Merge branch 'main' into issue-461

Author: aryasoni98

README.md

@@ -278,6 +278,23 @@ docker run -i --rm \
   ghcr.io/github/github-mcp-server
 ```
 
+## Read-Only Mode
+
+To run the server in read-only mode, you can use the `--read-only` flag. This will only offer read-only tools, preventing any modifications to repositories, issues, pull requests, etc.
+
+```bash
+./github-mcp-server --read-only
+```
+
+When using Docker, you can pass the read-only mode as an environment variable:
+
+```bash
+docker run -i --rm \
+  -e GITHUB_PERSONAL_ACCESS_TOKEN=<your-token> \
+  -e GITHUB_READ_ONLY=1 \
+  ghcr.io/github/github-mcp-server
+```
+
 ## GitHub Enterprise Server and Enterprise Cloud with data residency (ghe.com)
 
 The flag `--gh-host` and the environment variable `GITHUB_HOST` can be used to set

pkg/github/code_scanning.go

@@ -90,14 +90,14 @@ func ListCodeScanningAlerts(getClient GetClientFn, t translations.TranslationHel
 				mcp.Required(),
 				mcp.Description("The name of the repository."),
 			),
-			mcp.WithString("ref",
-				mcp.Description("The Git reference for the results you want to list."),
-			),
 			mcp.WithString("state",
 				mcp.Description("Filter code scanning alerts by state. Defaults to open"),
 				mcp.DefaultString("open"),
 				mcp.Enum("open", "closed", "dismissed", "fixed"),
 			),
+			mcp.WithString("ref",
+				mcp.Description("The Git reference for the results you want to list."),
+			),
 			mcp.WithString("severity",
 				mcp.Description("Filter code scanning alerts by severity"),
 				mcp.Enum("critical", "high", "medium", "low", "warning", "note", "error"),