Serialization: Bring back shadowing but only after the filtering

lib/Serialization/Deserialization.cpp

@@ -2766,6 +2766,12 @@ ModuleFile::resolveCrossReference(ModuleID MID, uint32_t pathLen) {
   if (M)
     return diagnoseFatal();
 
+  if (values.size() > 1) {
+    // Apply shadowing filtering after other local filters so we don't rule out
+    // valid candidates shadowed by invalid ones.
+    removeShadowedDecls(values, baseModule);
+  }
+
   // When all is said and done, we should have a single value here to return.
   if (values.size() != 1) {
     return llvm::make_error<XRefError>("result is ambiguous", pathTrace,

test/Serialization/shadowed-class-vs-protocol.swift

@@ -0,0 +1,50 @@
+/// Ensure cross references to shadowed decls take into account the shadowing
+/// after the custom deserialization filtering.
+
+// RUN: %empty-directory(%t)
+// RUN: split-file %s %t
+// REQUIRES: objc_interop
+
+// RUN: %target-swift-frontend(mock-sdk: %clang-importer-sdk) \
+// RUN:   %t/SwiftLib.swift -I %t -emit-module-path %t/SwiftLib.swiftmodule
+// RUN: %target-swift-frontend(mock-sdk: %clang-importer-sdk) \
+// RUN:   -typecheck %t/Client.swift -I %t
+
+//--- module.modulemap
+module RootLib {
+  header "RootLib.h"
+}
+
+module MiddleLib {
+  header "MiddleLib.h"
+  export *
+}
+
+//--- RootLib.h
+__attribute__((swift_name("ShadowedProtocol")))
+@protocol Shadowed
+@end
+
+//--- MiddleLib.h
+@import Foundation;
+#include "RootLib.h"
+
+@interface Shadowed: NSObject <Shadowed>
+@end
+
+//--- SwiftLib.swift
+import MiddleLib
+
+public func funcRef() -> Shadowed { fatalError() }
+
+extension Shadowed {
+    public func method() -> Shadowed { fatalError() }
+}
+
+//--- Client.swift
+import SwiftLib
+
+@inlinable
+public func bar() {
+    let _ = funcRef().method()
+}