diff --git a/Packages/src/Cli~/src/__tests__/package-metadata.test.ts b/Packages/src/Cli~/src/__tests__/package-metadata.test.ts
index de5f92e22..ee9820dd1 100644
--- a/Packages/src/Cli~/src/__tests__/package-metadata.test.ts
+++ b/Packages/src/Cli~/src/__tests__/package-metadata.test.ts
@@ -23,6 +23,33 @@ type AssemblyDefinition = {
 
 const TEST_FRAMEWORK_PACKAGE_NAME = 'com.unity.test-framework';
 const TEST_FRAMEWORK_DEFINE = 'ULOOPMCP_HAS_TEST_FRAMEWORK';
+const METADATA_VALIDATION_DEPENDENCY_META_PATHS = [
+  'Editor/MetadataValidation/Dependencies/uLoopMCP.System.Collections.Immutable.dll.meta',
+  'Editor/MetadataValidation/Dependencies/uLoopMCP.System.Reflection.Metadata.dll.meta',
+  'Editor/MetadataValidation/Dependencies/uLoopMCP.System.Runtime.CompilerServices.Unsafe.dll.meta',
+] as const;
+const METADATA_VALIDATION_PRIVATE_ASSEMBLIES = [
+  {
+    relativePath:
+      'Editor/MetadataValidation/Dependencies/uLoopMCP.System.Collections.Immutable.dll',
+    assemblyName: 'uLoopMCP.System.Collections.Immutable',
+    assemblyReferences: ['uLoopMCP.System.Runtime.CompilerServices.Unsafe'],
+  },
+  {
+    relativePath: 'Editor/MetadataValidation/Dependencies/uLoopMCP.System.Reflection.Metadata.dll',
+    assemblyName: 'uLoopMCP.System.Reflection.Metadata',
+    assemblyReferences: [
+      'uLoopMCP.System.Collections.Immutable',
+      'uLoopMCP.System.Runtime.CompilerServices.Unsafe',
+    ],
+  },
+  {
+    relativePath:
+      'Editor/MetadataValidation/Dependencies/uLoopMCP.System.Runtime.CompilerServices.Unsafe.dll',
+    assemblyName: 'uLoopMCP.System.Runtime.CompilerServices.Unsafe',
+    assemblyReferences: [],
+  },
+] as const;
 
 function loadPackageManifest(): PackageManifest {
   const packageJsonPath = join(__dirname, '..', '..', 'package.json');
@@ -45,6 +72,18 @@ function loadEditorAssemblyDefinition(): AssemblyDefinition {
   return JSON.parse(asmdefText) as AssemblyDefinition;
 }
 
+function loadUnityPackageText(relativePath: string): string {
+  const assetPath = join(__dirname, '..', '..', '..', relativePath);
+  // eslint-disable-next-line security/detect-non-literal-fs-filename
+  return readFileSync(assetPath, 'utf8');
+}
+
+function loadUnityPackageBytes(relativePath: string): Buffer {
+  const assetPath = join(__dirname, '..', '..', '..', relativePath);
+  // eslint-disable-next-line security/detect-non-literal-fs-filename
+  return readFileSync(assetPath);
+}
+
 describe('package metadata', () => {
   it('avoids bin target prefixes that npm normalizes during publish', () => {
     const packageManifest = loadPackageManifest();
@@ -75,4 +114,27 @@ describe('package metadata', () => {
       }),
     );
   });
+
+  it('keeps bundled metadata validation dependencies out of implicit project references', () => {
+    for (const metaPath of METADATA_VALIDATION_DEPENDENCY_META_PATHS) {
+      const metaText = loadUnityPackageText(metaPath);
+
+      expect(metaText).toContain('isExplicitlyReferenced: 1');
+    }
+  });
+
+  it('uses private assembly identities for metadata validation dependencies', () => {
+    for (const assembly of METADATA_VALIDATION_PRIVATE_ASSEMBLIES) {
+      const dllBytes = loadUnityPackageBytes(assembly.relativePath);
+
+      expect(dllBytes.includes(Buffer.from(assembly.assemblyName))).toBe(true);
+      for (const assemblyReference of assembly.assemblyReferences) {
+        expect(dllBytes.includes(Buffer.from(assemblyReference))).toBe(true);
+      }
+    }
+  });
+
+  it('does not keep orphaned plugin folder metadata', () => {
+    expect(() => loadUnityPackageText('Plugins.meta')).toThrow();
+  });
 });
diff --git a/Packages/src/Plugins.meta b/Packages/src/Editor/MetadataValidation/Dependencies.meta
similarity index 77%
rename from Packages/src/Plugins.meta
rename to Packages/src/Editor/MetadataValidation/Dependencies.meta
index 5f3a8083a..4b430975f 100644
--- a/Packages/src/Plugins.meta
+++ b/Packages/src/Editor/MetadataValidation/Dependencies.meta
@@ -1,5 +1,5 @@
 fileFormatVersion: 2
-guid: 216dff41199af460685390e0306583dc
+guid: 1650e75bb20ee4fffb2b799dec3cdcf8
 folderAsset: yes
 DefaultImporter:
   externalObjects: {}
diff --git a/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Collections.Immutable.dll b/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Collections.Immutable.dll
new file mode 100644
index 000000000..7b2498cc9
Binary files /dev/null and b/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Collections.Immutable.dll differ
diff --git a/Packages/src/Plugins/CodeAnalysis/System.Collections.Immutable.dll.meta b/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Collections.Immutable.dll.meta
similarity index 95%
rename from Packages/src/Plugins/CodeAnalysis/System.Collections.Immutable.dll.meta
rename to Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Collections.Immutable.dll.meta
index 4edf008b1..de331eca7 100644
--- a/Packages/src/Plugins/CodeAnalysis/System.Collections.Immutable.dll.meta
+++ b/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Collections.Immutable.dll.meta
@@ -8,7 +8,7 @@ PluginImporter:
   defineConstraints: []
   isPreloaded: 0
   isOverridable: 1
-  isExplicitlyReferenced: 0
+  isExplicitlyReferenced: 1
   validateReferences: 1
   platformData:
   - first:
diff --git a/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Reflection.Metadata.dll b/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Reflection.Metadata.dll
new file mode 100644
index 000000000..472779dfc
Binary files /dev/null and b/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Reflection.Metadata.dll differ
diff --git a/Packages/src/Plugins/CodeAnalysis/System.Reflection.Metadata.dll.meta b/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Reflection.Metadata.dll.meta
similarity index 95%
rename from Packages/src/Plugins/CodeAnalysis/System.Reflection.Metadata.dll.meta
rename to Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Reflection.Metadata.dll.meta
index 28f6b86c5..26f38e959 100644
--- a/Packages/src/Plugins/CodeAnalysis/System.Reflection.Metadata.dll.meta
+++ b/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Reflection.Metadata.dll.meta
@@ -8,7 +8,7 @@ PluginImporter:
   defineConstraints: []
   isPreloaded: 0
   isOverridable: 1
-  isExplicitlyReferenced: 0
+  isExplicitlyReferenced: 1
   validateReferences: 1
   platformData:
   - first:
diff --git a/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Runtime.CompilerServices.Unsafe.dll b/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Runtime.CompilerServices.Unsafe.dll
new file mode 100644
index 000000000..d0f5b6c04
Binary files /dev/null and b/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Runtime.CompilerServices.Unsafe.dll differ
diff --git a/Packages/src/Plugins/CodeAnalysis/System.Runtime.CompilerServices.Unsafe.dll.meta b/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Runtime.CompilerServices.Unsafe.dll.meta
similarity index 95%
rename from Packages/src/Plugins/CodeAnalysis/System.Runtime.CompilerServices.Unsafe.dll.meta
rename to Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Runtime.CompilerServices.Unsafe.dll.meta
index 97ecb26fd..77a7e2719 100644
--- a/Packages/src/Plugins/CodeAnalysis/System.Runtime.CompilerServices.Unsafe.dll.meta
+++ b/Packages/src/Editor/MetadataValidation/Dependencies/uLoopMCP.System.Runtime.CompilerServices.Unsafe.dll.meta
@@ -8,7 +8,7 @@ PluginImporter:
   defineConstraints: []
   isPreloaded: 0
   isOverridable: 1
-  isExplicitlyReferenced: 0
+  isExplicitlyReferenced: 1
   validateReferences: 1
   platformData:
   - first:
diff --git a/Packages/src/Editor/MetadataValidation/uLoopMCP.Editor.MetadataValidation.asmdef b/Packages/src/Editor/MetadataValidation/uLoopMCP.Editor.MetadataValidation.asmdef
index f9e3f533b..cb47c086b 100644
--- a/Packages/src/Editor/MetadataValidation/uLoopMCP.Editor.MetadataValidation.asmdef
+++ b/Packages/src/Editor/MetadataValidation/uLoopMCP.Editor.MetadataValidation.asmdef
@@ -11,9 +11,9 @@
     "allowUnsafeCode": false,
     "overrideReferences": true,
     "precompiledReferences": [
-        "System.Collections.Immutable.dll",
-        "System.Runtime.CompilerServices.Unsafe.dll",
-        "System.Reflection.Metadata.dll"
+        "uLoopMCP.System.Collections.Immutable.dll",
+        "uLoopMCP.System.Runtime.CompilerServices.Unsafe.dll",
+        "uLoopMCP.System.Reflection.Metadata.dll"
     ],
     "autoReferenced": true,
     "defineConstraints": [],
diff --git a/Packages/src/Plugins/CodeAnalysis.meta b/Packages/src/Plugins/CodeAnalysis.meta
deleted file mode 100644
index d79e38e77..000000000
--- a/Packages/src/Plugins/CodeAnalysis.meta
+++ /dev/null
@@ -1,8 +0,0 @@
-fileFormatVersion: 2
-guid: d3f5f7720247b4c0e96b55df9c13bfe8
-folderAsset: yes
-DefaultImporter:
-  externalObjects: {}
-  userData: 
-  assetBundleName: 
-  assetBundleVariant: 
diff --git a/Packages/src/Plugins/CodeAnalysis/System.Collections.Immutable.dll b/Packages/src/Plugins/CodeAnalysis/System.Collections.Immutable.dll
deleted file mode 100644
index ad944dff1..000000000
Binary files a/Packages/src/Plugins/CodeAnalysis/System.Collections.Immutable.dll and /dev/null differ
diff --git a/Packages/src/Plugins/CodeAnalysis/System.Reflection.Metadata.dll b/Packages/src/Plugins/CodeAnalysis/System.Reflection.Metadata.dll
deleted file mode 100644
index 34d543160..000000000
Binary files a/Packages/src/Plugins/CodeAnalysis/System.Reflection.Metadata.dll and /dev/null differ
diff --git a/Packages/src/Plugins/CodeAnalysis/System.Runtime.CompilerServices.Unsafe.dll b/Packages/src/Plugins/CodeAnalysis/System.Runtime.CompilerServices.Unsafe.dll
deleted file mode 100644
index 070abc296..000000000
Binary files a/Packages/src/Plugins/CodeAnalysis/System.Runtime.CompilerServices.Unsafe.dll and /dev/null differ