$reproduciblify`, and, if you installed `galaxy-dev-skills`, `$tool-dev` and
+`$nf-to-galaxy`. Codex also selects skills implicitly from their descriptions.
 
 Codex scans plugin skill directories recursively, so the sub-skills nested
 under `nf-to-galaxy` and `galaxy-integration` (for example

docs/cursor.md

@@ -81,10 +81,10 @@ the agent through diagnosing the connection.
 
 ## Use the skills
 
-Type `/` in Agent chat and pick a skill, for example `/tool-dev`,
-`/udt-authoring`, `/nf-to-galaxy`, `/galaxy-transform-collection`,
-`/galaxy-integration`, `/reproduciblify`, `/pipeline-nextflow-to-galaxy`,
-`/discover-shed-tool`. The agent also applies skills on its own when a request
+Type `/` in Agent chat and pick a skill, for example `/galaxy-integration`,
+`/galaxy-mcp-reference`, `/collection-manipulation`, `/udt-authoring`,
+`/reproduciblify`, `/tool-dev`, `/nf-to-galaxy`,
+`/pipeline-nextflow-to-galaxy`, `/discover-shed-tool`. The agent also applies skills on its own when a request
 matches a description. Installed skills are listed under **Customize > Skills**.
 
 ## Skills without the plugins

docs/pi.md

@@ -60,9 +60,10 @@ through diagnosing the connection.
 
 ## Use the skills
 
-Skills register as `/skill:<name>` commands, for example `/skill:tool-dev`,
-`/skill:udt-authoring`, `/skill:nf-to-galaxy`, `/skill:collection-manipulation`,
-`/skill:galaxy-integration`, `/skill:reproduciblify`,
+Skills register as `/skill:<name>` commands, for example
+`/skill:galaxy-integration`, `/skill:galaxy-mcp-reference`,
+`/skill:collection-manipulation`, `/skill:udt-authoring`,
+`/skill:reproduciblify`, `/skill:tool-dev`, `/skill:nf-to-galaxy`,
 `/skill:pipeline-nextflow-to-galaxy`, `/skill:discover-shed-tool`. The agent
 also loads skills on its own when a request matches a description.
 

package.json

@@ -20,11 +20,11 @@
       "./plugins/galaxy-mcp/skills",
       "./plugins/galaxy-skills/skills",
       "./plugins/galaxy-skills/skills/galaxy-integration/jupyterlite",
-      "./plugins/galaxy-skills/skills/galaxy-integration/mcp-reference",
-      "./plugins/galaxy-skills/skills/nf-to-galaxy/nf-pipeline-to-galaxy-workflow",
-      "./plugins/galaxy-skills/skills/nf-to-galaxy/nf-process-to-galaxy-tool",
-      "./plugins/galaxy-skills/skills/nf-to-galaxy/nf-subworkflow-to-galaxy-workflow",
-      "./plugins/galaxy-skills/skills/tool-dev/tool-selection-diagram",
+      "./plugins/galaxy-dev-skills/skills",
+      "./plugins/galaxy-dev-skills/skills/nf-to-galaxy/nf-pipeline-to-galaxy-workflow",
+      "./plugins/galaxy-dev-skills/skills/nf-to-galaxy/nf-process-to-galaxy-tool",
+      "./plugins/galaxy-dev-skills/skills/nf-to-galaxy/nf-subworkflow-to-galaxy-workflow",
+      "./plugins/galaxy-dev-skills/skills/tool-dev/tool-selection-diagram",
       "./plugins/foundry-skills/skills"
     ],
     "mcp": "./plugins/galaxy-mcp/mcp/pi.json"

plugins/galaxy-dev-skills/.claude-plugin/plugin.json

@@ -0,0 +1,25 @@
+{
+  "name": "galaxy-dev-skills",
+  "version": "2026.9.16",
+  "description": "Galaxy development skills: tool XML wrappers, Nextflow-to-Galaxy conversion, ToolShed revisions in usegalaxy-tools, UCSC track hubs and Galaxy Hub news posts. Mirror of galaxyproject/galaxy-skills (dev-skills/).",
+  "author": {
+    "name": "The Galaxy Project",
+    "url": "https://galaxyproject.org"
+  },
+  "homepage": "https://github.com/galaxyproject/galaxy-skills",
+  "repository": "https://github.com/galaxyproject/agentic-plugins",
+  "license": "MIT",
+  "keywords": [
+    "galaxy",
+    "bioinformatics",
+    "skills",
+    "tool-development",
+    "nextflow"
+  ],
+  "skills": [
+    "./skills/nf-to-galaxy/nf-pipeline-to-galaxy-workflow",
+    "./skills/nf-to-galaxy/nf-process-to-galaxy-tool",
+    "./skills/nf-to-galaxy/nf-subworkflow-to-galaxy-workflow",
+    "./skills/tool-dev/tool-selection-diagram"
+  ]
+}

plugins/galaxy-dev-skills/.codex-plugin/plugin.json

@@ -0,0 +1,37 @@
+{
+  "name": "galaxy-dev-skills",
+  "version": "2026.9.16",
+  "description": "Galaxy development skills: tool XML wrappers, Nextflow-to-Galaxy conversion, ToolShed revisions in usegalaxy-tools, UCSC track hubs and Galaxy Hub news posts. Mirror of galaxyproject/galaxy-skills (dev-skills/).",
+  "author": {
+    "name": "The Galaxy Project",
+    "url": "https://galaxyproject.org"
+  },
+  "homepage": "https://github.com/galaxyproject/galaxy-skills",
+  "repository": "https://github.com/galaxyproject/agentic-plugins",
+  "license": "MIT",
+  "keywords": [
+    "galaxy",
+    "bioinformatics",
+    "skills",
+    "tool-development",
+    "nextflow"
+  ],
+  "skills": "./skills/",
+  "interface": {
+    "displayName": "Galaxy Dev Skills",
+    "shortDescription": "Skills for building Galaxy tools and workflows",
+    "longDescription": "Skills for the work that produces Galaxy itself rather than an analysis: writing and testing tool XML wrappers, converting Nextflow processes and pipelines, adding ToolShed revisions to usegalaxy-tools, publishing UCSC track hubs and writing Galaxy Hub news posts. Mirrored from galaxyproject/galaxy-skills.",
+    "developerName": "The Galaxy Project",
+    "category": "Developer Tools",
+    "capabilities": [
+      "Read",
+      "Write"
+    ],
+    "websiteURL": "https://galaxyproject.org/",
+    "defaultPrompt": [
+      "Update the ncbi-datasets Galaxy tool to the latest version.",
+      "Convert this Nextflow process to a Galaxy tool.",
+      "Add a ToolShed revision for this tool to usegalaxy-tools."
+    ]
+  }
+}