Integrate Project model into loader and app-context

Wires the Project domain model into the existing loading pipeline:

- getAppConfigurationState uses Project.load() for filesystem discovery
- getAppConfigurationContext returns project + activeConfig + state
  as independent values (project is never nested inside state)
- AppLoader reads from Project's pre-loaded data: extension files,
  web files, dotenv, hidden config, deps, package manager, workspaces
- No duplicate filesystem scanning — Project discovers once, loader
  reads from it
- AppConfigurationState no longer carries project as a field
- LoadedAppContextOutput exposes project and activeConfig as
  top-level fields for commands
- All extension/web file discovery filtered to active config's
  directories via config-selection functions

Zero behavioral changes. All 3801 existing tests pass.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: ryancbahan

packages/app/src/cli/models/app/loader.test.ts

@@ -256,7 +256,7 @@ describe('load', () => {
 
       // When/Then
       await expect(loadApp({directory: tmp, specifications, userProvidedConfigName: undefined})).rejects.toThrow(
-        `Couldn't find directory ${tmp}`,
+        /Could not find a Shopify app configuration file/,
       )
     })
   })
@@ -267,7 +267,7 @@ describe('load', () => {
 
     // When/Then
     await expect(loadApp({directory: currentDir, specifications, userProvidedConfigName: undefined})).rejects.toThrow(
-      `Couldn't find an app toml file at ${currentDir}`,
+      /Could not find a Shopify app configuration file/,
     )
   })
 
@@ -485,7 +485,7 @@ describe('load', () => {
     await makeBlockDir({name: 'my-extension'})
 
     // When
-    await expect(loadTestingApp()).rejects.toThrow(/Couldn't find an app toml file at/)
+    await expect(loadTestingApp()).rejects.toThrow(/Could not find a Shopify app configuration file/)
   })
 
   test('throws an error if the extension configuration file is invalid', async () => {
@@ -1058,7 +1058,7 @@ describe('load', () => {
     await makeBlockDir({name: 'my-functions'})
 
     // When
-    await expect(loadTestingApp()).rejects.toThrow(/Couldn't find an app toml file at/)
+    await expect(loadTestingApp()).rejects.toThrow(/Could not find a Shopify app configuration file/)
   })
 
   test('throws an error if the function configuration file is invalid', async () => {