fix(session): compare entrypoint file identity

Fixes #8844
Supersedes #8849

Co-Authored-By: gensokyo-dev <342580529+gensokyo-dev@users.noreply.github.com>

src/serverIdentity.ts

@@ -1,3 +1,4 @@
+import { statSync } from "node:fs";
 import { dirname, basename, resolve } from "node:path";
 import { fileURLToPath } from "node:url";
 
@@ -24,6 +25,24 @@ const packageRoot = (): string => {
     : resolve(moduleDirectory, "..");
 };
 
+const compareServerPaths = (
+  expected: string,
+  observed: string,
+): "aligned" | "mismatch" | "unknown" => {
+  if (expected === observed) return "aligned";
+  if (process.platform === "win32")
+    return resolve(expected) === observed ? "aligned" : "mismatch";
+  try {
+    const selected = statSync(expected, { bigint: true });
+    const running = statSync(observed, { bigint: true });
+    return selected.dev === running.dev && selected.ino === running.ino
+      ? "aligned"
+      : "mismatch";
+  } catch {
+    return "unknown";
+  }
+};
+
 /** Build one runtime identity without claiming alignment from absent observations. */
 export const createServerIdentity = (input: {
   readonly startedAt: string;
@@ -35,6 +54,10 @@ export const createServerIdentity = (input: {
 }) => {
   const catalog = input.catalog;
   const serverPath = input.commandPath || undefined;
+  const pathComparison =
+    input.expected?.server_path === undefined || serverPath === undefined
+      ? "unknown"
+      : compareServerPaths(input.expected.server_path, serverPath);
   const reasons: string[] = [];
   if (
     input.expected?.package_version !== undefined &&
@@ -46,17 +69,12 @@ export const createServerIdentity = (input: {
     input.expected.catalog_digest !== catalog.digests.combined_sha256
   )
     reasons.push("catalog_digest_mismatch");
-  if (
-    input.expected?.server_path !== undefined &&
-    serverPath !== undefined &&
-    resolve(input.expected.server_path) !== serverPath
-  )
-    reasons.push("registration_path_mismatch");
+  if (pathComparison === "mismatch") reasons.push("registration_path_mismatch");
   const observedExpectation =
     input.expected !== undefined &&
     Object.values(input.expected).some((value) => value !== undefined);
   const pathComparable =
-    input.expected?.server_path === undefined || serverPath !== undefined;
+    input.expected?.server_path === undefined || pathComparison !== "unknown";
   return {
     package: {
       name: PRODUCT_IDENTITY.packageName,
@@ -105,7 +123,10 @@ export const createServerIdentity = (input: {
             : input.expected?.server_path !== undefined &&
                 serverPath === undefined
               ? "The server entrypoint path is unavailable, so registration identity cannot be compared."
-              : "Supply expected package, catalog, or registration identity to compare the live server.",
+              : input.expected?.server_path !== undefined &&
+                  pathComparison === "unknown"
+                ? "The expected or running server entrypoint could not be inspected, so registration identity cannot be compared."
+                : "Supply expected package, catalog, or registration identity to compare the live server.",
     },
   } as const;
 };

tests/boundary/mcp/serverIdentity.test.ts

@@ -1,6 +1,6 @@
 import { parseMcpToolError } from "../../fixtures/mcpToolError.js";
 import { ok as resultOk } from "../../../src/domain/result.js";
-import { readFile, writeFile } from "node:fs/promises";
+import { mkdir, readFile, symlink, writeFile } from "node:fs/promises";
 import { join } from "node:path";
 
 import { Client, InMemoryTransport } from "@modelcontextprotocol/client";
@@ -245,6 +245,43 @@ describe("server and catalog identity", () => {
   });
 });
 
+it.skipIf(process.platform === "win32")(
+  "compares the selected entrypoint through symlink and parent traversal",
+  async () => {
+    const root = await createTestTempDirectory("server-identity-path-");
+    const scripts = join(root, "package", "scripts");
+    const scratch = join(root, "scratch");
+    await mkdir(scripts, { recursive: true });
+    await mkdir(scratch);
+    const canonical = join(scripts, "rea.mjs");
+    const other = join(root, "other.mjs");
+    await writeFile(canonical, "entrypoint");
+    await writeFile(other, "other entrypoint");
+    await symlink(scripts, join(scratch, "link"));
+    const selected = `${scratch}/link/../scripts/rea.mjs`;
+    const identity = (server_path: string) =>
+      createServerIdentity({
+        catalog: DEFAULT_CATALOG_IDENTITY,
+        startedAt: "2026-07-13T00:00:00.000Z",
+        commandPath: canonical,
+        expected: { server_path },
+      });
+
+    expect(identity(selected).alignment).toMatchObject({
+      state: "aligned",
+      reasons: [],
+    });
+    expect(identity(other).alignment).toMatchObject({
+      state: "mcp_server_restart_required",
+      reasons: ["registration_path_mismatch"],
+    });
+    expect(identity(join(root, "missing.mjs")).alignment).toMatchObject({
+      state: "unknown",
+      reasons: [],
+    });
+  },
+);
+
 describe("provider capability inventory", () => {
   it("reports composed, host, and target-specific availability truthfully", () => {
     const policy = {