Fix uid placement for single-entry [[extensions]] TOMLs

addUidToToml branched on `extensionsArray.length > 1` to decide between
the regex-based positional insertion (inside the matching [[extensions]]
block) and a top-level WASM patch. A single-entry [[extensions]] array
fell into the top-level branch, so `uid` was written outside the
[[extensions]] block — the wrong location.

This is the shape produced by current `shopify app init` templates
(e.g. ui_extension app-home), so every newly-init'd app from those
templates ended up with a top-level `uid` after the first
`linkedAppContext` run.

Fix: branch on whether `extensionsArray` exists at all. Any array shape
(length 1 or many) gets the regex insertion path. Legacy single-extension
TOMLs with top-level `type`/`handle` fields still get the top-level
`file.patch` path.

Adds a regression test using the exact app init template TOML shape.

Co-authored-by: Nick Wesselman <nick.wesselman@shopify.com>

Author: shopify-river

.changeset/fix-uid-placement-single-extension-array.md

@@ -0,0 +1,5 @@
+---
+'@shopify/app': patch
+---
+
+Fix `uid` being inserted at the top level of extension TOML files (outside the `[[extensions]]` block) during `shopify app init` and other `linkedAppContext` flows when the TOML uses the modern `[[extensions]]` array-of-tables shape with a single entry — the shape produced by current `app init` templates. Previously, single-entry arrays fell into the legacy top-level `file.patch` branch; `uid` is now inserted inside the `[[extensions]]` block (after `handle`) for any array shape, regardless of length. Legacy single-extension TOMLs with top-level `type`/`handle` fields continue to use the top-level patch path.

packages/app/src/cli/services/app/add-uid-to-extension-toml.test.ts

@@ -67,6 +67,63 @@ describe('addUidToTomlsIfNecessary', () => {
     })
   })
 
+  test('adds uid inside the [[extensions]] block for a single-entry array TOML (matching the app init template shape)', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given — a TOML using the modern `[[extensions]]` array-of-tables shape with a
+      // single extension. This is the shape produced by `shopify app init` templates.
+      const tomlPath = joinPath(tmpDir, 'shopify.extension.toml')
+      const tomlContent = `api_version = "2026-07"
+
+[[extensions]]
+# Change the merchant-facing name of the extension in locales/en.default.json
+name = "t:name"
+handle = "app-home"
+type = "ui_extension"
+
+[[extensions.targeting]]
+module = "./src/AppHome.jsx"
+target = "admin.app.home.render"
+
+[access_scopes]
+scopes = "write_metaobject_definitions,write_metaobjects,write_products"
+`
+      await writeFile(tomlPath, tomlContent)
+
+      const extension = {
+        configurationPath: tomlPath,
+        handle: 'app-home',
+        isUUIDStrategyExtension: true,
+        uid: 'abc-123',
+        configuration: {},
+      } as ExtensionInstance
+
+      const client = testDeveloperPlatformClient({supportsAtomicDeployments: true})
+
+      // When
+      await addUidToTomlsIfNecessary([extension], client)
+
+      // Then — uid must be inside the [[extensions]] block (right after handle), not at
+      // the top level of the file.
+      const updatedContent = await readFile(tomlPath)
+      expect(updatedContent).toBe(`api_version = "2026-07"
+
+[[extensions]]
+# Change the merchant-facing name of the extension in locales/en.default.json
+name = "t:name"
+handle = "app-home"
+uid = "abc-123"
+type = "ui_extension"
+
+[[extensions.targeting]]
+module = "./src/AppHome.jsx"
+target = "admin.app.home.render"
+
+[access_scopes]
+scopes = "write_metaobject_definitions,write_metaobjects,write_products"
+`)
+    })
+  })
+
   test('adds uid to multi-extension TOML', async () => {
     await inTemporaryDirectory(async (tmpDir) => {
       // Given

packages/app/src/cli/services/app/add-uid-to-extension-toml.ts

@@ -28,17 +28,20 @@ async function addUidToToml(extension: ExtensionInstance) {
     if (currentExtension && 'uid' in currentExtension) return
   }
 
-  if (extensionsArray && extensionsArray.length > 1) {
-    // Multi-extension TOML: use regex to insert uid after the correct handle.
+  if (extensionsArray) {
+    // [[extensions]] array-of-tables TOML: use regex to insert uid after the correct handle.
     // updateTomlValues (WASM) doesn't support patching individual array-of-tables entries,
-    // so transformRaw with positional insertion is the pragmatic choice here.
+    // so transformRaw with positional insertion is the pragmatic choice here. This applies
+    // whether the array has one entry or many — putting `uid` at the top level of the file
+    // would place it outside the [[extensions]] block, which is the wrong location.
     const handle = extension.handle
     await file.transformRaw((raw) => {
       const regex = new RegExp(`(\\n?(\\s*)handle\\s*=\\s*"${handle}")`)
       return raw.replace(regex, `$1\n$2uid = "${extension.uid}"`)
     })
   } else {
-    // Single extension (or no extensions array): add uid at the top level via WASM patch
+    // Legacy single-extension TOML with top-level `type`/`handle` fields: add uid at the
+    // top level via WASM patch.
     await file.patch({uid: extension.uid})
   }
 }