fix: add smithery.yaml for stdio publishing, fix publish command

Smithery was trying to scan servers via HTTP because `mcp publish <url>`
treats them as external servers. Stdio servers need a smithery.yaml with
startCommand config and must be published from the project directory
without a URL argument.

Author: JaimeCernuda

.github/workflows/publish.yml

@@ -236,18 +236,20 @@ jobs:
         SMITHERY_API_KEY: ${{ secrets.SMITHERY_TOKEN }}
       run: |
         FAILURES=0
+        PUBLISHED=0
         for server_dir in clio-kit-mcp-servers/*/; do
-          if [ ! -f "$server_dir/server.json" ]; then continue; fi
+          if [ ! -f "$server_dir/smithery.yaml" ]; then continue; fi
           server_name=$(basename "$server_dir")
           echo "Publishing $server_name to Smithery..."
-          if smithery mcp publish "https://github.com/${{ github.repository }}" \
-            -n "iowarp/${server_name}-mcp"; then
+          if (cd "$server_dir" && smithery mcp publish -n "iowarp/${server_name}-mcp"); then
             echo "Published $server_name to Smithery"
+            PUBLISHED=$((PUBLISHED + 1))
           else
             echo "::error::Failed to publish $server_name to Smithery"
             FAILURES=$((FAILURES + 1))
           fi
         done
+        echo "Smithery: $PUBLISHED published, $FAILURES failed"
         if [ $FAILURES -gt 0 ]; then
           echo "::error::$FAILURES server(s) failed to publish to Smithery"
           exit 1

clio-kit-mcp-servers/adios/smithery.yaml

@@ -0,0 +1,8 @@
+# Smithery configuration: https://smithery.ai/docs/config#smitheryyaml
+startCommand:
+  type: stdio
+  configSchema:
+    type: object
+    properties: {}
+  commandFunction: |-
+    config => ({ command: 'uvx', args: ['clio-kit', 'adios'] })

clio-kit-mcp-servers/arxiv/smithery.yaml

@@ -0,0 +1,8 @@
+# Smithery configuration: https://smithery.ai/docs/config#smitheryyaml
+startCommand:
+  type: stdio
+  configSchema:
+    type: object
+    properties: {}
+  commandFunction: |-
+    config => ({ command: 'uvx', args: ['clio-kit', 'arxiv'] })

clio-kit-mcp-servers/chronolog/smithery.yaml

@@ -0,0 +1,8 @@
+# Smithery configuration: https://smithery.ai/docs/config#smitheryyaml
+startCommand:
+  type: stdio
+  configSchema:
+    type: object
+    properties: {}
+  commandFunction: |-
+    config => ({ command: 'uvx', args: ['clio-kit', 'chronolog'] })

clio-kit-mcp-servers/compression/smithery.yaml

@@ -0,0 +1,8 @@
+# Smithery configuration: https://smithery.ai/docs/config#smitheryyaml
+startCommand:
+  type: stdio
+  configSchema:
+    type: object
+    properties: {}
+  commandFunction: |-
+    config => ({ command: 'uvx', args: ['clio-kit', 'compression'] })

clio-kit-mcp-servers/darshan/smithery.yaml

@@ -0,0 +1,8 @@
+# Smithery configuration: https://smithery.ai/docs/config#smitheryyaml
+startCommand:
+  type: stdio
+  configSchema:
+    type: object
+    properties: {}
+  commandFunction: |-
+    config => ({ command: 'uvx', args: ['clio-kit', 'darshan'] })

clio-kit-mcp-servers/hdf5/smithery.yaml

@@ -0,0 +1,8 @@
+# Smithery configuration: https://smithery.ai/docs/config#smitheryyaml
+startCommand:
+  type: stdio
+  configSchema:
+    type: object
+    properties: {}
+  commandFunction: |-
+    config => ({ command: 'uvx', args: ['clio-kit', 'hdf5'] })

clio-kit-mcp-servers/jarvis/smithery.yaml

@@ -0,0 +1,8 @@
+# Smithery configuration: https://smithery.ai/docs/config#smitheryyaml
+startCommand:
+  type: stdio
+  configSchema:
+    type: object
+    properties: {}
+  commandFunction: |-
+    config => ({ command: 'uvx', args: ['clio-kit', 'jarvis'] })

clio-kit-mcp-servers/lmod/smithery.yaml

@@ -0,0 +1,8 @@
+# Smithery configuration: https://smithery.ai/docs/config#smitheryyaml
+startCommand:
+  type: stdio
+  configSchema:
+    type: object
+    properties: {}
+  commandFunction: |-
+    config => ({ command: 'uvx', args: ['clio-kit', 'lmod'] })

clio-kit-mcp-servers/ndp/smithery.yaml

@@ -0,0 +1,8 @@
+# Smithery configuration: https://smithery.ai/docs/config#smitheryyaml
+startCommand:
+  type: stdio
+  configSchema:
+    type: object
+    properties: {}
+  commandFunction: |-
+    config => ({ command: 'uvx', args: ['clio-kit', 'ndp'] })