Serialize UUID for non-library modules (#9057)

Missing ID's in IR meant that instrumentation wouldn't be applied for loaded modules. This is the reason why after a restart engine wouldn't send **any** expression updates.

Closes #8689.

# Important Notes
After the change
[Kazam_screencast_00038.webm](https://github.com/enso-org/enso/assets/292128/4249287b-6c41-4c9d-b138-e7af59512566)

The video somehow doesn't show that all nodes are loaded after the restart, but once I moved the screen they are there. This appears to be a bug in the recording somehow.

engine/runtime-compiler/src/main/scala/org/enso/compiler/data/BindingsMap.scala

@@ -23,7 +23,7 @@ import scala.annotation.unused
   */
 
 @SerialVersionUID(
-  8160L // Use BindingsMap
+  9057L // Use BindingsMap
 )
 case class BindingsMap(
   definedEntities: List[DefinedEntity],

engine/runtime-parser/src/main/java/org/enso/compiler/core/IR.java

@@ -30,7 +30,7 @@ import scala.collection.immutable.List;
  */
 public interface IR extends Serializable {
 
-  long serialVersionUID = 8145L; // Scala to Java
+  long serialVersionUID = 9057L; // Scala to Java
 
   /**
    * Storage for metadata that the node has been tagged with as the result of various compiler

engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Module.scala

@@ -20,7 +20,7 @@ import java.util.UUID
   * @param diagnostics compiler diagnostics for this node
   */
 @SerialVersionUID(
-  8160L // Use BindingsMap
+  9057L // Use BindingsMap
 )       // prevents reading broken caches, see PR-3692 for details
 final case class Module(
   imports: List[Import],

engine/runtime/src/main/java/org/enso/interpreter/caches/CacheUtils.java

@@ -1,5 +1,6 @@
 package org.enso.interpreter.caches;
 
+import com.oracle.truffle.api.TruffleFile;
 import java.io.IOException;
 import java.nio.ByteBuffer;
 import java.security.MessageDigest;
@@ -8,40 +9,38 @@ import java.util.Comparator;
 import java.util.List;
 import java.util.UUID;
 import java.util.function.Function;
-
 import org.enso.compiler.context.CompilerContext;
 import org.enso.compiler.core.ir.ProcessingPass;
 import org.enso.pkg.SourceFile;
 import org.enso.text.Hex;
 
-import com.oracle.truffle.api.TruffleFile;
-
 final class CacheUtils {
-  private CacheUtils() {
-  }
+  private CacheUtils() {}
 
-  static Function<Object, Object> writeReplace(CompilerContext context) {
-    return (obj) -> switch (obj) {
-      case ProcessingPass.Metadata metadata -> metadata.prepareForSerialization(context);
-      case UUID _ -> null;
-      case null -> null;
-      default -> obj;
-    };
+  static Function<Object, Object> writeReplace(CompilerContext context, boolean keepUUIDs) {
+    return (obj) ->
+        switch (obj) {
+          case ProcessingPass.Metadata metadata -> metadata.prepareForSerialization(context);
+          case UUID id -> keepUUIDs ? id : null;
+          case null -> null;
+          default -> obj;
+        };
   }
 
   static Function<Object, Object> readResolve(CompilerContext context) {
-    return (obj) -> switch (obj) {
-      case ProcessingPass.Metadata metadata -> {
-        var option = metadata.restoreFromSerialization(context);
-        if (option.nonEmpty()) {
-          yield option.get();
-        } else {
-          throw raise(RuntimeException.class, new IOException("Cannot convert " + metadata));
-        }
-      }
-      case null -> null;
-      default -> obj;
-    };
+    return (obj) ->
+        switch (obj) {
+          case ProcessingPass.Metadata metadata -> {
+            var option = metadata.restoreFromSerialization(context);
+            if (option.nonEmpty()) {
+              yield option.get();
+            } else {
+              throw raise(RuntimeException.class, new IOException("Cannot convert " + metadata));
+            }
+          }
+          case null -> null;
+          default -> obj;
+        };
   }
 
   /**
@@ -75,9 +74,7 @@ final class CacheUtils {
    * @param pkgSources the list of package sources
    * @return string representation of bytes' hash
    */
-  static final String computeDigestOfLibrarySources(
-    List<SourceFile<TruffleFile>> pkgSources
-  ) {
+  static final String computeDigestOfLibrarySources(List<SourceFile<TruffleFile>> pkgSources) {
     pkgSources.sort(Comparator.comparing(o -> o.qualifiedName().toString()));
 
     try {
@@ -95,5 +92,4 @@ final class CacheUtils {
   static <T extends Exception> T raise(Class<T> cls, Exception e) throws T {
     throw (T) e;
   }
-
 }

engine/runtime/src/main/java/org/enso/interpreter/caches/ImportExportCache.java

@@ -65,7 +65,7 @@ public final class ImportExportCache
   public byte[] serialize(EnsoContext context, CachedBindings entry) throws IOException {
     var arr =
         Persistance.write(
-            entry.bindings(), CacheUtils.writeReplace(context.getCompiler().context()));
+            entry.bindings(), CacheUtils.writeReplace(context.getCompiler().context(), false));
     return arr;
   }
 

engine/runtime/src/main/java/org/enso/interpreter/caches/ModuleCache.java

@@ -60,7 +60,7 @@ public final class ModuleCache
   public byte[] serialize(EnsoContext context, CachedModule entry) throws IOException {
     var arr =
         Persistance.write(
-            entry.moduleIR(), CacheUtils.writeReplace(context.getCompiler().context()));
+            entry.moduleIR(), CacheUtils.writeReplace(context.getCompiler().context(), true));
     return arr;
   }