diff --git a/src/lib/standalone.ts b/src/lib/standalone.ts
index 72cc9f36183..efd397bd3bc 100644
--- a/src/lib/standalone.ts
+++ b/src/lib/standalone.ts
@@ -7,7 +7,15 @@ export function isStandaloneBinary(): boolean {
 }
 
 export function isStandaloneModuleUrl(url: string): boolean {
-  return url.includes("/$bunfs/") || /^file:\/\/\/[A-Za-z]:\/~BUN\//.test(url);
+  try {
+    const parsed = new URL(url);
+    if (parsed.protocol !== "file:" || parsed.host !== "") return false;
+    // Bun may encode the Windows virtual root's tilde; decode one URL layer only.
+    const path = decodeURIComponent(parsed.pathname);
+    return path.startsWith("/$bunfs/") || /^\/[A-Za-z]:\/~BUN\//.test(path);
+  } catch {
+    return false;
+  }
 }
 
 /** Directory containing the compiled executable and its copied runtime assets. */
diff --git a/structure/INDEX.md b/structure/INDEX.md
index d1a258a6810..a0dbbf3ea74 100644
--- a/structure/INDEX.md
+++ b/structure/INDEX.md
@@ -132,7 +132,7 @@ A source area can be described by more than one doc, because these docs are orga
 | `src/index.ts` | [`runtime.md`](runtime.md) |
 | `src/integrations/` | [`clients/integrations.md`](clients/integrations.md) |
 | `src/lab/` | [`runtime.md`](runtime.md)<br>[`adapters/compatibility-lab.md`](adapters/compatibility-lab.md) |
-| `src/lib/` | [`overview.md`](overview.md)<br>[`runtime.md`](runtime.md)<br>[`transports/byte-accounting.md`](transports/byte-accounting.md)<br>[`transports/responses-wire-shapes.md`](transports/responses-wire-shapes.md)<br>[`transports/responses-failover.md`](transports/responses-failover.md)<br>[`transports/responses-spend.md`](transports/responses-spend.md)<br>[`transports/inventory.md`](transports/inventory.md)<br>[`gui-and-management-api.md`](gui-and-management-api.md)<br>[`dashboard-and-usage.md`](dashboard-and-usage.md)<br>[`clients/integrations.md`](clients/integrations.md)<br>[`ops/docs-and-release.md`](ops/docs-and-release.md) |
+| `src/lib/` | [`overview.md`](overview.md)<br>[`runtime.md`](runtime.md)<br>[`transports/byte-accounting.md`](transports/byte-accounting.md)<br>[`transports/responses-wire-shapes.md`](transports/responses-wire-shapes.md)<br>[`transports/responses-failover.md`](transports/responses-failover.md)<br>[`transports/responses-spend.md`](transports/responses-spend.md)<br>[`transports/inventory.md`](transports/inventory.md)<br>[`gui-and-management-api.md`](gui-and-management-api.md)<br>[`dashboard-and-usage.md`](dashboard-and-usage.md)<br>[`clients/integrations.md`](clients/integrations.md)<br>[`ops/service-and-sidecars.md`](ops/service-and-sidecars.md)<br>[`ops/docs-and-release.md`](ops/docs-and-release.md) |
 | `src/link/` | [`remote-link.md`](remote-link.md) |
 | `src/oauth/` | [`runtime.md`](runtime.md)<br>[`transports/inventory.md`](transports/inventory.md)<br>[`providers-and-adapters.md`](providers-and-adapters.md)<br>[`providers/xai-grok.md`](providers/xai-grok.md) |
 | `src/plugins/` | [`ops/plugins.md`](ops/plugins.md) |
diff --git a/structure/manifest.json b/structure/manifest.json
index 5201bb9bf71..0057a6464e4 100644
--- a/structure/manifest.json
+++ b/structure/manifest.json
@@ -450,6 +450,7 @@
       "title": "Background Service And Sidecars",
       "scope": "Service install/repair, platform launchers, tray, and sidecar processes.",
       "documents": [
+        "src/lib/",
         "src/server/",
         "src/service-manager-probe.ts",
         "src/sidecar/",
diff --git a/structure/ops/service-and-sidecars.md b/structure/ops/service-and-sidecars.md
index 8a2d164a7f6..e2a6f218789 100644
--- a/structure/ops/service-and-sidecars.md
+++ b/structure/ops/service-and-sidecars.md
@@ -233,9 +233,12 @@ The service loads the optional `compactionRouting` block from persisted configur
 [Responses ingress](../transports/responses-failover.md#compaction-routing-overrides) applies it to individual compaction
 requests whose trigger the block names.
 
-Standalone binaries use `src/lib/standalone.ts` to detect the Bun `$bunfs` runtime and
-`src/service/state.ts` to compose durable service commands as `<execPath> start`, without a
-source-tree CLI path. The copied `gui/dist` directory is located by `src/server/gui-static.ts`;
+Standalone binaries use `src/lib/standalone.ts` to recognize hostless `file:` module URLs
+whose decoded pathname begins at Bun's `$bunfs` or Windows `~BUN` virtual root. The helper
+decodes one URL layer, so encoded Windows tildes work while network-host and nested source
+paths do not impersonate a bundled module. `src/service/state.ts` composes durable service
+commands as `<execPath> start`, without a source-tree CLI path. The copied `gui/dist`
+directory is located by `src/server/gui-static.ts`;
 `OPENCODEX_GUI_DIST` remains an explicit override.
 
 ## Bun updater ownership transaction
diff --git a/tests/lib/standalone.test.ts b/tests/lib/standalone.test.ts
index d58c3a7aa0d..b8d29b70a6e 100644
--- a/tests/lib/standalone.test.ts
+++ b/tests/lib/standalone.test.ts
@@ -17,6 +17,19 @@ test("compiled module URL markers are recognized on POSIX and Windows", () => {
   expect(isStandaloneModuleUrl("file:///Users/x/src/lib/standalone.ts")).toBe(false);
 });
 
+test("encoded Windows Bun virtual roots are recognized once", () => {
+  expect(isStandaloneModuleUrl("file:///B:/%7EBUN/root/ocx.exe")).toBe(true);
+  expect(isStandaloneModuleUrl("file:///B:/%7eBUN/root/ocx.exe")).toBe(true);
+  expect(isStandaloneModuleUrl("file:///B:/%257EBUN/root/ocx.exe")).toBe(false);
+});
+
+test("network hosts and nested Bun markers remain source URLs", () => {
+  expect(isStandaloneModuleUrl("file://server/$bunfs/root/index.ts")).toBe(false);
+  expect(isStandaloneModuleUrl("file:///Users/x/$bunfs/root/index.ts")).toBe(false);
+  expect(isStandaloneModuleUrl("https://example.test/$bunfs/root/index.ts")).toBe(false);
+  expect(isStandaloneModuleUrl("file:///B:/%XXBUN/root/index.ts")).toBe(false);
+});
+
 test("standaloneRoot follows the running executable", () => {
   expect(standaloneRoot()).toBe(dirname(realpathSync(process.execPath)));
 });