diff --git a/.changeset/fix-init-install-in-place.md b/.changeset/fix-init-install-in-place.md
deleted file mode 100644
index 3da21318a54..00000000000
--- a/.changeset/fix-init-install-in-place.md
+++ /dev/null
@@ -1,5 +0,0 @@
----
-'@shopify/app': patch
----
-
-Fix `shopify app init` leaving dangling `node_modules` symlinks on Windows when using `pnpm` (and similarly affected package managers). The scaffolded project is now moved to its final directory before dependencies are installed, so package-manager-managed symlinks/junctions resolve to the final location instead of the temporary scaffold path.
diff --git a/.changeset/ninety-doodles-scream.md b/.changeset/ninety-doodles-scream.md
deleted file mode 100644
index ec3bd6005cc..00000000000
--- a/.changeset/ninety-doodles-scream.md
+++ /dev/null
@@ -1,6 +0,0 @@
----
-'@shopify/cli-kit': minor
-'@shopify/app': minor
----
-
-Update extension-only template to include app home by default
diff --git a/.changeset/old-poems-speak.md b/.changeset/old-poems-speak.md
deleted file mode 100644
index c1fdb616962..00000000000
--- a/.changeset/old-poems-speak.md
+++ /dev/null
@@ -1,5 +0,0 @@
----
-'@shopify/cli-kit': patch
----
-
-Fix error reporting of cli-kit methods that try to run git when git is unavailable
diff --git a/packages/app/CHANGELOG.md b/packages/app/CHANGELOG.md
index b83be944ca8..c757598cb01 100644
--- a/packages/app/CHANGELOG.md
+++ b/packages/app/CHANGELOG.md
@@ -1,5 +1,20 @@
 # @shopify/app
 
+## 4.1.0
+
+### Minor Changes
+
+- 8943b19: Update extension-only template to include app home by default
+
+### Patch Changes
+
+- 45b1884: Fix `shopify app init` leaving dangling `node_modules` symlinks on Windows when using `pnpm` (and similarly affected package managers). The scaffolded project is now moved to its final directory before dependencies are installed, so package-manager-managed symlinks/junctions resolve to the final location instead of the temporary scaffold path.
+- Updated dependencies [8943b19]
+- Updated dependencies [5156580]
+  - @shopify/cli-kit@4.1.0
+  - @shopify/plugin-cloudflare@4.1.0
+  - @shopify/theme@4.1.0
+
 ## 4.0.0
 
 ### Major Changes
diff --git a/packages/app/package.json b/packages/app/package.json
index 0e61bf9703f..4982e0af5c5 100644
--- a/packages/app/package.json
+++ b/packages/app/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@shopify/app",
-  "version": "4.0.0",
+  "version": "4.1.0",
   "packageManager": "pnpm@10.11.1",
   "description": "Utilities for loading, building, and publishing apps.",
   "homepage": "https://github.com/shopify/cli#readme",
@@ -61,11 +61,11 @@
     "@graphql-typed-document-node/core": "3.2.0",
     "@luckycatfactory/esbuild-graphql-loader": "3.8.1",
     "@oclif/core": "4.5.3",
-    "@shopify/cli-kit": "4.0.0",
-    "@shopify/plugin-cloudflare": "4.0.0",
+    "@shopify/cli-kit": "4.1.0",
+    "@shopify/plugin-cloudflare": "4.1.0",
     "@shopify/polaris": "12.27.0",
     "@shopify/polaris-icons": "8.11.1",
-    "@shopify/theme": "4.0.0",
+    "@shopify/theme": "4.1.0",
     "@shopify/theme-check-node": "3.25.0",
     "@shopify/toml-patch": "0.3.0",
     "chokidar": "3.6.0",
diff --git a/packages/cli-kit/CHANGELOG.md b/packages/cli-kit/CHANGELOG.md
index 1b1a8f240db..c4fefc436ab 100644
--- a/packages/cli-kit/CHANGELOG.md
+++ b/packages/cli-kit/CHANGELOG.md
@@ -1,5 +1,15 @@
 # @shopify/cli-kit
 
+## 4.1.0
+
+### Minor Changes
+
+- 8943b19: Update extension-only template to include app home by default
+
+### Patch Changes
+
+- 5156580: Fix error reporting of cli-kit methods that try to run git when git is unavailable
+
 ## 4.0.0
 
 ### Major Changes
diff --git a/packages/cli-kit/package.json b/packages/cli-kit/package.json
index 1e16879a782..1725431d06d 100644
--- a/packages/cli-kit/package.json
+++ b/packages/cli-kit/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@shopify/cli-kit",
-  "version": "4.0.0",
+  "version": "4.1.0",
   "packageManager": "pnpm@10.11.1",
   "private": false,
   "description": "A set of utilities, interfaces, and models that are common across all the platform features",
diff --git a/packages/cli-kit/src/public/common/version.ts b/packages/cli-kit/src/public/common/version.ts
index 83295a299b6..4bbf1317055 100644
--- a/packages/cli-kit/src/public/common/version.ts
+++ b/packages/cli-kit/src/public/common/version.ts
@@ -1 +1 @@
-export const CLI_KIT_VERSION = '4.0.0'
+export const CLI_KIT_VERSION = '4.1.0'
diff --git a/packages/cli/CHANGELOG.md b/packages/cli/CHANGELOG.md
index 23b88cf5590..81eab1996d1 100644
--- a/packages/cli/CHANGELOG.md
+++ b/packages/cli/CHANGELOG.md
@@ -1,5 +1,7 @@
 # @shopify/cli
 
+## 4.1.0
+
 ## 4.0.0
 
 ### Major Changes
diff --git a/packages/cli/oclif.manifest.json b/packages/cli/oclif.manifest.json
index 046ac204728..b73dd5a6473 100644
--- a/packages/cli/oclif.manifest.json
+++ b/packages/cli/oclif.manifest.json
@@ -7986,5 +7986,5 @@
       "strict": true
     }
   },
-  "version": "4.0.0"
+  "version": "4.1.0"
 }
\ No newline at end of file
diff --git a/packages/cli/package.json b/packages/cli/package.json
index 1554432da6d..76c20094422 100644
--- a/packages/cli/package.json
+++ b/packages/cli/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@shopify/cli",
-  "version": "4.0.0",
+  "version": "4.1.0",
   "packageManager": "pnpm@10.11.1",
   "private": false,
   "description": "A CLI tool to build for the Shopify platform",
@@ -60,12 +60,12 @@
     "@oclif/core": "4.5.3",
     "@oclif/plugin-commands": "4.1.33",
     "@oclif/plugin-plugins": "5.4.47",
-    "@shopify/app": "4.0.0",
-    "@shopify/store": "4.0.0",
-    "@shopify/cli-kit": "4.0.0",
-    "@shopify/plugin-cloudflare": "4.0.0",
-    "@shopify/plugin-did-you-mean": "4.0.0",
-    "@shopify/theme": "4.0.0",
+    "@shopify/app": "4.1.0",
+    "@shopify/store": "4.1.0",
+    "@shopify/cli-kit": "4.1.0",
+    "@shopify/plugin-cloudflare": "4.1.0",
+    "@shopify/plugin-did-you-mean": "4.1.0",
+    "@shopify/theme": "4.1.0",
     "@shopify/cli-hydrogen": "11.1.10",
     "@types/global-agent": "3.0.0",
     "@vitest/coverage-istanbul": "^3.1.4",
diff --git a/packages/create-app/CHANGELOG.md b/packages/create-app/CHANGELOG.md
index fb3fe2fb97e..a3a14db9ebf 100644
--- a/packages/create-app/CHANGELOG.md
+++ b/packages/create-app/CHANGELOG.md
@@ -1,5 +1,7 @@
 # @shopify/create-app
 
+## 4.1.0
+
 ## 4.0.0
 
 ### Major Changes
diff --git a/packages/create-app/oclif.manifest.json b/packages/create-app/oclif.manifest.json
index c211a5cba70..cd0d4e684b6 100644
--- a/packages/create-app/oclif.manifest.json
+++ b/packages/create-app/oclif.manifest.json
@@ -117,5 +117,5 @@
       "summary": "Create a new app project"
     }
   },
-  "version": "4.0.0"
+  "version": "4.1.0"
 }
\ No newline at end of file
diff --git a/packages/create-app/package.json b/packages/create-app/package.json
index 25db5d6db57..b11886362ca 100644
--- a/packages/create-app/package.json
+++ b/packages/create-app/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@shopify/create-app",
-  "version": "4.0.0",
+  "version": "4.1.0",
   "packageManager": "pnpm@10.11.1",
   "private": false,
   "description": "A CLI tool to create a new Shopify app.",
@@ -58,8 +58,8 @@
     "esbuild": "0.28.0"
   },
   "devDependencies": {
-    "@shopify/cli-kit": "4.0.0",
-    "@shopify/app": "4.0.0",
+    "@shopify/cli-kit": "4.1.0",
+    "@shopify/app": "4.1.0",
     "esbuild-plugin-copy": "^2.1.1",
     "@vitest/coverage-istanbul": "^3.1.4"
   },
diff --git a/packages/plugin-cloudflare/CHANGELOG.md b/packages/plugin-cloudflare/CHANGELOG.md
index e92b3cbbc95..a046342194a 100644
--- a/packages/plugin-cloudflare/CHANGELOG.md
+++ b/packages/plugin-cloudflare/CHANGELOG.md
@@ -1,5 +1,13 @@
 # @shopify/plugin-cloudflare
 
+## 4.1.0
+
+### Patch Changes
+
+- Updated dependencies [8943b19]
+- Updated dependencies [5156580]
+  - @shopify/cli-kit@4.1.0
+
 ## 4.0.0
 
 ### Major Changes
diff --git a/packages/plugin-cloudflare/package.json b/packages/plugin-cloudflare/package.json
index ea7073326e9..1da70bb1c4d 100644
--- a/packages/plugin-cloudflare/package.json
+++ b/packages/plugin-cloudflare/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@shopify/plugin-cloudflare",
-  "version": "4.0.0",
+  "version": "4.1.0",
   "packageManager": "pnpm@10.11.1",
   "description": "Enables the creation of Cloudflare tunnels from `shopify app dev`, allowing previews from any device",
   "keywords": [
@@ -46,7 +46,7 @@
   },
   "dependencies": {
     "@oclif/core": "4.5.3",
-    "@shopify/cli-kit": "4.0.0"
+    "@shopify/cli-kit": "4.1.0"
   },
   "devDependencies": {
     "@vitest/coverage-istanbul": "^3.1.4"
diff --git a/packages/plugin-did-you-mean/CHANGELOG.md b/packages/plugin-did-you-mean/CHANGELOG.md
index 9df3d293fc6..bbf66025c2f 100644
--- a/packages/plugin-did-you-mean/CHANGELOG.md
+++ b/packages/plugin-did-you-mean/CHANGELOG.md
@@ -1,5 +1,13 @@
 # @shopify/plugin-did-you-mean
 
+## 4.1.0
+
+### Patch Changes
+
+- Updated dependencies [8943b19]
+- Updated dependencies [5156580]
+  - @shopify/cli-kit@4.1.0
+
 ## 4.0.0
 
 ### Major Changes
diff --git a/packages/plugin-did-you-mean/package.json b/packages/plugin-did-you-mean/package.json
index 7236be5ac47..bfb4c63ad8c 100644
--- a/packages/plugin-did-you-mean/package.json
+++ b/packages/plugin-did-you-mean/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@shopify/plugin-did-you-mean",
-  "version": "4.0.0",
+  "version": "4.1.0",
   "packageManager": "pnpm@10.11.1",
   "private": true,
   "bugs": {
@@ -41,7 +41,7 @@
   },
   "dependencies": {
     "@oclif/core": "4.5.3",
-    "@shopify/cli-kit": "4.0.0",
+    "@shopify/cli-kit": "4.1.0",
     "n-gram": "2.0.2"
   },
   "devDependencies": {
diff --git a/packages/store/CHANGELOG.md b/packages/store/CHANGELOG.md
index dbefcb4ccaf..8108024b9c4 100644
--- a/packages/store/CHANGELOG.md
+++ b/packages/store/CHANGELOG.md
@@ -1,5 +1,13 @@
 # @shopify/store
 
+## 4.1.0
+
+### Patch Changes
+
+- Updated dependencies [8943b19]
+- Updated dependencies [5156580]
+  - @shopify/cli-kit@4.1.0
+
 ## 4.0.0
 
 ### Major Changes
diff --git a/packages/store/package.json b/packages/store/package.json
index f800c0d56a4..b1843e78742 100644
--- a/packages/store/package.json
+++ b/packages/store/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@shopify/store",
-  "version": "4.0.0",
+  "version": "4.1.0",
   "packageManager": "pnpm@10.11.1",
   "private": true,
   "description": "Utilities for working with Shopify stores",
@@ -40,7 +40,7 @@
   },
   "dependencies": {
     "@oclif/core": "4.5.3",
-    "@shopify/cli-kit": "4.0.0"
+    "@shopify/cli-kit": "4.1.0"
   },
   "devDependencies": {
     "@vitest/coverage-istanbul": "^3.1.4"
diff --git a/packages/theme/CHANGELOG.md b/packages/theme/CHANGELOG.md
index 2bbb62a6d83..1269daddb49 100644
--- a/packages/theme/CHANGELOG.md
+++ b/packages/theme/CHANGELOG.md
@@ -1,5 +1,13 @@
 # @shopify/theme
 
+## 4.1.0
+
+### Patch Changes
+
+- Updated dependencies [8943b19]
+- Updated dependencies [5156580]
+  - @shopify/cli-kit@4.1.0
+
 ## 4.0.0
 
 ### Major Changes
diff --git a/packages/theme/package.json b/packages/theme/package.json
index f32429dc4ef..76c8842fd5a 100644
--- a/packages/theme/package.json
+++ b/packages/theme/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@shopify/theme",
-  "version": "4.0.0",
+  "version": "4.1.0",
   "packageManager": "pnpm@10.11.1",
   "private": true,
   "description": "Utilities for building and publishing themes",
@@ -41,7 +41,7 @@
   },
   "dependencies": {
     "@oclif/core": "4.5.3",
-    "@shopify/cli-kit": "4.0.0",
+    "@shopify/cli-kit": "4.1.0",
     "@shopify/theme-check-node": "3.25.0",
     "@shopify/theme-language-server-node": "2.21.0",
     "chokidar": "3.6.0",
diff --git a/packages/ui-extensions-dev-console/CHANGELOG.md b/packages/ui-extensions-dev-console/CHANGELOG.md
index 8b287bca15b..af9a03f899c 100644
--- a/packages/ui-extensions-dev-console/CHANGELOG.md
+++ b/packages/ui-extensions-dev-console/CHANGELOG.md
@@ -1,5 +1,7 @@
 # @shopify/ui-extensions-dev-console-app
 
+## 4.1.0
+
 ## 4.0.0
 
 ## 3.94.0
diff --git a/packages/ui-extensions-dev-console/package.json b/packages/ui-extensions-dev-console/package.json
index da58af0034f..7c9109dc81f 100644
--- a/packages/ui-extensions-dev-console/package.json
+++ b/packages/ui-extensions-dev-console/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@shopify/ui-extensions-dev-console-app",
-  "version": "4.0.0",
+  "version": "4.1.0",
   "packageManager": "pnpm@10.11.1",
   "private": true,
   "scripts": {
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 48ce89ec5d1..46d9a04578f 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -155,10 +155,10 @@ importers:
         specifier: 4.5.3
         version: 4.5.3
       '@shopify/cli-kit':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../cli-kit
       '@shopify/plugin-cloudflare':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../plugin-cloudflare
       '@shopify/polaris':
         specifier: 12.27.0
@@ -167,7 +167,7 @@ importers:
         specifier: 8.11.1
         version: 8.11.1(react@19.2.4)
       '@shopify/theme':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../theme
       '@shopify/theme-check-node':
         specifier: 3.25.0
@@ -262,25 +262,25 @@ importers:
         specifier: 5.4.47
         version: 5.4.47
       '@shopify/app':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../app
       '@shopify/cli-hydrogen':
         specifier: 11.1.10
         version: 11.1.10(@graphql-codegen/cli@6.0.1(@parcel/watcher@2.5.6)(@types/node@18.19.70)(crossws@0.3.5)(graphql@16.10.0)(typescript@5.9.3))(graphql-config@5.1.5(@types/node@22.19.17)(crossws@0.3.5)(graphql@16.10.0)(typescript@5.9.3))(graphql@16.10.0)(react-dom@19.2.4(react@18.3.1))(react@18.3.1)(vite@6.4.1(@types/node@22.19.17)(jiti@2.6.1)(sass@1.97.3)(tsx@4.21.0)(yaml@2.8.3))
       '@shopify/cli-kit':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../cli-kit
       '@shopify/plugin-cloudflare':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../plugin-cloudflare
       '@shopify/plugin-did-you-mean':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../plugin-did-you-mean
       '@shopify/store':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../store
       '@shopify/theme':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../theme
       '@types/global-agent':
         specifier: 3.0.0
@@ -507,10 +507,10 @@ importers:
         version: 0.28.0
     devDependencies:
       '@shopify/app':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../app
       '@shopify/cli-kit':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../cli-kit
       '@vitest/coverage-istanbul':
         specifier: ^3.1.4
@@ -604,7 +604,7 @@ importers:
         specifier: 4.5.3
         version: 4.5.3
       '@shopify/cli-kit':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../cli-kit
     devDependencies:
       '@vitest/coverage-istanbul':
@@ -617,7 +617,7 @@ importers:
         specifier: 4.5.3
         version: 4.5.3
       '@shopify/cli-kit':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../cli-kit
       n-gram:
         specifier: 2.0.2
@@ -633,7 +633,7 @@ importers:
         specifier: 4.5.3
         version: 4.5.3
       '@shopify/cli-kit':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../cli-kit
     devDependencies:
       '@vitest/coverage-istanbul':
@@ -646,7 +646,7 @@ importers:
         specifier: 4.5.3
         version: 4.5.3
       '@shopify/cli-kit':
-        specifier: 4.0.0
+        specifier: 4.1.0
         version: link:../cli-kit
       '@shopify/theme-check-node':
         specifier: 3.25.0