diff --git a/packages/app/src/cli/commands/app/build.ts b/packages/app/src/cli/commands/app/build.ts
index 0cff69a8e8a..bfef69c1ed5 100644
--- a/packages/app/src/cli/commands/app/build.ts
+++ b/packages/app/src/cli/commands/app/build.ts
@@ -34,12 +34,12 @@ export default class Build extends AppUnlinkedCommand {
       cmd_app_dependency_installation_skipped: flags['skip-dependencies-installation'],
     }))
 
-    const app = await localAppContext({
+    const {app, project} = await localAppContext({
       directory: flags.path,
       userProvidedConfigName: flags.config,
     })
 
-    await build({app, skipDependenciesInstallation: flags['skip-dependencies-installation'], apiKey: clientId})
+    await build({app, project, skipDependenciesInstallation: flags['skip-dependencies-installation'], apiKey: clientId})
 
     return {app}
   }
diff --git a/packages/app/src/cli/commands/app/config/use.ts b/packages/app/src/cli/commands/app/config/use.ts
index 7854466879c..448b565fb29 100644
--- a/packages/app/src/cli/commands/app/config/use.ts
+++ b/packages/app/src/cli/commands/app/config/use.ts
@@ -35,7 +35,7 @@ export default class ConfigUse extends AppUnlinkedCommand {
   public async run(): Promise<AppUnlinkedCommandOutput> {
     const {flags, args} = await this.parse(ConfigUse)
 
-    const app = await localAppContext({
+    const {app} = await localAppContext({
       directory: flags.path,
       userProvidedConfigName: args.config,
     })
diff --git a/packages/app/src/cli/commands/app/deploy.ts b/packages/app/src/cli/commands/app/deploy.ts
index 1f7ec37618b..62f59dc70ee 100644
--- a/packages/app/src/cli/commands/app/deploy.ts
+++ b/packages/app/src/cli/commands/app/deploy.ts
@@ -104,7 +104,7 @@ export default class Deploy extends AppLinkedCommand {
     }
     this.failMissingNonTTYFlags(flags, requiredNonTTYFlags)
 
-    const {app, remoteApp, developerPlatformClient, organization} = await linkedAppContext({
+    const {app, project, remoteApp, developerPlatformClient, organization} = await linkedAppContext({
       directory: flags.path,
       clientId,
       forceRelink: flags.reset,
@@ -116,6 +116,7 @@ export default class Deploy extends AppLinkedCommand {
 
     const result = await deploy({
       app,
+      project,
       remoteApp,
       organization,
       developerPlatformClient,
diff --git a/packages/app/src/cli/commands/app/function/build.ts b/packages/app/src/cli/commands/app/function/build.ts
index 4b96ce1d8c0..7e7e821dd65 100644
--- a/packages/app/src/cli/commands/app/function/build.ts
+++ b/packages/app/src/cli/commands/app/function/build.ts
@@ -22,7 +22,7 @@ export default class FunctionBuild extends AppUnlinkedCommand {
   public async run(): Promise<AppUnlinkedCommandOutput> {
     const {flags} = await this.parse(FunctionBuild)
 
-    const app = await localAppContext({
+    const {app} = await localAppContext({
       directory: flags.path,
       userProvidedConfigName: flags.config,
     })
diff --git a/packages/app/src/cli/commands/app/function/info.ts b/packages/app/src/cli/commands/app/function/info.ts
index 28b72502b13..345c0790f26 100644
--- a/packages/app/src/cli/commands/app/function/info.ts
+++ b/packages/app/src/cli/commands/app/function/info.ts
@@ -33,7 +33,7 @@ export default class FunctionInfo extends AppUnlinkedCommand {
   public async run(): Promise<AppUnlinkedCommandOutput> {
     const {flags} = await this.parse(FunctionInfo)
 
-    const app = await localAppContext({
+    const {app} = await localAppContext({
       directory: flags.path,
       userProvidedConfigName: flags.config,
     })
diff --git a/packages/app/src/cli/commands/app/function/run.ts b/packages/app/src/cli/commands/app/function/run.ts
index 2e5ea046c2a..b4efc67d9d7 100644
--- a/packages/app/src/cli/commands/app/function/run.ts
+++ b/packages/app/src/cli/commands/app/function/run.ts
@@ -40,7 +40,7 @@ export default class FunctionRun extends AppUnlinkedCommand {
 
     let functionExport = DEFAULT_FUNCTION_EXPORT
 
-    const app = await localAppContext({
+    const {app} = await localAppContext({
       directory: flags.path,
       userProvidedConfigName: flags.config,
     })
diff --git a/packages/app/src/cli/commands/app/function/typegen.ts b/packages/app/src/cli/commands/app/function/typegen.ts
index 9fd9a738cc4..527c5a1d1bf 100644
--- a/packages/app/src/cli/commands/app/function/typegen.ts
+++ b/packages/app/src/cli/commands/app/function/typegen.ts
@@ -22,7 +22,7 @@ export default class FunctionTypegen extends AppUnlinkedCommand {
   public async run(): Promise<AppUnlinkedCommandOutput> {
     const {flags} = await this.parse(FunctionTypegen)
 
-    const app = await localAppContext({
+    const {app} = await localAppContext({
       directory: flags.path,
       userProvidedConfigName: flags.config,
     })
diff --git a/packages/app/src/cli/commands/app/generate/extension.ts b/packages/app/src/cli/commands/app/generate/extension.ts
index ffb81c0ec65..25629eec374 100644
--- a/packages/app/src/cli/commands/app/generate/extension.ts
+++ b/packages/app/src/cli/commands/app/generate/extension.ts
@@ -77,7 +77,7 @@ export default class AppGenerateExtension extends AppLinkedCommand {
 
     await checkFolderIsValidApp(flags.path)
 
-    const {app, specifications, remoteApp, developerPlatformClient} = await linkedAppContext({
+    const {app, project, specifications, remoteApp, developerPlatformClient} = await linkedAppContext({
       directory: flags.path,
       clientId: flags['client-id'],
       forceRelink: flags.reset,
@@ -92,6 +92,7 @@ export default class AppGenerateExtension extends AppLinkedCommand {
       template: flags.template,
       flavor: flags.flavor,
       app,
+      project,
       specifications,
       remoteApp,
       developerPlatformClient,
diff --git a/packages/app/src/cli/commands/app/info.ts b/packages/app/src/cli/commands/app/info.ts
index c25b331400f..b629828e5d3 100644
--- a/packages/app/src/cli/commands/app/info.ts
+++ b/packages/app/src/cli/commands/app/info.ts
@@ -34,14 +34,14 @@ export default class AppInfo extends AppLinkedCommand {
   public async run(): Promise<AppLinkedCommandOutput> {
     const {flags} = await this.parse(AppInfo)
 
-    const {app, remoteApp, organization, developerPlatformClient} = await linkedAppContext({
+    const {app, project, remoteApp, organization, developerPlatformClient} = await linkedAppContext({
       directory: flags.path,
       clientId: flags['client-id'],
       forceRelink: flags.reset,
       userProvidedConfigName: flags.config,
       unsafeReportMode: true,
     })
-    const results = await info(app, remoteApp, organization, {
+    const results = await info(app, remoteApp, organization, project, {
       format: (flags.json ? 'json' : 'text') as Format,
       webEnv: flags['web-env'],
       configName: flags.config,
diff --git a/packages/app/src/cli/models/app/app.test-data.ts b/packages/app/src/cli/models/app/app.test-data.ts
index 2747cd6c5e7..e963d5964bb 100644
--- a/packages/app/src/cli/models/app/app.test-data.ts
+++ b/packages/app/src/cli/models/app/app.test-data.ts
@@ -74,12 +74,14 @@ import {SchemaDefinitionByTargetQueryVariables} from '../../api/graphql/function
 import {SchemaDefinitionByApiTypeQueryVariables} from '../../api/graphql/functions/generated/schema-definition-by-api-type.js'
 import {AppHomeSpecIdentifier} from '../extensions/specifications/app_config_app_home.js'
 import {AppProxySpecIdentifier} from '../extensions/specifications/app_config_app_proxy.js'
-import {ExtensionSpecification, isAppConfigSpecification} from '../extensions/specification.js'
+import {ExtensionSpecification} from '../extensions/specification.js'
 import {AppLogsOptions} from '../../services/app-logs/utils.js'
 import {AppLogsSubscribeMutationVariables} from '../../api/graphql/app-management/generated/app-logs-subscribe.js'
+import {Project} from '../project/project.js'
 import {Session} from '@shopify/cli-kit/node/session'
 import {vi} from 'vitest'
 import {joinPath} from '@shopify/cli-kit/node/path'
+import {PackageManager} from '@shopify/cli-kit/node/node-package-manager'
 
 export const DEFAULT_CONFIG = {
   application_url: 'https://myapp.com',
@@ -104,9 +106,7 @@ export function testApp(app: Partial<AppInterface> = {}): AppInterface {
     name: app.name ?? 'App',
     directory: app.directory ?? '/tmp/project',
     configPath: app.configPath ?? '/tmp/project/shopify.app.toml',
-    packageManager: app.packageManager ?? 'yarn',
     configuration: app.configuration ?? getConfig(),
-    nodeDependencies: app.nodeDependencies ?? {},
     webs: app.webs ?? [
       {
         directory: '',
@@ -117,7 +117,6 @@ export function testApp(app: Partial<AppInterface> = {}): AppInterface {
       },
     ],
     modules: app.allExtensions ?? [],
-    usesWorkspaces: app.usesWorkspaces ?? false,
     dotenv: app.dotenv,
     errors: app.errors,
     specifications: app.specifications ?? [],
@@ -127,9 +126,6 @@ export function testApp(app: Partial<AppInterface> = {}): AppInterface {
     devApplicationURLs: app.devApplicationURLs,
   })
 
-  if (app.updateDependencies) {
-    Object.getPrototypeOf(newApp).updateDependencies = app.updateDependencies
-  }
   if (app.extensionsForType) {
     Object.getPrototypeOf(newApp).extensionsForType = app.extensionsForType
   }
@@ -155,6 +151,34 @@ export function testAppWithConfig(options?: TestAppWithConfigOptions): AppLinked
   return app
 }
 
+interface TestProjectOptions {
+  directory?: string
+  packageManager?: PackageManager
+  nodeDependencies?: Record<string, string>
+  usesWorkspaces?: boolean
+}
+
+/**
+ * Creates a minimal Project mock for testing.
+ * Use this when a service needs a Project for packageManager, usesWorkspaces, or directory.
+ */
+export function testProject(options: TestProjectOptions = {}): Project {
+  return {
+    directory: options.directory ?? '/tmp/project',
+    packageManager: options.packageManager ?? 'yarn',
+    nodeDependencies: options.nodeDependencies ?? {},
+    usesWorkspaces: options.usesWorkspaces ?? false,
+    appConfigFiles: [],
+    extensionConfigFiles: [],
+    webConfigFiles: [],
+    dotenvFiles: new Map(),
+    hiddenConfigRaw: {},
+    appConfigByName: () => undefined,
+    appConfigByClientId: () => undefined,
+    defaultAppConfig: undefined,
+  } as unknown as Project
+}
+
 export function getWebhookConfig(webhookConfigOverrides?: WebhooksConfig): CurrentAppConfiguration {
   return {
     ...DEFAULT_CONFIG,
@@ -1526,5 +1550,5 @@ export async function buildVersionedAppSchema() {
 }
 
 export async function configurationSpecifications() {
-  return (await loadLocalExtensionsSpecifications()).filter(isAppConfigSpecification)
+  return (await loadLocalExtensionsSpecifications()).filter((spec) => spec.uidStrategy === 'single')
 }
diff --git a/packages/app/src/cli/models/app/app.ts b/packages/app/src/cli/models/app/app.ts
index d5e0edfeb14..6cf75077a34 100644
--- a/packages/app/src/cli/models/app/app.ts
+++ b/packages/app/src/cli/models/app/app.ts
@@ -16,7 +16,7 @@ import {WebhookSubscription} from '../extensions/specifications/types/app_config
 import {joinPath} from '@shopify/cli-kit/node/path'
 import {ZodObjectOf, zod} from '@shopify/cli-kit/node/schema'
 import {DotEnvFile} from '@shopify/cli-kit/node/dot-env'
-import {getDependencies, PackageManager, readAndParsePackageJson} from '@shopify/cli-kit/node/node-package-manager'
+import {readAndParsePackageJson} from '@shopify/cli-kit/node/node-package-manager'
 import {
   fileExistsSync,
   fileRealPath,
@@ -222,11 +222,8 @@ export interface AppInterface<
   TModuleSpec extends ExtensionSpecification = ExtensionSpecification,
 > extends AppConfigurationInterface<TConfig, TModuleSpec> {
   name: string
-  packageManager: PackageManager
   idEnvironmentVariableName: 'SHOPIFY_API_KEY'
-  nodeDependencies: {[key: string]: string}
   webs: Web[]
-  usesWorkspaces: boolean
   dotenv?: DotEnvFile
   allExtensions: ExtensionInstance[]
   realExtensions: ExtensionInstance[]
@@ -236,7 +233,6 @@ export interface AppInterface<
   hiddenConfig: AppHiddenConfig
   includeConfigOnDeploy: boolean | undefined
   readonly devApplicationURLs?: ApplicationURLs
-  updateDependencies: () => Promise<void>
   extensionsForType: (spec: {identifier: string; externalIdentifier: string}) => ExtensionInstance[]
   updateExtensionUUIDS: (uuids: {[key: string]: string}) => void
   preDeployValidation: () => Promise<void>
@@ -264,11 +260,8 @@ type AppConstructor<
   TModuleSpec extends ExtensionSpecification = ExtensionSpecification,
 > = AppConfigurationInterface<TConfig, TModuleSpec> & {
   name: string
-  packageManager: PackageManager
-  nodeDependencies: {[key: string]: string}
   webs: Web[]
   modules: ExtensionInstance[]
-  usesWorkspaces: boolean
   dotenv?: DotEnvFile
   errors?: AppErrors
   specifications: ExtensionSpecification[]
@@ -285,11 +278,8 @@ export class App<
   idEnvironmentVariableName: 'SHOPIFY_API_KEY' = 'SHOPIFY_API_KEY' as const
   directory: string
   configPath: string
-  packageManager: PackageManager
   configuration: TConfig
-  nodeDependencies: {[key: string]: string}
   webs: Web[]
-  usesWorkspaces: boolean
   dotenv?: DotEnvFile
   errors?: AppErrors
   specifications: TModuleSpec[]
@@ -303,12 +293,9 @@ export class App<
     name,
     directory,
     configPath,
-    packageManager,
     configuration,
-    nodeDependencies,
     webs,
     modules,
-    usesWorkspaces,
     dotenv,
     errors,
     specifications,
@@ -320,14 +307,11 @@ export class App<
     this.name = name
     this.directory = directory
     this.configPath = configPath
-    this.packageManager = packageManager
     this.configuration = configuration
-    this.nodeDependencies = nodeDependencies
     this.webs = webs
     this.dotenv = dotenv
     this.realExtensions = modules
     this.errors = errors
-    this.usesWorkspaces = usesWorkspaces
     this.specifications = specifications
     this.configSchema = configSchema ?? AppSchema
     this.remoteFlags = remoteFlags ?? []
@@ -381,11 +365,6 @@ export class App<
     }
   }
 
-  async updateDependencies() {
-    const nodeDependencies = await getDependencies(joinPath(this.directory, 'package.json'))
-    this.nodeDependencies = nodeDependencies
-  }
-
   get hiddenConfig() {
     return this._hiddenConfig
   }
diff --git a/packages/app/src/cli/models/app/loader.test.ts b/packages/app/src/cli/models/app/loader.test.ts
index d5c3c321930..585316f9d2e 100644
--- a/packages/app/src/cli/models/app/loader.test.ts
+++ b/packages/app/src/cli/models/app/loader.test.ts
@@ -24,13 +24,7 @@ import {WebhooksSchema} from '../extensions/specifications/app_config_webhook_sc
 import {WebhooksConfig} from '../extensions/specifications/types/app_config_webhook.js'
 import {Flag} from '../../utilities/developer-platform-client.js'
 import {describe, expect, beforeEach, afterEach, beforeAll, test, vi} from 'vitest'
-import {
-  installNodeModules,
-  yarnLockfile,
-  pnpmLockfile,
-  PackageJson,
-  pnpmWorkspaceFile,
-} from '@shopify/cli-kit/node/node-package-manager'
+import {installNodeModules, PackageJson} from '@shopify/cli-kit/node/node-package-manager'
 import {inTemporaryDirectory, moveFile, mkdir, mkTmpDir, rmdir, writeFile} from '@shopify/cli-kit/node/fs'
 import {joinPath, dirname, cwd, normalizePath} from '@shopify/cli-kit/node/path'
 import {platformAndArch} from '@shopify/cli-kit/node/os'
@@ -39,7 +33,6 @@ import {zod} from '@shopify/cli-kit/node/schema'
 import colors from '@shopify/cli-kit/node/colors'
 import {showMultipleCLIWarningIfNeeded} from '@shopify/cli-kit/node/multiple-installation-warning'
 import {AbortError} from '@shopify/cli-kit/node/error'
-import {captureOutput} from '@shopify/cli-kit/node/system'
 
 vi.mock('../../services/local-storage.js')
 // Mock captureOutput to prevent executing `npm prefix` inside getPackageManager
@@ -354,72 +347,9 @@ describe('load', () => {
     expect(app.name).toBe('config-name')
   })
 
-  test('defaults to npm as the package manager when the configuration is valid', async () => {
-    // Given
-    await writeConfig(appConfiguration)
-    vi.mocked(captureOutput).mockResolvedValue(tmpDir)
-
-    // When
-    const app = await loadTestingApp()
-
-    // Then
-    expect(app.packageManager).toBe('npm')
-  })
-
-  test('defaults to yarn as the package manager when yarn.lock is present, the configuration is valid, and has no blocks', async () => {
-    // Given
-    await writeConfig(appConfiguration)
-    const yarnLockPath = joinPath(tmpDir, yarnLockfile)
-    await writeFile(yarnLockPath, '')
-    vi.mocked(captureOutput).mockResolvedValue(tmpDir)
-
-    // When
-    const app = await loadTestingApp()
-
-    // Then
-    expect(app.packageManager).toBe('yarn')
-  })
-
-  test('defaults to pnpm as the package manager when pnpm lockfile is present, the configuration is valid, and has no blocks', async () => {
-    // Given
-    await writeConfig(appConfiguration)
-    const pnpmLockPath = joinPath(tmpDir, pnpmLockfile)
-    await writeFile(pnpmLockPath, '')
-    vi.mocked(captureOutput).mockResolvedValue(tmpDir)
-
-    // When
-    const app = await loadTestingApp()
-
-    // Then
-    expect(app.packageManager).toBe('pnpm')
-  })
-
-  test("identifies if the app doesn't use workspaces", async () => {
-    // Given
-    await writeConfig(appConfiguration)
-
-    // When
-    const app = await loadTestingApp()
-
-    // Then
-    expect(app.usesWorkspaces).toBe(false)
-  })
-
-  test('identifies if the app uses yarn or npm workspaces', async () => {
-    // Given
-    await writeConfig(appConfiguration, {
-      workspaces: ['packages/*'],
-      name: 'my_app',
-      dependencies: {},
-      devDependencies: {},
-    })
+  // packageManager is now owned by Project and tested in project.test.ts
 
-    // When
-    const app = await loadTestingApp()
-
-    // Then
-    expect(app.usesWorkspaces).toBe(true)
-  })
+  // usesWorkspaces is now owned by Project and tested in project.test.ts
 
   test('checks for multiple CLI installations', async () => {
     // Given
@@ -437,19 +367,6 @@ describe('load', () => {
     expect(showMultipleCLIWarningIfNeeded).toHaveBeenCalled()
   })
 
-  test('identifies if the app uses pnpm workspaces', async () => {
-    // Given
-    await writeConfig(appConfiguration)
-    const pnpmWorkspaceFilePath = joinPath(tmpDir, pnpmWorkspaceFile)
-    await writeFile(pnpmWorkspaceFilePath, '')
-
-    // When
-    const app = await loadTestingApp()
-
-    // Then
-    expect(app.usesWorkspaces).toBe(true)
-  })
-
   test('does not double-count webs defined in workspaces', async () => {
     // Given
     await writeConfig(appConfiguration, {
@@ -474,7 +391,6 @@ describe('load', () => {
     app = await loadTestingApp()
 
     // Then
-    expect(app.usesWorkspaces).toBe(true)
     expect(app.webs.length).toBe(1)
   }, 30000)
 
@@ -2552,9 +2468,6 @@ describe('load', () => {
       },
     })
     expect(reloadedApp.name).toBe(app.name)
-    expect(reloadedApp.packageManager).toBe(app.packageManager)
-    expect(reloadedApp.nodeDependencies).toEqual(app.nodeDependencies)
-    expect(reloadedApp.usesWorkspaces).toBe(app.usesWorkspaces)
   })
 
   test('call app.generateExtensionTypes', async () => {
diff --git a/packages/app/src/cli/models/app/loader.ts b/packages/app/src/cli/models/app/loader.ts
index ff61fdf6cd6..943a2fd6d74 100644
--- a/packages/app/src/cli/models/app/loader.ts
+++ b/packages/app/src/cli/models/app/loader.ts
@@ -287,8 +287,6 @@ export async function loadAppFromContext<TModuleSpec extends ExtensionSpecificat
   if (clientIdOverride) {
     rawConfig.client_id = clientIdOverride
   }
-  delete rawConfig.path
-
   const appVersionedSchema = getAppVersionedSchema(specifications)
   const configSchema = appVersionedSchema as SchemaForConfig<CurrentAppConfiguration>
   const configurationPath = activeConfig.file.path
@@ -352,6 +350,7 @@ export type OpaqueAppLoadResult =
       state: 'loaded-app'
       app: AppInterface
       configuration: CurrentAppConfiguration
+      packageManager: PackageManager
     }
   | {
       state: 'loaded-template'
@@ -393,14 +392,15 @@ export async function loadOpaqueApp(options: {
 }): Promise<OpaqueAppLoadResult> {
   // Try to load the app normally first
   try {
-    const app = await loadApp({
-      directory: options.directory,
-      userProvidedConfigName: options.configName,
+    const {project, activeConfig} = await getAppConfigurationContext(options.directory, options.configName)
+    const app = await loadAppFromContext({
+      project,
+      activeConfig,
       specifications: options.specifications,
       remoteFlags: options.remoteFlags,
       mode: options.mode ?? 'report',
     })
-    return {state: 'loaded-app', app, configuration: app.configuration}
+    return {state: 'loaded-app', app, configuration: app.configuration, packageManager: project.packageManager}
     // eslint-disable-next-line no-catch-all/no-catch-all
   } catch {
     // loadApp failed - try loading as raw template config
@@ -480,14 +480,11 @@ class AppLoader<TConfig extends CurrentAppConfiguration, TModuleSpec extends Ext
     const configName = configuration.name
     const configHandle: string | undefined = configuration.handle
     const name: string = configHandle ?? configName ?? ''
-    const nodeDependencies = this.project.nodeDependencies
-    const packageManager = this.project.packageManager
-    const usesWorkspaces = this.project.usesWorkspaces
 
     const hiddenConfig = await resolveHiddenConfig(this.project, configuration.client_id)
 
     if (!this.reloadState) {
-      await showMultipleCLIWarningIfNeeded(directory, nodeDependencies)
+      await showMultipleCLIWarningIfNeeded(directory, this.project.nodeDependencies)
     }
 
     const {webs, usedCustomLayout: usedCustomLayoutForWeb} = await this.loadWebs(
@@ -499,12 +496,9 @@ class AppLoader<TConfig extends CurrentAppConfiguration, TModuleSpec extends Ext
       name,
       directory,
       configPath,
-      packageManager,
       configuration,
-      nodeDependencies,
       webs,
       modules: extensions,
-      usesWorkspaces,
       dotenv,
       specifications: this.specifications,
       configSchema,
@@ -519,7 +513,7 @@ class AppLoader<TConfig extends CurrentAppConfiguration, TModuleSpec extends Ext
 
     if (!this.errors.isEmpty()) appClass.errors = this.errors
 
-    await logMetadataForLoadedApp(appClass, {
+    await logMetadataForLoadedApp(appClass, this.project.usesWorkspaces, {
       usedCustomLayoutForWeb,
       usedCustomLayoutForExtensions: configuration.extension_directories !== undefined,
     })
@@ -638,7 +632,7 @@ class AppLoader<TConfig extends CurrentAppConfiguration, TModuleSpec extends Ext
   private async loadExtensions(appDirectory: string, appConfiguration: TConfig): Promise<ExtensionInstance[]> {
     if (this.specifications.length === 0) return []
 
-    const extensionPromises = await this.createExtensionInstances(appDirectory, appConfiguration.extension_directories)
+    const extensionPromises = await this.createExtensionInstances(appDirectory)
     const configExtensionPromises = await this.createConfigExtensionInstances(appDirectory, appConfiguration)
 
     const webhookPromises = this.createWebhookSubscriptionInstances(appDirectory, appConfiguration)
@@ -668,7 +662,7 @@ class AppLoader<TConfig extends CurrentAppConfiguration, TModuleSpec extends Ext
     return allExtensions
   }
 
-  private async createExtensionInstances(appDirectory: string, _extensionDirectories?: string[]) {
+  private async createExtensionInstances(appDirectory: string) {
     // Use pre-discovered extension files from Project, filtered by active config
     const activeConfig = this.activeConfigFile
     const extensionFiles = activeConfig
@@ -735,9 +729,9 @@ class AppLoader<TConfig extends CurrentAppConfiguration, TModuleSpec extends Ext
   }
 
   private createWebhookSubscriptionInstances(directory: string, appConfiguration: TConfig) {
+    const configPath = this.loadedConfiguration.configPath
     const specification = this.findSpecificationForType(WebhookSubscriptionSpecIdentifier)
     if (!specification) return []
-    const configPath = this.loadedConfiguration.configPath
     const specConfiguration = parseConfigurationObject(
       WebhooksSchema,
       configPath,
@@ -1016,6 +1010,7 @@ export function isWebType(web: Web, type: WebType): boolean {
 
 async function logMetadataForLoadedApp(
   app: AppInterface,
+  usesWorkspaces: boolean,
   loadingStrategy: {
     usedCustomLayoutForWeb: boolean
     usedCustomLayoutForExtensions: boolean
@@ -1027,7 +1022,6 @@ async function logMetadataForLoadedApp(
   const appName = app.name
   const appDirectory = app.directory
   const sortedAppScopes = getAppScopesArray(app.configuration).sort()
-  const appUsesWorkspaces = app.usesWorkspaces
 
   await logMetadataForLoadedAppUsingRawValues(
     webs,
@@ -1036,7 +1030,7 @@ async function logMetadataForLoadedApp(
     appName,
     appDirectory,
     sortedAppScopes,
-    appUsesWorkspaces,
+    usesWorkspaces,
   )
 }
 
diff --git a/packages/app/src/cli/models/project/project-integration.test.ts b/packages/app/src/cli/models/project/project-integration.test.ts
index f0805cbbc1c..9f895d9c829 100644
--- a/packages/app/src/cli/models/project/project-integration.test.ts
+++ b/packages/app/src/cli/models/project/project-integration.test.ts
@@ -187,22 +187,15 @@ describe('Project integration', () => {
     })
   })
 
-  test('Project metadata matches the old loader metadata', async () => {
+  test('Project loads correct metadata from filesystem', async () => {
     await inTemporaryDirectory(async (dir) => {
       await setupRealApp(dir)
-      const specifications = await loadLocalExtensionsSpecifications()
 
       const project = await Project.load(dir)
-      const app = await loadApp({
-        directory: dir,
-        userProvidedConfigName: undefined,
-        specifications,
-        mode: 'report',
-      })
 
-      expect(project.packageManager).toBe(app.packageManager)
-      expect(project.nodeDependencies).toStrictEqual(app.nodeDependencies)
-      expect(project.usesWorkspaces).toBe(app.usesWorkspaces)
+      expect(project.packageManager).toBe('npm')
+      expect(project.nodeDependencies).toStrictEqual({})
+      expect(project.usesWorkspaces).toBe(false)
     })
   })
 
diff --git a/packages/app/src/cli/services/app-context.test.ts b/packages/app/src/cli/services/app-context.test.ts
index 40b41159915..18753cb4983 100644
--- a/packages/app/src/cli/services/app-context.test.ts
+++ b/packages/app/src/cli/services/app-context.test.ts
@@ -65,10 +65,11 @@ client_id="test-api-key"`
       // Then
       expect(result).toEqual({
         app: expect.objectContaining({
-          configuration: {
+          configPath: normalizePath(joinPath(tmp, 'shopify.app.toml')),
+          configuration: expect.objectContaining({
             client_id: 'test-api-key',
             name: 'test-app',
-          },
+          }),
         }),
         remoteApp: mockRemoteApp,
         developerPlatformClient: expect.any(Object),
@@ -282,14 +283,14 @@ describe('localAppContext', () => {
 
       // Then
       expect(result).toBeDefined()
-      expect(result.name).toEqual(expect.any(String))
-      expect(result.directory).toEqual(normalizePath(tmp))
-      expect(result.configuration).toEqual(
+      expect(result.app.name).toEqual(expect.any(String))
+      expect(result.app.directory).toEqual(normalizePath(tmp))
+      expect(result.app.configuration).toEqual(
         expect.objectContaining({
           name: 'test-app',
         }),
       )
-      expect(result.configPath).toEqual(normalizePath(joinPath(tmp, 'shopify.app.toml')))
+      expect(result.app.configPath).toEqual(normalizePath(joinPath(tmp, 'shopify.app.toml')))
       // Verify no network calls were made
       expect(appFromIdentifiers).not.toHaveBeenCalled()
       expect(fetchOrgFromId).not.toHaveBeenCalled()
@@ -322,12 +323,12 @@ describe('localAppContext', () => {
 
       // Then
       expect(result).toBeDefined()
-      expect(result.configuration).toEqual(
+      expect(result.app.configuration).toEqual(
         expect.objectContaining({
           name: 'test-app-custom',
         }),
       )
-      expect(result.configPath).toEqual(normalizePath(joinPath(tmp, 'shopify.app.custom.toml')))
+      expect(result.app.configPath).toEqual(normalizePath(joinPath(tmp, 'shopify.app.custom.toml')))
     })
   })
 
@@ -427,7 +428,7 @@ describe('localAppContext', () => {
       })
 
       // Then
-      const realExtensions = result.allExtensions.filter((ext) => !ext.isAppConfigExtension)
+      const realExtensions = result.app.allExtensions.filter((ext) => ext.specification.experience !== 'configuration')
       expect(realExtensions).toHaveLength(1)
       expect(realExtensions[0]).toEqual(
         expect.objectContaining({
diff --git a/packages/app/src/cli/services/app-context.ts b/packages/app/src/cli/services/app-context.ts
index bf9bc4144a3..22367657c56 100644
--- a/packages/app/src/cli/services/app-context.ts
+++ b/packages/app/src/cli/services/app-context.ts
@@ -7,7 +7,7 @@ import {addUidToTomlsIfNecessary} from './app/add-uid-to-extension-toml.js'
 import {loadLocalExtensionsSpecifications} from '../models/extensions/load-specifications.js'
 import {Organization, OrganizationApp, OrganizationSource} from '../models/organization.js'
 import {DeveloperPlatformClient} from '../utilities/developer-platform-client.js'
-import {getAppConfigurationContext, loadApp, loadAppFromContext} from '../models/app/loader.js'
+import {getAppConfigurationContext, loadAppFromContext} from '../models/app/loader.js'
 import {RemoteAwareExtensionSpecification} from '../models/extensions/specification.js'
 import {AppLinkedInterface, AppInterface} from '../models/app/app.js'
 import {Project} from '../models/project/project.js'
@@ -87,8 +87,9 @@ export async function linkedAppContext({
   }
 
   // Determine the effective client ID
-  const configClientId = activeConfig.file.content.client_id as string
-  const effectiveClientId = clientId ?? configClientId
+  const configClientId =
+    typeof activeConfig.file.content.client_id === 'string' ? activeConfig.file.content.client_id : ''
+  const effectiveClientId = clientId || configClientId
 
   // Fetch the remote app, using a different clientID if provided via flag.
   if (!remoteApp) {
@@ -146,24 +147,23 @@ async function logMetadata(app: {apiKey: string}, organization: Organization, re
   }))
 }
 
+interface LocalAppContextOutput {
+  app: AppInterface
+  project: Project
+}
+
 /**
  * This function loads an app locally without making any network calls.
  * It uses local specifications and doesn't require the app to be linked.
  *
- * @returns The local app instance.
+ * @returns The local app and project instances.
  */
 export async function localAppContext({
   directory,
   userProvidedConfigName,
-}: LocalAppContextOptions): Promise<AppInterface> {
-  // Load local specifications only
+}: LocalAppContextOptions): Promise<LocalAppContextOutput> {
+  const {project, activeConfig} = await getAppConfigurationContext(directory, userProvidedConfigName)
   const specifications = await loadLocalExtensionsSpecifications()
-
-  // Load the local app using the specifications
-  return loadApp({
-    directory,
-    userProvidedConfigName,
-    specifications,
-    mode: 'local',
-  })
+  const app = await loadAppFromContext({project, activeConfig, specifications, mode: 'local'})
+  return {app, project}
 }
diff --git a/packages/app/src/cli/services/app/config/link.test.ts b/packages/app/src/cli/services/app/config/link.test.ts
index 83a2a57d21d..48e243bdccd 100644
--- a/packages/app/src/cli/services/app/config/link.test.ts
+++ b/packages/app/src/cli/services/app/config/link.test.ts
@@ -1859,6 +1859,7 @@ async function mockLoadOpaqueAppWithApp(
     state: 'loaded-app',
     app: mockedApp,
     configuration: mockedApp.configuration,
+    packageManager: 'yarn',
   })
   // Also mock loadApp for backward compatibility with getAppCreationDefaultsFromLocalApp
   vi.mocked(loadApp).mockResolvedValue(mockedApp)
diff --git a/packages/app/src/cli/services/app/config/link.ts b/packages/app/src/cli/services/app/config/link.ts
index 7d57920934a..52aaf375ebd 100644
--- a/packages/app/src/cli/services/app/config/link.ts
+++ b/packages/app/src/cli/services/app/config/link.ts
@@ -247,7 +247,7 @@ export async function loadLocalAppOptions(
           existingBuildOptions: configuration.build,
           existingConfig: {...configuration},
           appDirectory: app.directory,
-          packageManager: app.packageManager,
+          packageManager: result.packageManager,
         }
       }
       return {
diff --git a/packages/app/src/cli/services/app/env/pull.test.ts b/packages/app/src/cli/services/app/env/pull.test.ts
index 2d9d18e49dd..c8fd46e2488 100644
--- a/packages/app/src/cli/services/app/env/pull.test.ts
+++ b/packages/app/src/cli/services/app/env/pull.test.ts
@@ -100,9 +100,7 @@ describe('env pull', () => {
   })
 })
 
-function mockApp(currentVersion = '2.2.2'): AppInterface {
-  const nodeDependencies: {[key: string]: string} = {}
-  nodeDependencies['@shopify/cli'] = currentVersion
+function mockApp(): AppInterface {
   return testApp({
     name: 'myapp',
     directory: '/',
@@ -116,6 +114,5 @@ function mockApp(currentVersion = '2.2.2'): AppInterface {
       },
       extension_directories: ['extensions/*'],
     },
-    nodeDependencies,
   })
 }
diff --git a/packages/app/src/cli/services/app/env/show.test.ts b/packages/app/src/cli/services/app/env/show.test.ts
index 67225c2811f..7a0a8e3b2f2 100644
--- a/packages/app/src/cli/services/app/env/show.test.ts
+++ b/packages/app/src/cli/services/app/env/show.test.ts
@@ -45,9 +45,7 @@ describe('env show', () => {
   })
 })
 
-function mockApp(currentVersion = '2.2.2'): AppInterface {
-  const nodeDependencies: {[key: string]: string} = {}
-  nodeDependencies['@shopify/cli'] = currentVersion
+function mockApp(): AppInterface {
   return testApp({
     name: 'myapp',
     directory: '/',
@@ -60,6 +58,5 @@ function mockApp(currentVersion = '2.2.2'): AppInterface {
         scopes: 'my-scope',
       },
     },
-    nodeDependencies,
   })
 }
diff --git a/packages/app/src/cli/services/build.ts b/packages/app/src/cli/services/build.ts
index 2e172c78fac..e1b0e597f7a 100644
--- a/packages/app/src/cli/services/build.ts
+++ b/packages/app/src/cli/services/build.ts
@@ -2,19 +2,21 @@ import buildWeb from './web.js'
 import {installAppDependencies} from './dependencies.js'
 import {installJavy} from './function/build.js'
 import {AppInterface, Web} from '../models/app/app.js'
+import {Project} from '../models/project/project.js'
 import {renderConcurrent, renderSuccess} from '@shopify/cli-kit/node/ui'
 import {AbortSignal} from '@shopify/cli-kit/node/abort'
 import {Writable} from 'stream'
 
 interface BuildOptions {
   app: AppInterface
+  project: Project
   skipDependenciesInstallation: boolean
   apiKey?: string
 }
 
 async function build(options: BuildOptions) {
-  if (!options.skipDependenciesInstallation && !options.app.usesWorkspaces) {
-    await installAppDependencies(options.app)
+  if (!options.skipDependenciesInstallation && !options.project.usesWorkspaces) {
+    await installAppDependencies(options.project)
   }
 
   const env: {SHOPIFY_API_KEY?: string} = {}
diff --git a/packages/app/src/cli/services/context.test.ts b/packages/app/src/cli/services/context.test.ts
index 340d205a472..c1c4b257701 100644
--- a/packages/app/src/cli/services/context.test.ts
+++ b/packages/app/src/cli/services/context.test.ts
@@ -22,6 +22,7 @@ import {
   testAppWithConfig,
   testOrganizationApp,
   testThemeExtensions,
+  testProject,
 } from '../models/app/app.test-data.js'
 import metadata from '../metadata.js'
 import {getAppConfigurationFileName, isWebType, loadApp} from '../models/app/loader.js'
@@ -79,6 +80,7 @@ const STORE1: OrganizationStore = {
 const deployOptions = (app: AppLinkedInterface, reset = false, force = false): DeployOptions => {
   return {
     app,
+    project: testProject(),
     remoteApp: APP2,
     organization: ORG1,
     reset,
@@ -416,6 +418,7 @@ describe('ensureDeployContext', () => {
     // When
     const options = {
       app,
+      project: testProject(),
       remoteApp: APP2,
       organization: ORG1,
       reset: false,
@@ -458,6 +461,7 @@ describe('ensureDeployContext', () => {
     // When
     const options = {
       app,
+      project: testProject(),
       remoteApp: APP2,
       organization: ORG1,
       reset: false,
@@ -517,6 +521,7 @@ describe('ensureDeployContext', () => {
     // When
     const result = await ensureDeployContext({
       app,
+      project: testProject(),
       remoteApp: APP2,
       organization: ORG1,
       reset: false,
@@ -563,6 +568,7 @@ describe('ensureDeployContext', () => {
     // When
     const result = await ensureDeployContext({
       app,
+      project: testProject(),
       remoteApp: APP2,
       organization: ORG1,
       reset: false,
diff --git a/packages/app/src/cli/services/dependencies.test.ts b/packages/app/src/cli/services/dependencies.test.ts
index 780ae365d14..363bbe98c25 100644
--- a/packages/app/src/cli/services/dependencies.test.ts
+++ b/packages/app/src/cli/services/dependencies.test.ts
@@ -1,6 +1,5 @@
 import {installAppDependencies} from './dependencies.js'
-import {AppInterface} from '../models/app/app.js'
-import {testApp} from '../models/app/app.test-data.js'
+import {testProject} from '../models/app/app.test-data.js'
 import {describe, expect, test, vi} from 'vitest'
 import {installNPMDependenciesRecursively} from '@shopify/cli-kit/node/node-package-manager'
 import {renderTasks} from '@shopify/cli-kit/node/ui'
@@ -11,10 +10,10 @@ vi.mock('@shopify/cli-kit/node/ui')
 describe('installAppDependencies', () => {
   test('installs dependencies recursively', async () => {
     // Given
-    const app: AppInterface = testApp({updateDependencies: () => Promise.resolve()})
+    const project = testProject({packageManager: 'yarn', directory: '/tmp/project'})
 
     // When
-    await installAppDependencies(app)
+    await installAppDependencies(project)
 
     // Then
     expect(vi.mocked(renderTasks).mock.calls.length).toEqual(1)
diff --git a/packages/app/src/cli/services/dependencies.ts b/packages/app/src/cli/services/dependencies.ts
index 53253be4b37..5ef3b16f0b4 100644
--- a/packages/app/src/cli/services/dependencies.ts
+++ b/packages/app/src/cli/services/dependencies.ts
@@ -1,28 +1,25 @@
-import {AppInterface} from '../models/app/app.js'
+import {Project} from '../models/project/project.js'
 import {installNPMDependenciesRecursively} from '@shopify/cli-kit/node/node-package-manager'
 import {renderTasks} from '@shopify/cli-kit/node/ui'
 
 /**
- * Given an app, it installs its NPM dependencies by traversing
+ * Given a project, it installs its NPM dependencies by traversing
  * the sub-directories and finding the ones that have NPM dependencies
  * defined in package.json files.
- * @param app - App whose dependencies will be installed.
- * @returns An copy of the app with the Node dependencies updated.
+ * @param project - Project whose dependencies will be installed.
  */
-export async function installAppDependencies(app: AppInterface) {
+export async function installAppDependencies(project: Project) {
   const tasks = [
     {
       title: 'Installing dependencies',
       task: async () => {
         await installNPMDependenciesRecursively({
-          packageManager: app.packageManager,
-          directory: app.directory,
+          packageManager: project.packageManager,
+          directory: project.directory,
           deep: 3,
         })
       },
     },
   ]
   await renderTasks(tasks)
-  await app.updateDependencies()
-  return app
 }
diff --git a/packages/app/src/cli/services/deploy.test.ts b/packages/app/src/cli/services/deploy.test.ts
index 3718bc092b6..8a695e91e60 100644
--- a/packages/app/src/cli/services/deploy.test.ts
+++ b/packages/app/src/cli/services/deploy.test.ts
@@ -15,6 +15,7 @@ import {
   testDeveloperPlatformClient,
   testAppLinked,
   testOrganization,
+  testProject,
 } from '../models/app/app.test-data.js'
 import {updateAppIdentifiers} from '../models/app/identifiers.js'
 import {AppInterface, AppLinkedInterface} from '../models/app/app.js'
@@ -614,7 +615,13 @@ describe('deploy', () => {
       nextSteps: [
         [
           'Run',
-          {command: formatPackageManagerCommand(app.packageManager, 'shopify app release', `--version=${versionTag}`)},
+          {
+            command: formatPackageManagerCommand(
+              testProject().packageManager,
+              'shopify app release',
+              `--version=${versionTag}`,
+            ),
+          },
           'to release this version to users.',
         ],
       ],
@@ -650,7 +657,7 @@ describe('deploy', () => {
           title: 'Next steps',
           body: [
             '• Map extension IDs to other copies of your app by running',
-            {command: formatPackageManagerCommand(app.packageManager, 'shopify app deploy')},
+            {command: formatPackageManagerCommand(testProject().packageManager, 'shopify app deploy')},
             'for: ',
             {list: {items: ['shopify.app.prod.toml', 'shopify.app.stg.toml']}},
             "• Commit to source control to ensure your extension IDs aren't regenerated on the next deploy.",
@@ -728,6 +735,7 @@ async function testDeployBundle({
 
   await deploy({
     app,
+    project: testProject(),
     remoteApp,
     organization: testOrganization(),
     reset: false,
diff --git a/packages/app/src/cli/services/deploy.ts b/packages/app/src/cli/services/deploy.ts
index 5cda1effbf9..66848fa8666 100644
--- a/packages/app/src/cli/services/deploy.ts
+++ b/packages/app/src/cli/services/deploy.ts
@@ -5,6 +5,7 @@ import {bundleAndBuildExtensions} from './deploy/bundle.js'
 import {allExtensionTypes, filterOutImportedExtensions, importAllExtensions} from './import-extensions.js'
 import {getExtensions} from './fetch-extensions.js'
 import {AppLinkedInterface} from '../models/app/app.js'
+import {Project} from '../models/project/project.js'
 import {updateAppIdentifiers} from '../models/app/identifiers.js'
 import {DeveloperPlatformClient} from '../utilities/developer-platform-client.js'
 import {Organization, OrganizationApp} from '../models/organization.js'
@@ -23,6 +24,9 @@ export interface DeployOptions {
   /** The app to be built and uploaded */
   app: AppLinkedInterface
 
+  /** The project environment (packageManager, directory, etc.) */
+  project: Project
+
   /** The remote app to be deployed */
   remoteApp: OrganizationApp
 
@@ -277,6 +281,7 @@ export async function deploy(options: DeployOptions) {
 
     await outputCompletionMessage({
       app,
+      project: options.project,
       release,
       uploadExtensionsBundleResult,
       didMigrateExtensionsToDevDash,
@@ -297,11 +302,13 @@ export async function deploy(options: DeployOptions) {
 
 async function outputCompletionMessage({
   app,
+  project,
   release,
   uploadExtensionsBundleResult,
   didMigrateExtensionsToDevDash,
 }: {
   app: AppLinkedInterface
+  project: Project
   release: boolean
   uploadExtensionsBundleResult: UploadExtensionsBundleOutput
   didMigrateExtensionsToDevDash: boolean
@@ -320,7 +327,7 @@ async function outputCompletionMessage({
       body.push(
         '• Map extension IDs to other copies of your app by running',
         {
-          command: formatPackageManagerCommand(app.packageManager, 'shopify app deploy'),
+          command: formatPackageManagerCommand(project.packageManager, 'shopify app deploy'),
         },
         'for: ',
         {
@@ -372,7 +379,7 @@ async function outputCompletionMessage({
         'Run',
         {
           command: formatPackageManagerCommand(
-            app.packageManager,
+            project.packageManager,
             'shopify app release',
             `--version=${uploadExtensionsBundleResult.versionTag}`,
           ),
diff --git a/packages/app/src/cli/services/dev.test.ts b/packages/app/src/cli/services/dev.test.ts
index 781ab61ee2d..c1a7888f892 100644
--- a/packages/app/src/cli/services/dev.test.ts
+++ b/packages/app/src/cli/services/dev.test.ts
@@ -1,5 +1,10 @@
 import {warnIfScopesDifferBeforeDev, blockIfMigrationIncomplete} from './dev.js'
-import {testAppLinked, testDeveloperPlatformClient, testOrganizationApp} from '../models/app/app.test-data.js'
+import {
+  testAppLinked,
+  testDeveloperPlatformClient,
+  testOrganizationApp,
+  testProject,
+} from '../models/app/app.test-data.js'
 import {describe, expect, test, vi} from 'vitest'
 import {mockAndCaptureOutput} from '@shopify/cli-kit/node/testing/output'
 
@@ -33,7 +38,11 @@ describe('warnIfScopesDifferBeforeDev', () => {
     // When
     const mockOutput = mockAndCaptureOutput()
     mockOutput.clear()
-    await warnIfScopesDifferBeforeDev({...apps, developerPlatformClient})
+    await warnIfScopesDifferBeforeDev({
+      ...apps,
+      developerPlatformClient,
+      commandOptions: {project: testProject()} as any,
+    })
 
     // Then
     expect(mockOutput.warn()).toBe('')
@@ -47,7 +56,11 @@ describe('warnIfScopesDifferBeforeDev', () => {
     // When
     const mockOutput = mockAndCaptureOutput()
     mockOutput.clear()
-    await warnIfScopesDifferBeforeDev({...apps, developerPlatformClient})
+    await warnIfScopesDifferBeforeDev({
+      ...apps,
+      developerPlatformClient,
+      commandOptions: {project: testProject()} as any,
+    })
 
     // Then
     expect(mockOutput.warn()).toContain("The scopes in your TOML don't match")
@@ -61,7 +74,11 @@ describe('warnIfScopesDifferBeforeDev', () => {
     // When
     const mockOutput = mockAndCaptureOutput()
     mockOutput.clear()
-    await warnIfScopesDifferBeforeDev({...apps, developerPlatformClient})
+    await warnIfScopesDifferBeforeDev({
+      ...apps,
+      developerPlatformClient,
+      commandOptions: {project: testProject()} as any,
+    })
 
     // Then
     expect(mockOutput.warn()).toBe('')
diff --git a/packages/app/src/cli/services/dev.ts b/packages/app/src/cli/services/dev.ts
index 0b946cb0be3..620d7a86e05 100644
--- a/packages/app/src/cli/services/dev.ts
+++ b/packages/app/src/cli/services/dev.ts
@@ -29,6 +29,7 @@ import {TunnelMode} from './dev/tunnel-mode.js'
 import {PortDetail, renderPortWarnings} from './dev/port-warnings.js'
 import {DeveloperPlatformClient} from '../utilities/developer-platform-client.js'
 import {Web, getAppScopesArray, AppLinkedInterface} from '../models/app/app.js'
+import {Project} from '../models/project/project.js'
 import {Organization, OrganizationApp, OrganizationStore} from '../models/organization.js'
 import {getAnalyticsTunnelType} from '../utilities/analytics.js'
 import metadata from '../metadata.js'
@@ -52,6 +53,7 @@ import {AbortError} from '@shopify/cli-kit/node/error'
 
 export interface DevOptions {
   app: AppLinkedInterface
+  project: Project
   remoteApp: OrganizationApp
   organization: Organization
   specifications: RemoteAwareExtensionSpecification[]
@@ -118,8 +120,8 @@ async function prepareForDev(commandOptions: DevOptions): Promise<DevConfig> {
     await configFile.patch({build: {dev_store_url: store.shopDomain}})
   }
 
-  if (!commandOptions.skipDependenciesInstallation && !app.usesWorkspaces) {
-    await installAppDependencies(app)
+  if (!commandOptions.skipDependenciesInstallation && !commandOptions.project.usesWorkspaces) {
+    await installAppDependencies(commandOptions.project)
   }
 
   const graphiqlPort = commandOptions.graphiqlPort ?? (await getAvailableTCPPort(ports.graphiql))
@@ -198,7 +200,8 @@ export async function warnIfScopesDifferBeforeDev({
   localApp,
   remoteApp,
   developerPlatformClient,
-}: Pick<DevConfig, 'localApp' | 'remoteApp' | 'developerPlatformClient'>) {
+  commandOptions,
+}: Pick<DevConfig, 'localApp' | 'remoteApp' | 'developerPlatformClient' | 'commandOptions'>) {
   if (developerPlatformClient.supportsDevSessions) return
   const localAccess = localApp.configuration.access_scopes
   const remoteAccess = remoteApp.configuration?.access_scopes
@@ -218,7 +221,7 @@ export async function warnIfScopesDifferBeforeDev({
     const nextSteps = [
       [
         'Run',
-        {command: formatPackageManagerCommand(localApp.packageManager, 'shopify app deploy')},
+        {command: formatPackageManagerCommand(commandOptions.project.packageManager, 'shopify app deploy')},
         'to push your scopes to the Partner Dashboard',
       ],
     ]
diff --git a/packages/app/src/cli/services/dev/processes/setup-dev-processes.test.ts b/packages/app/src/cli/services/dev/processes/setup-dev-processes.test.ts
index cad404fc6c6..add3d387079 100644
--- a/packages/app/src/cli/services/dev/processes/setup-dev-processes.test.ts
+++ b/packages/app/src/cli/services/dev/processes/setup-dev-processes.test.ts
@@ -24,6 +24,7 @@ import {
   testAppLinked,
   testOrganization,
   testOrganizationStore,
+  testProject,
 } from '../../../models/app/app.test-data.js'
 import {WebType} from '../../../models/app/app.js'
 import {ensureDeploymentIdsPresence} from '../../context/identifiers.js'
@@ -85,6 +86,7 @@ beforeEach(() => {
 
 const appContextResult = {
   app: testAppLinked(),
+  project: testProject(),
   remoteApp: testOrganizationApp(),
   developerPlatformClient: testDeveloperPlatformClient(),
   organization: testOrganization(),
diff --git a/packages/app/src/cli/services/generate.test.ts b/packages/app/src/cli/services/generate.test.ts
index b84a5dfd548..f9379ae3066 100644
--- a/packages/app/src/cli/services/generate.test.ts
+++ b/packages/app/src/cli/services/generate.test.ts
@@ -9,6 +9,7 @@ import {
   testOrganizationApp,
   testRemoteExtensionTemplates,
   testUIExtension,
+  testProject,
 } from '../models/app/app.test-data.js'
 import {ExtensionInstance} from '../models/extensions/extension-instance.js'
 import generateExtensionPrompts from '../prompts/generate/extension.js'
@@ -60,7 +61,15 @@ describe('generate', () => {
     const outputInfo = await mockSuccessfulCommandExecution('subscription_ui')
 
     // When
-    await generate({directory: '/', reset: false, app, remoteApp, specifications, developerPlatformClient})
+    await generate({
+      directory: '/',
+      reset: false,
+      app,
+      project: testProject(),
+      remoteApp,
+      specifications,
+      developerPlatformClient,
+    })
 
     // Then
     expect(outputInfo.info()).toMatchInlineSnapshot(`
@@ -82,7 +91,15 @@ describe('generate', () => {
     const outputInfo = await mockSuccessfulCommandExecution('theme_app_extension')
 
     // When
-    await generate({directory: '/', reset: false, app, remoteApp, specifications, developerPlatformClient})
+    await generate({
+      directory: '/',
+      reset: false,
+      app,
+      project: testProject(),
+      remoteApp,
+      specifications,
+      developerPlatformClient,
+    })
 
     // Then
     expect(outputInfo.info()).toMatchInlineSnapshot(`
@@ -104,7 +121,15 @@ describe('generate', () => {
     const outputInfo = await mockSuccessfulCommandExecution('product_discounts')
 
     // When
-    await generate({directory: '/', reset: false, app, remoteApp, specifications, developerPlatformClient})
+    await generate({
+      directory: '/',
+      reset: false,
+      app,
+      project: testProject(),
+      remoteApp,
+      specifications,
+      developerPlatformClient,
+    })
 
     // Then
     expect(outputInfo.info()).toMatchInlineSnapshot(`
@@ -129,6 +154,7 @@ describe('generate', () => {
       directory: '/',
       reset: false,
       app,
+      project: testProject(),
       remoteApp,
       specifications,
       developerPlatformClient,
@@ -149,6 +175,7 @@ describe('generate', () => {
       directory: '/',
       reset: false,
       app,
+      project: testProject(),
       remoteApp,
       specifications,
       developerPlatformClient,
@@ -169,6 +196,7 @@ describe('generate', () => {
       directory: '/',
       reset: false,
       app,
+      project: testProject(),
       remoteApp,
       specifications,
       developerPlatformClient,
@@ -188,6 +216,7 @@ describe('generate', () => {
       directory: '/',
       reset: false,
       app,
+      project: testProject(),
       remoteApp,
       specifications,
       developerPlatformClient,
diff --git a/packages/app/src/cli/services/generate.ts b/packages/app/src/cli/services/generate.ts
index 50c6cc5bfd1..e0500470739 100644
--- a/packages/app/src/cli/services/generate.ts
+++ b/packages/app/src/cli/services/generate.ts
@@ -7,6 +7,7 @@ import {
 } from './generate/extension.js'
 import {DeveloperPlatformClient} from '../utilities/developer-platform-client.js'
 import {AppInterface, AppLinkedInterface} from '../models/app/app.js'
+import {Project} from '../models/project/project.js'
 import generateExtensionPrompts, {
   GenerateExtensionPromptOptions,
   GenerateExtensionPromptOutput,
@@ -25,6 +26,7 @@ import {groupBy} from '@shopify/cli-kit/common/collection'
 
 interface GenerateOptions {
   app: AppLinkedInterface
+  project: Project
   specifications: RemoteAwareExtensionSpecification[]
   remoteApp: OrganizationApp
   developerPlatformClient: DeveloperPlatformClient
@@ -54,7 +56,7 @@ async function generate(options: GenerateOptions) {
   const generateExtensionOptions = buildGenerateOptions(promptAnswers, app, options, developerPlatformClient)
   const generatedExtension = await generateExtensionTemplate(generateExtensionOptions)
 
-  renderSuccessMessage(generatedExtension, app.packageManager)
+  renderSuccessMessage(generatedExtension, options.project.packageManager)
 }
 
 async function buildPromptOptions(
@@ -118,6 +120,7 @@ function buildGenerateOptions(
 ): GenerateExtensionTemplateOptions {
   return {
     app,
+    project: options.project,
     cloneUrl: options.cloneUrl,
     extensionChoices: promptAnswers.extensionContent,
     extensionTemplate: promptAnswers.extensionTemplate,
@@ -125,7 +128,7 @@ function buildGenerateOptions(
   }
 }
 
-function renderSuccessMessage(extension: GeneratedExtension, packageManager: AppInterface['packageManager']) {
+function renderSuccessMessage(extension: GeneratedExtension, packageManager: PackageManager) {
   const formattedSuccessfulMessage = formatSuccessfulRunMessage(
     extension.extensionTemplate,
     extension.directory,
diff --git a/packages/app/src/cli/services/generate/extension.test.ts b/packages/app/src/cli/services/generate/extension.test.ts
index 7b7f7d1882b..8c97436e93d 100644
--- a/packages/app/src/cli/services/generate/extension.test.ts
+++ b/packages/app/src/cli/services/generate/extension.test.ts
@@ -17,6 +17,7 @@ import {ExtensionTemplate} from '../../models/app/template.js'
 import {ExtensionSpecification} from '../../models/extensions/specification.js'
 import {loadLocalExtensionsSpecifications} from '../../models/extensions/load-specifications.js'
 import {AppLinkedInterface} from '../../models/app/app.js'
+import {Project} from '../../models/project/project.js'
 import {DeveloperPlatformClient} from '../../utilities/developer-platform-client.js'
 import {describe, expect, vi, test} from 'vitest'
 import * as output from '@shopify/cli-kit/node/output'
@@ -559,6 +560,7 @@ async function createFromTemplate({
   onGetTemplateRepository,
   developerPlatformClient = testDeveloperPlatformClient(),
 }: CreateFromTemplateOptions): Promise<string> {
+  const project = await Project.load(appDirectory)
   const result = await generateExtensionTemplate({
     extensionTemplate: specification,
     app: (await loadApp({
@@ -566,6 +568,7 @@ async function createFromTemplate({
       specifications,
       userProvidedConfigName: undefined,
     })) as AppLinkedInterface,
+    project,
     extensionChoices: {name, flavor: extensionFlavor},
     developerPlatformClient,
     onGetTemplateRepository,
diff --git a/packages/app/src/cli/services/generate/extension.ts b/packages/app/src/cli/services/generate/extension.ts
index 3a47ee52d64..06e89ffd9ae 100644
--- a/packages/app/src/cli/services/generate/extension.ts
+++ b/packages/app/src/cli/services/generate/extension.ts
@@ -1,5 +1,6 @@
 import {configurationFileNames, versions} from '../../constants.js'
 import {AppLinkedInterface} from '../../models/app/app.js'
+import {Project} from '../../models/project/project.js'
 import {buildGraphqlTypes, PREFERRED_FUNCTION_NPM_PACKAGE_MAJOR_VERSION} from '../function/build.js'
 import {GenerateExtensionContentOutput} from '../../prompts/generate/extension.js'
 import {ExtensionFlavor, ExtensionTemplate} from '../../models/app/template.js'
@@ -23,6 +24,7 @@ import {nonRandomUUID} from '@shopify/cli-kit/node/crypto'
 
 export interface GenerateExtensionTemplateOptions {
   app: AppLinkedInterface
+  project: Project
   cloneUrl?: string
   extensionChoices: GenerateExtensionContentOutput
   extensionTemplate: ExtensionTemplate
@@ -69,6 +71,7 @@ interface ExtensionInitOptions {
   directory: string
   url: string
   app: AppLinkedInterface
+  project: Project
   type: string
   name: string
   extensionFlavor: ExtensionFlavor | undefined
@@ -90,6 +93,7 @@ export async function generateExtensionTemplate(
     directory,
     url,
     app: options.app,
+    project: options.project,
     type: options.extensionTemplate.type,
     name: extensionName,
     extensionFlavor,
@@ -147,6 +151,7 @@ async function functionExtensionInit({
   directory,
   url,
   app,
+  project,
   name,
   extensionFlavor,
   onGetTemplateRepository,
@@ -184,15 +189,15 @@ async function functionExtensionInit({
       title: 'Installing additional dependencies',
       task: async () => {
         // We need to run install once to setup the workspace correctly
-        if (app.usesWorkspaces) {
-          await installNodeModules({packageManager: app.packageManager, directory: app.directory})
+        if (project.usesWorkspaces) {
+          await installNodeModules({packageManager: project.packageManager, directory: project.directory})
         }
 
         const requiredDependencies = getFunctionRuntimeDependencies(templateLanguage)
         await addNPMDependenciesIfNeeded(requiredDependencies, {
-          packageManager: app.packageManager,
+          packageManager: project.packageManager,
           type: 'prod',
-          directory: app.usesWorkspaces ? directory : app.directory,
+          directory: project.usesWorkspaces ? directory : project.directory,
         })
       },
     })
@@ -214,6 +219,7 @@ async function uiExtensionInit({
   directory,
   url,
   app,
+  project,
   name,
   extensionFlavor,
   onGetTemplateRepository,
@@ -250,23 +256,23 @@ async function uiExtensionInit({
     {
       title: 'Installing dependencies',
       task: async () => {
-        const packageManager = app.packageManager
-        if (app.usesWorkspaces) {
+        const packageManager = project.packageManager
+        if (project.usesWorkspaces) {
           // Only install dependencies if the extension is javascript
           if (getTemplateLanguage(extensionFlavor?.value) === 'javascript') {
             await installNodeModules({
               packageManager,
-              directory: app.directory,
+              directory: project.directory,
             })
           }
         } else {
-          await addResolutionOrOverrideIfNeeded(app.directory, extensionFlavor?.value)
+          await addResolutionOrOverrideIfNeeded(project.directory, extensionFlavor?.value)
           const extensionPackageJsonPath = joinPath(directory, 'package.json')
           const requiredDependencies = await getProdDependencies(extensionPackageJsonPath)
           await addNPMDependenciesIfNeeded(requiredDependencies, {
             packageManager,
             type: 'prod',
-            directory: app.directory,
+            directory: project.directory,
           })
           await removeFile(extensionPackageJsonPath)
         }
diff --git a/packages/app/src/cli/services/info.test.ts b/packages/app/src/cli/services/info.test.ts
index 35e4758d21e..6edfc42dec8 100644
--- a/packages/app/src/cli/services/info.test.ts
+++ b/packages/app/src/cli/services/info.test.ts
@@ -8,6 +8,7 @@ import {
   testUIExtension,
   testAppConfigExtensions,
   testAppLinked,
+  testProject,
 } from '../models/app/app.test-data.js'
 import {AppErrors} from '../models/app/loader.js'
 import {DeveloperPlatformClient} from '../utilities/developer-platform-client.js'
@@ -87,7 +88,10 @@ describe('info', () => {
       vi.mocked(selectOrganizationPrompt).mockResolvedValue(ORG1)
 
       // When
-      const result = (await info(app, remoteApp, ORG1, {...infoOptions(), webEnv: true})) as OutputMessage
+      const result = (await info(app, remoteApp, ORG1, testProject(), {
+        ...infoOptions(),
+        webEnv: true,
+      })) as OutputMessage
 
       // Then
       expect(unstyled(stringifyMessage(result))).toMatchInlineSnapshot(`
@@ -107,7 +111,7 @@ describe('info', () => {
       vi.mocked(selectOrganizationPrompt).mockResolvedValue(ORG1)
 
       // When
-      const result = (await info(app, remoteApp, ORG1, {
+      const result = (await info(app, remoteApp, ORG1, testProject(), {
         ...infoOptions(),
         format: 'json',
         webEnv: true,
@@ -159,7 +163,7 @@ describe('info', () => {
       vi.mocked(selectOrganizationPrompt).mockResolvedValue(ORG1)
 
       // When
-      const result = (await info(app, remoteApp, ORG1, infoOptions())) as AlertCustomSection[]
+      const result = (await info(app, remoteApp, ORG1, testProject(), infoOptions())) as AlertCustomSection[]
       const uiData = tabularDataSectionFromInfo(result, 'ui_extension_external')
       const checkoutData = tabularDataSectionFromInfo(result, 'checkout_ui_extension_external')
 
@@ -207,7 +211,7 @@ describe('info', () => {
       vi.mocked(selectOrganizationPrompt).mockResolvedValue(ORG1)
 
       // When
-      const result = (await info(app, remoteApp, ORG1, infoOptions())) as AlertCustomSection[]
+      const result = (await info(app, remoteApp, ORG1, testProject(), infoOptions())) as AlertCustomSection[]
       const uiExtensionsData = tabularDataSectionFromInfo(result, 'ui_extension_external')
       const relevantExtension = extensionTitleRow(uiExtensionsData, 'handle-for-extension-1')
       const irrelevantExtension = extensionTitleRow(uiExtensionsData, 'point_of_sale')
@@ -241,7 +245,11 @@ describe('info', () => {
       vi.mocked(selectOrganizationPrompt).mockResolvedValue(ORG1)
 
       // When
-      const result = await info(app, remoteApp, ORG1, {format: 'json', webEnv: false, developerPlatformClient})
+      const result = await info(app, remoteApp, ORG1, testProject(), {
+        format: 'json',
+        webEnv: false,
+        developerPlatformClient,
+      })
 
       // Then
       expect(result).toBeInstanceOf(TokenizedString)
@@ -249,24 +257,25 @@ describe('info', () => {
       const extensionsIdentifiers = resultObject.allExtensions.map((extension) => extension.localIdentifier)
       expect(extensionsIdentifiers).toContain('handle-for-extension-1')
       expect(extensionsIdentifiers).not.toContain('point_of_sale')
+
+      // Verify backward-compat: project fields injected into JSON output
+      const rawResult = JSON.parse((result as TokenizedString).value)
+      expect(rawResult.packageManager).toBe('yarn')
+      expect(rawResult.nodeDependencies).toEqual({})
+      expect(rawResult.usesWorkspaces).toBe(false)
     })
   })
 })
 
 function mockApp({
   directory,
-  currentVersion = '2.2.2',
   configContents = 'scopes = "read_products"',
   app,
 }: {
   directory: string
-  currentVersion?: string
   configContents?: string
   app?: Partial<AppInterface>
 }): AppLinkedInterface {
-  const nodeDependencies: {[key: string]: string} = {}
-  nodeDependencies['@shopify/cli'] = currentVersion
-
   writeFileSync(joinPath(directory, 'shopify.app.toml'), configContents)
 
   return testAppLinked({
@@ -283,7 +292,6 @@ function mockApp({
       },
       extension_directories: ['extensions/*'],
     },
-    nodeDependencies,
     ...(app ? app : {}),
   })
 }
diff --git a/packages/app/src/cli/services/info.ts b/packages/app/src/cli/services/info.ts
index 3b2718a6629..7b2e8985cba 100644
--- a/packages/app/src/cli/services/info.ts
+++ b/packages/app/src/cli/services/info.ts
@@ -1,6 +1,7 @@
 import {outputEnv} from './app/env/show.js'
 import {DeveloperPlatformClient} from '../utilities/developer-platform-client.js'
 import {AppLinkedInterface, getAppScopes} from '../models/app/app.js'
+import {Project} from '../models/project/project.js'
 import {configurationFileNames} from '../constants.js'
 import {ExtensionInstance} from '../models/extensions/extension-instance.js'
 import {Organization, OrganizationApp} from '../models/organization.js'
@@ -30,12 +31,13 @@ export async function info(
   app: AppLinkedInterface,
   remoteApp: OrganizationApp,
   organization: Organization,
+  project: Project,
   options: InfoOptions,
 ): Promise<OutputMessage | AlertCustomSection[]> {
   if (options.webEnv) {
     return infoWeb(app, remoteApp, organization, options)
   } else {
-    return infoApp(app, remoteApp, options)
+    return infoApp(app, remoteApp, project, options)
   }
 }
 
@@ -51,12 +53,16 @@ async function infoWeb(
 async function infoApp(
   app: AppLinkedInterface,
   remoteApp: OrganizationApp,
+  project: Project,
   options: InfoOptions,
 ): Promise<OutputMessage | AlertCustomSection[]> {
   if (options.format === 'json') {
     const extensionsInfo = withPurgedSchemas(app.allExtensions.filter((ext) => ext.isReturnedAsInfo()))
     let appWithSupportedExtensions = {
       ...app,
+      packageManager: project.packageManager,
+      nodeDependencies: project.nodeDependencies,
+      usesWorkspaces: project.usesWorkspaces,
       allExtensions: extensionsInfo,
     }
     if ('realExtensions' in appWithSupportedExtensions) {
@@ -82,7 +88,7 @@ async function infoApp(
       2,
     )}`
   } else {
-    const appInfo = new AppInfo(app, remoteApp, options)
+    const appInfo = new AppInfo(app, remoteApp, project, options)
     return appInfo.output()
   }
 }
@@ -114,11 +120,13 @@ const NOT_LOADED_TEXT = 'NOT LOADED'
 class AppInfo {
   private readonly app: AppLinkedInterface
   private readonly remoteApp: OrganizationApp
+  private readonly project: Project
   private readonly options: InfoOptions
 
-  constructor(app: AppLinkedInterface, remoteApp: OrganizationApp, options: InfoOptions) {
+  constructor(app: AppLinkedInterface, remoteApp: OrganizationApp, project: Project, options: InfoOptions) {
     this.app = app
     this.remoteApp = remoteApp
+    this.project = project
     this.options = options
   }
 
@@ -165,7 +173,7 @@ class AppInfo {
       {
         body: [
           '💡 To change these, run',
-          {command: formatPackageManagerCommand(this.app.packageManager, 'shopify app config link')},
+          {command: formatPackageManagerCommand(this.project.packageManager, 'shopify app config link')},
         ],
       },
     ]
@@ -266,7 +274,7 @@ class AppInfo {
     const {platform, arch} = platformAndArch()
     return this.tableSection('Tooling and System', [
       ['Shopify CLI', CLI_KIT_VERSION],
-      ['Package manager', this.app.packageManager],
+      ['Package manager', this.project.packageManager],
       ['OS', `${platform}-${arch}`],
       ['Shell', process.env.SHELL ?? 'unknown'],
       ['Node version', process.version],