Add marketplace plugin structure and bump to 0.3.0-beta.7

ammawla · ammawla · commit 4cbf4de4166d · 2026-03-11T15:32:57.000-07:00
- Add plugin/ subdirectory with .claude-plugin/plugin.json, .mcp.json,
  and symlinks to skills/ and CLAUDE.md for marketplace installation
- Update marketplace.json to point source to ./plugin
- Clear root .mcp.json (MCP config lives in plugin/.mcp.json)
- Bump version to 0.3.0-beta.7 across all manifests
diff --git a/.claude-plugin/marketplace.json b/.claude-plugin/marketplace.json
@@ -3,10 +3,15 @@
   "owner": {
     "name": "Dr. Alex M. Mawla, PhD"
   },
+  "metadata": {
+    "description": "ENCODE Project genomics research infrastructure for Claude Code",
+    "homepage": "https://github.com/ammawla/encode-toolkit"
+  },
   "plugins": [
     {
       "name": "encode-toolkit",
-      "source": ".",
+      "version": "0.3.0",
+      "source": "./plugin",
       "description": "20 ENCODE API tools + 48 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases."
     }
   ]
diff --git a/.claude-plugin/plugin.json b/.claude-plugin/plugin.json
@@ -1,7 +1,7 @@
 {
   "name": "encode-toolkit",
   "description": "20 ENCODE API tools + 48 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.",
-  "version": "0.3.0-beta.6",
+  "version": "0.3.0-beta.7",
   "author": {
     "name": "Dr. Alex M. Mawla, PhD",
     "email": "ammawla@ucdavis.edu"
diff --git a/.gitignore b/.gitignore
@@ -66,3 +66,4 @@ package-lock.json
 # OS
 .DS_Store
 Thumbs.db
+buildwithclaude/
diff --git a/.mcp.json b/.mcp.json
@@ -1,8 +1,3 @@
 {
-  "mcpServers": {
-    "encode": {
-      "command": "encode-toolkit",
-      "args": []
-    }
-  }
+  "mcpServers": {}
 }
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "encode-toolkit",
-  "version": "0.3.0-beta.6",
+  "version": "0.3.0-beta.7",
   "mcpName": "io.github.ammawla/encode-toolkit",
   "description": "ENCODE Toolkit — Genomics research infrastructure with 20 MCP tools, 47 skills, 14 database integrations, and 7 pipelines for Claude Code",
   "main": "index.js",
diff --git a/plugin/.claude-plugin/plugin.json b/plugin/.claude-plugin/plugin.json
@@ -0,0 +1,22 @@
+{
+  "name": "encode-toolkit",
+  "version": "0.3.0",
+  "description": "20 ENCODE API tools + 48 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.",
+  "author": {
+    "name": "Dr. Alex M. Mawla, PhD",
+    "url": "https://github.com/ammawla/encode-toolkit"
+  },
+  "repository": "https://github.com/ammawla/encode-toolkit",
+  "license": "CC-BY-NC-ND-4.0",
+  "keywords": [
+    "genomics",
+    "encode",
+    "bioinformatics",
+    "epigenomics",
+    "chip-seq",
+    "atac-seq",
+    "rna-seq",
+    "pipelines",
+    "science"
+  ]
+}
diff --git a/plugin/.mcp.json b/plugin/.mcp.json
@@ -0,0 +1,9 @@
+{
+  "mcpServers": {
+    "encode-toolkit": {
+      "type": "stdio",
+      "command": "npx",
+      "args": ["-y", "encode-toolkit@latest"]
+    }
+  }
+}
diff --git a/plugin/CLAUDE.md b/plugin/CLAUDE.md
@@ -0,0 +1 @@
+../CLAUDE.md
diff --git a/plugin/skills b/plugin/skills
@@ -0,0 +1 @@
+../skills
diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "encode-toolkit"
-version = "0.3.0b6"
+version = "0.3.0b7"
 description = "MCP server for querying and downloading ENCODE Project genomics data directly from Claude"
 readme = "README.md"
 license = "CC-BY-NC-ND-4.0"
diff --git a/server.json b/server.json
@@ -7,20 +7,20 @@
     "url": "https://github.com/ammawla/encode-toolkit",
     "source": "github"
   },
-  "version": "0.3.0-beta.6",
+  "version": "0.3.0-beta.7",
   "packages": [
     {
       "registryType": "npm",
       "identifier": "encode-toolkit",
-      "version": "0.3.0-beta.6",
+      "version": "0.3.0-beta.7",
       "transport": {
         "type": "stdio"
       }
     },
     {
       "registryType": "pypi",
       "identifier": "encode-toolkit",
-      "version": "0.3.0b6",
+      "version": "0.3.0b7",
       "transport": {
         "type": "stdio"
       }

Original file line number	Diff line number	Diff line change
`@@ -3,10 +3,15 @@`
`3`	`3`	`"owner": {`
`4`	`4`	`"name": "Dr. Alex M. Mawla, PhD"`
`5`	`5`	`},`
	`6`	`+ "metadata": {`
	`7`	`+ "description": "ENCODE Project genomics research infrastructure for Claude Code",`
	`8`	`+ "homepage": "https://github.com/ammawla/encode-toolkit"`
	`9`	`+ },`
`6`	`10`	`"plugins": [`
`7`	`11`	`{`
`8`	`12`	`"name": "encode-toolkit",`
`9`		`- "source": ".",`
	`13`	`+ "version": "0.3.0",`
	`14`	`+ "source": "./plugin",`
`10`	`15`	`"description": "20 ENCODE API tools + 48 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases."`
`11`	`16`	`}`
`12`	`17`	`]`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "encode-toolkit",`
`3`	`3`	`"description": "20 ENCODE API tools + 48 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.",`
`4`		`- "version": "0.3.0-beta.6",`
	`4`	`+ "version": "0.3.0-beta.7",`
`5`	`5`	`"author": {`
`6`	`6`	`"name": "Dr. Alex M. Mawla, PhD",`
`7`	`7`	`"email": "ammawla@ucdavis.edu"`
Original file line number	Diff line number	Diff line change
`@@ -1,8 +1,3 @@`
`1`	`1`	`{`
`2`		`- "mcpServers": {`
`3`		`- "encode": {`
`4`		`- "command": "encode-toolkit",`
`5`		`- "args": []`
`6`		`- }`
`7`		`- }`
	`2`	`+ "mcpServers": {}`
`8`	`3`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "encode-toolkit",`
`3`		`- "version": "0.3.0-beta.6",`
	`3`	`+ "version": "0.3.0-beta.7",`
`4`	`4`	`"mcpName": "io.github.ammawla/encode-toolkit",`
`5`	`5`	`"description": "ENCODE Toolkit — Genomics research infrastructure with 20 MCP tools, 47 skills, 14 database integrations, and 7 pipelines for Claude Code",`
`6`	`6`	`"main": "index.js",`