@@ -0,0 +1,4 @@
+---
+category: minorAnalysis
+---
+* Added modeling of the `@modelcontextprotocol/sdk` and `@modelcontextprotocol/server` (the official Model Context Protocol SDK) and `fastmcp` npm packages. The arguments of MCP tool, resource and prompt callbacks, the requests that handlers of the low-level `Server` receive, and the request headers and bearer token that the SDK passes to a callback, are now sources of the `remote` threat model.
@@ -0,0 +1,4 @@
+---
+category: minorAnalysis
+---
+* Added flow summaries for schema parsing with the `zod` npm package: data now flows from the argument of `parse`, `safeParse`, `parseAsync` and `safeParseAsync` to the parsed result.
@@ -0,0 +1,15 @@
+# Sources for MCP servers built with the npm package "fastmcp": the arguments of tools, resource
+# templates and prompts.
+extensions:
+  - addsTo:
+      pack: codeql/javascript-all
+      extensible: typeModel
+    data:
+      - ["fastmcp.FastMCP", "fastmcp", "Member[FastMCP].Instance"]
+
+  - addsTo:
+      pack: codeql/javascript-all
+      extensible: sourceModel
+    data:
+      - ["fastmcp.FastMCP", "Member[addTool].Argument[0].Member[execute].Parameter[0]", "remote"]
+      - ["fastmcp.FastMCP", "Member[addResourceTemplate,addPrompt].Argument[0].Member[load].Parameter[0]", "remote"]
@@ -0,0 +1,36 @@
+# Sources for MCP servers built with the TypeScript SDK: "@modelcontextprotocol/sdk" (1.x) and
+# "@modelcontextprotocol/server" (2.x). The arguments of tool, prompt and resource callbacks are
+# input the server receives through MCP, and so are the transport headers and the bearer token the
+# SDK hands to a callback.
+#
+# A package name that contains a dot must be quoted with single quotes; otherwise CodeQL reads the
+# text after the first dot as a type name.
+extensions:
+  - addsTo:
+      pack: codeql/javascript-all
+      extensible: typeModel
+    data:
+      - ["@modelcontextprotocol/sdk.McpServer", "'@modelcontextprotocol/sdk/server/mcp.js'", "Member[McpServer].Instance"]
+      - ["@modelcontextprotocol/sdk.McpServer", "@modelcontextprotocol/sdk/server/mcp", "Member[McpServer].Instance"]
+      - ["@modelcontextprotocol/sdk.McpServer", "@modelcontextprotocol/server", "Member[McpServer].Instance"]
+      - ["@modelcontextprotocol/sdk.McpServer", "'@modelcontextprotocol/sdk/server/mcp.js'.McpServer", ""]
+      - ["@modelcontextprotocol/sdk.Server", "'@modelcontextprotocol/sdk/server/index.js'", "Member[Server].Instance"]
+      - ["@modelcontextprotocol/sdk.Server", "@modelcontextprotocol/sdk/server/index", "Member[Server].Instance"]
+      - ["@modelcontextprotocol/sdk.Server", "@modelcontextprotocol/server", "Member[Server].Instance"]
+      - ["@modelcontextprotocol/sdk.Server", "@modelcontextprotocol/sdk.McpServer", "Member[server]"]
+
+  - addsTo:
+      pack: codeql/javascript-all
+      extensible: sourceModel
+    data:
+      # High-level server: the callback is the last argument; its first parameter holds the arguments
+      - ["@modelcontextprotocol/sdk.McpServer", "Member[tool,registerTool,prompt,registerPrompt].Argument[1..].Parameter[0]", "remote"]
+      - ["@modelcontextprotocol/sdk.McpServer", "Member[resource,registerResource].Argument[1..].Parameter[0,1]", "remote"]
+      # Transport headers and the bearer token: `extra` in 1.x, `ctx` in 2.x
+      - ["@modelcontextprotocol/sdk.McpServer", "Member[tool,registerTool,prompt,registerPrompt].Argument[1..].Parameter[1,2].Member[requestInfo].Member[headers]", "remote"]
+      - ["@modelcontextprotocol/sdk.McpServer", "Member[tool,registerTool,prompt,registerPrompt].Argument[1..].Parameter[1,2].Member[authInfo].Member[token]", "remote"]
+      - ["@modelcontextprotocol/sdk.McpServer", "Member[tool,registerTool,prompt,registerPrompt].Argument[1..].Parameter[1,2].Member[http].Member[req].Member[headers].Member[get].ReturnValue", "remote"]
+      - ["@modelcontextprotocol/sdk.McpServer", "Member[tool,registerTool,prompt,registerPrompt].Argument[1..].Parameter[1,2].Member[http].Member[authInfo].Member[token]", "remote"]
+      # Low-level server: request handlers receive the request; custom methods (2.x) its params
+      - ["@modelcontextprotocol/sdk.Server", "Member[setRequestHandler].Argument[1].Parameter[0].Member[params]", "remote"]
+      - ["@modelcontextprotocol/sdk.Server", "Member[setRequestHandler].Argument[2].Parameter[0]", "remote"]
@@ -0,0 +1,16 @@
+extensions:
+  - addsTo:
+      pack: codeql/javascript-all
+      extensible: typeModel
+    data:
+      - ["zod", "zod/v3", ""]
+      - ["zod", "zod/v4", ""]
+
+  - addsTo:
+      pack: codeql/javascript-all
+      extensible: summaryModel
+    data:
+      - ["zod", "Fuzzy.Member[parse]", "Argument[0]", "ReturnValue", "value"]
+      - ["zod", "Fuzzy.Member[safeParse]", "Argument[0]", "ReturnValue.Member[data]", "value"]
+      - ["zod", "Fuzzy.Member[parseAsync]", "Argument[0]", "ReturnValue.Awaited", "value"]
+      - ["zod", "Fuzzy.Member[safeParseAsync]", "Argument[0]", "ReturnValue.Awaited.Member[data]", "value"]
@@ -0,0 +1,43 @@
+import { FastMCP } from "fastmcp";
+import { z } from "zod";
+
+declare function SINK(value: unknown): void;
+
+const server = new FastMCP({ name: "test", version: "1.0.0" });
+
+server.addTool({
+  name: "run",
+  parameters: z.object({ command: z.string() }),
+  execute: async (args) => { // $ threat-source=remote
+    SINK(args.command); // $ hasFlow
+    return "";
+  },
+});
+
+server.addResourceTemplate({
+  uriTemplate: "note://{name}",
+  name: "note",
+  arguments: [{ name: "name" }],
+  async load({ name }) { // $ threat-source=remote
+    SINK(name); // $ hasFlow
+    return { text: "" };
+  },
+});
+
+server.addPrompt({
+  name: "summarize",
+  arguments: [{ name: "topic" }],
+  load: async ({ topic }) => { // $ threat-source=remote
+    SINK(topic); // $ hasFlow
+    return "";
+  },
+});
+
+// A static resource takes no arguments: no source.
+server.addResource({
+  uri: "file:///log",
+  name: "log",
+  async load() {
+    return { text: "" };
+  },
+});
@@ -0,0 +1,112 @@
+import { Server } from "@modelcontextprotocol/sdk/server/index.js";
+import { McpServer, ResourceTemplate } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { McpServer as McpServerNoSuffix } from "@modelcontextprotocol/sdk/server/mcp";
+import { CallToolRequestSchema } from "@modelcontextprotocol/sdk/types.js";
+import { McpServer as McpServerV2, Server as ServerV2 } from "@modelcontextprotocol/server";
+import { z } from "zod";
+
+declare function SINK(value: unknown): void;
+
+const server = new McpServer({ name: "test", version: "1.0.0" });
+
+// Tools and prompts: the first parameter of the callback holds the arguments.
+server.tool("run", { command: z.string() }, async ({ command }) => { // $ threat-source=remote
+  SINK(command); // $ hasFlow
+  return { content: [] };
+});
+
+server.tool("read", "Read a file", { path: z.string() }, async (args) => { // $ threat-source=remote
+  SINK(args.path); // $ hasFlow
+  return { content: [] };
+});
+
+server.registerTool("fetch", { inputSchema: { url: z.string() } }, async ({ url }) => { // $ threat-source=remote
+  SINK(url); // $ hasFlow
+  return { content: [] };
+});
+
+async function namedHandler({ target }: { target: string }) { // $ threat-source=remote
+  SINK(target); // $ hasFlow
+  return { content: [] };
+}
+server.tool("remove", { target: z.string() }, namedHandler);
+
+server.prompt("summarize", { topic: z.string() }, ({ topic }) => { // $ threat-source=remote
+  SINK(topic); // $ hasFlow
+  return { messages: [] };
+});
+
+server.registerPrompt("explain", { argsSchema: { file: z.string() } }, ({ file }) => { // $ threat-source=remote
+  SINK(file); // $ hasFlow
+  return { messages: [] };
+});
+
+// Resources: the URI and the variables of the template.
+server.resource("note", new ResourceTemplate("note://{name}", { list: undefined }), async (uri, { name }) => { // $ threat-source=remote
+  SINK(uri.href); // $ hasFlow
+  SINK(name); // $ hasFlow
+  return { contents: [] };
+});
+
+server.registerResource("page", new ResourceTemplate("page://{host}", { list: undefined }), {}, async (uri, variables) => { // $ threat-source=remote
+  SINK(variables.host); // $ hasFlow
+  return { contents: [] };
+});
+
+// The request headers and the bearer token that the SDK hands to a callback.
+server.tool("forward", { id: z.string() }, async (_args, extra) => { // $ threat-source=remote
+  SINK(extra.requestInfo?.headers["x-target"]); // $ hasFlow threat-source=remote
+  SINK(extra.authInfo?.token); // $ hasFlow threat-source=remote
+  SINK(extra.sessionId);
+  return { content: [] };
+});
+
+// The low-level server: handlers receive the request.
+const lowLevel = new Server({ name: "test", version: "1.0.0" }, { capabilities: { tools: {} } });
+lowLevel.setRequestHandler(CallToolRequestSchema, async (request) => {
+  SINK(request.params.arguments?.command); // $ hasFlow threat-source=remote
+  return { content: [] };
+});
+
+server.server.setRequestHandler(CallToolRequestSchema, async (request) => {
+  SINK(request.params.name); // $ hasFlow threat-source=remote
+  return { content: [] };
+});
+
+// An import path without the file suffix, and a server that arrives as a typed parameter.
+new McpServerNoSuffix({ name: "test", version: "1.0.0" }).tool("run", { command: z.string() }, async ({ command }) => { // $ threat-source=remote
+  SINK(command); // $ hasFlow
+  return { content: [] };
+});
+
+export function register(target: McpServer) {
+  target.tool("run", { command: z.string() }, async ({ command }) => { // $ threat-source=remote
+    SINK(command); // $ hasFlow
+    return { content: [] };
+  });
+}
+
+// Version 2 of the SDK: one package, and a context object instead of `extra`.
+const serverV2 = new McpServerV2({ name: "test", version: "2.0.0" });
+serverV2.registerTool("fetch", { inputSchema: z.object({ url: z.string() }) }, async ({ url }, ctx) => { // $ threat-source=remote
+  SINK(url); // $ hasFlow
+  SINK(ctx.http?.req.headers.get("x-target")); // $ hasFlow threat-source=remote
+  SINK(ctx.http?.authInfo?.token); // $ hasFlow threat-source=remote
+  return { content: [] };
+});
+
+const lowLevelV2 = new ServerV2({ name: "test", version: "2.0.0" });
+lowLevelV2.setRequestHandler("tools/call", async (request) => {
+  SINK(request.params.arguments); // $ hasFlow threat-source=remote
+  return { content: [] };
+});
+
+lowLevelV2.setRequestHandler("acme/search", { params: z.object({ query: z.string() }), result: z.object({}) }, async (params) => { // $ threat-source=remote
+  SINK(params.query); // $ hasFlow
+  return {};
+});
+
+// Not registered with a server: no source.
+export function notAHandler(command: string) {
+  SINK(command);
+}
@@ -0,0 +1,30 @@
+import { z } from "zod";
+import * as z4 from "zod/v4";
+
+declare function SINK(value: unknown): void;
+
+const raw = JSON.parse(process.argv[2]); // $ threat-source=commandargs
+
+const Options = z.object({ command: z.string() });
+const NextOptions = z4.object({ command: z4.string() });
+
+SINK(Options.parse(raw).command); // $ hasFlow
+SINK(NextOptions.parse(raw).command); // $ hasFlow
+
+const checked = Options.safeParse(raw);
+if (checked.success) {
+  SINK(checked.data.command); // $ hasFlow
+}
+SINK(checked.error);
+
+async function later() {
+  SINK((await Options.parseAsync(raw)).command); // $ hasFlow
+
+  const result = await Options.safeParseAsync(raw);
+  if (result.success) {
+    SINK(result.data.command); // $ hasFlow
+  }
+}
+
+// A value that did not come from a source stays clean.
+SINK(Options.parse({ command: "ls" }).command);