diff --git a/docs/language-server/protocol-language-server.md b/docs/language-server/protocol-language-server.md
index 60b84deeec..75994d1bb4 100644
--- a/docs/language-server/protocol-language-server.md
+++ b/docs/language-server/protocol-language-server.md
@@ -28,6 +28,8 @@ transport formats, please look [here](./protocol-architecture).
   - [`SuggestionEntryArgument`](#suggestionentryargument)
   - [`SuggestionEntry`](#suggestionentry)
   - [`SuggestionEntryType`](#suggestionentrytype)
+  - [`SuggestionId`](#suggestionid)
+  - [`SuggestionsDatabaseEntry`](#suggestionsdatabaseentry)
   - [`SuggestionsDatabaseUpdate`](#suggestionsdatabaseupdate)
   - [`File`](#file)
   - [`DirectoryTree`](#directorytree)
@@ -203,8 +205,13 @@ Points to a method definition.
 
 ```typescript
 interface MethodPointer {
-  file: Path;
+  /** The fully qualified module name. */
+  module: String;
+
+  /** The type on which the method is defined. */
   definedOnType: String;
+
+  /** The method name. */
   name: String;
 }
 ```
@@ -216,8 +223,11 @@ interface ExpressionValueUpdate {
   /** The id of updated expression */
   expressionId: ExpressionId;
 
-  /** The updated suggestion id */
-  suggestionId: number;
+  /** The updated type of the expression */
+  type?: String;
+
+  /** The updated pointer to the method call */
+  methodPointer?: SuggestionId;
 }
 ```
 
@@ -335,6 +345,16 @@ The suggestion entry type that is used as a filter in search requests.
 type SuggestionEntryType = Atom | Method | Function | Local;
 ```
 
+### `SuggestionId`
+
+The suggestion entry id of the suggestions database.
+
+#### Format
+
+```typescript
+type SuggestionId = number;
+```
+
 ### `SuggestionsDatabaseEntry`
 
 #### Format
@@ -344,7 +364,7 @@ The entry in the suggestions database.
 ```typescript
 interface SuggestionsDatabaseEntry {
   // suggestion entry id
-  id: number;
+  id: SuggestionId;
   // suggestion entry
   suggestion: SuggestionEntry;
 }
@@ -362,19 +382,19 @@ type SuggestionsDatabaseUpdate = Add | Remove | Modify;
 
 interface Add {
   // suggestion entry id
-  id: number;
+  id: SuggestionId;
   // suggestion entry
   suggestion: SuggestionEntry;
 }
 
 interface Remove {
   // suggestion entry id
-  id: number;
+  id: SuggestionId;
 }
 
 interface Modify {
   // suggestion entry id
-  id: number;
+  id: SuggestionId;
   // new return type
   returnType: String;
 }
diff --git a/engine/language-server/src/main/scala/org/enso/languageserver/runtime/ContextEventsListener.scala b/engine/language-server/src/main/scala/org/enso/languageserver/runtime/ContextEventsListener.scala
index 02c1d9f0f8..17772d7413 100644
--- a/engine/language-server/src/main/scala/org/enso/languageserver/runtime/ContextEventsListener.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/runtime/ContextEventsListener.scala
@@ -89,16 +89,41 @@ final class ContextEventsListener(
       sessionRouter ! DeliverToBinaryController(rpcSession.clientId, payload)
 
     case RunExpressionUpdates if expressionUpdates.nonEmpty =>
-      val updatedExpressionIds = expressionUpdates.map(_.expressionId)
+      def toMethodPointer(call: Api.MethodPointer): (String, String, String) =
+        (call.module, call.definedOnType, call.name)
+      val methodPointerToExpression = expressionUpdates
+        .flatMap(update =>
+          update.methodCall.map(call =>
+            toMethodPointer(call) -> update.expressionId
+          )
+        )
+        .toMap
+      val methodPointers = methodPointerToExpression.keys.toSeq
       repo
-        .getAllByExternalIds(updatedExpressionIds)
+        .getAllMethods(methodPointers)
         .map { suggestionIds =>
-          val valueUpdates = updatedExpressionIds.zip(suggestionIds).flatMap {
-            case (expressionId, Some(suggestionId)) =>
-              Some(ExpressionValueUpdate(expressionId, suggestionId))
-            case (id, None) =>
-              log.error("Unable to find suggestion with expression id: {}", id)
-              None
+          val methodPointerToSuggestion =
+            methodPointers
+              .zip(suggestionIds)
+              .collect {
+                case (ptr, Some(suggestionId)) =>
+                  ptr -> suggestionId
+              }
+              .toMap
+          val valueUpdates = expressionUpdates.map { update =>
+            ExpressionValueUpdate(
+              update.expressionId,
+              update.expressionType,
+              update.methodCall.flatMap { call =>
+                val pointer = toMethodPointer(call)
+                methodPointerToSuggestion.get(pointer) match {
+                  case suggestionId @ Some(_) => suggestionId
+                  case None =>
+                    log.error(s"Unable to find suggestion for $pointer")
+                    None
+                }
+              }
+            )
           }
           val payload =
             ContextRegistryProtocol.ExpressionValuesComputedNotification(
diff --git a/engine/language-server/src/main/scala/org/enso/languageserver/runtime/ContextRegistry.scala b/engine/language-server/src/main/scala/org/enso/languageserver/runtime/ContextRegistry.scala
index f761a4f588..94968874ba 100644
--- a/engine/language-server/src/main/scala/org/enso/languageserver/runtime/ContextRegistry.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/runtime/ContextRegistry.scala
@@ -8,7 +8,6 @@ import org.enso.languageserver.event.{
   ExecutionContextCreated,
   ExecutionContextDestroyed
 }
-import org.enso.languageserver.filemanager.FileSystemFailure
 import org.enso.languageserver.monitoring.MonitoringProtocol.{Ping, Pong}
 import org.enso.languageserver.runtime.handler._
 import org.enso.languageserver.util.UnhandledLogging
@@ -134,14 +133,11 @@ final class ContextRegistry(
 
     case PushContextRequest(client, contextId, stackItem) =>
       if (store.hasContext(client.clientId, contextId)) {
-        getRuntimeStackItem(stackItem) match {
-          case Right(stackItem) =>
-            val handler =
-              context.actorOf(PushContextHandler.props(timeout, runtime))
-            handler.forward(Api.PushContextRequest(contextId, stackItem))
-          case Left(error) =>
-            sender() ! FileSystemError(error)
-        }
+        val item = getRuntimeStackItem(stackItem)
+        val handler =
+          context.actorOf(PushContextHandler.props(timeout, runtime))
+        handler.forward(Api.PushContextRequest(contextId, item))
+
       } else {
         sender() ! AccessDenied
       }
@@ -224,27 +220,24 @@ final class ContextRegistry(
 
   private def getRuntimeStackItem(
     stackItem: StackItem
-  ): Either[FileSystemFailure, Api.StackItem] =
+  ): Api.StackItem =
     stackItem match {
       case StackItem.ExplicitCall(pointer, argument, arguments) =>
-        getRuntimeMethodPointer(pointer).map { methodPointer =>
-          Api.StackItem.ExplicitCall(methodPointer, argument, arguments)
-        }
+        val methodPointer = getRuntimeMethodPointer(pointer)
+        Api.StackItem.ExplicitCall(methodPointer, argument, arguments)
 
       case StackItem.LocalCall(expressionId) =>
-        Right(Api.StackItem.LocalCall(expressionId))
+        Api.StackItem.LocalCall(expressionId)
     }
 
   private def getRuntimeMethodPointer(
     pointer: MethodPointer
-  ): Either[FileSystemFailure, Api.MethodPointer] =
-    config.findContentRoot(pointer.file.rootId).map { rootPath =>
-      Api.MethodPointer(
-        file          = pointer.file.toFile(rootPath),
-        definedOnType = pointer.definedOnType,
-        name          = pointer.name
-      )
-    }
+  ): Api.MethodPointer =
+    Api.MethodPointer(
+      module        = pointer.module,
+      definedOnType = pointer.definedOnType,
+      name          = pointer.name
+    )
 
   private def toRuntimeInvalidatedExpressions(
     expressions: InvalidatedExpressions
diff --git a/engine/language-server/src/main/scala/org/enso/languageserver/runtime/ExpressionValueUpdate.scala b/engine/language-server/src/main/scala/org/enso/languageserver/runtime/ExpressionValueUpdate.scala
index 4d6e34293a..6e8fa61653 100644
--- a/engine/language-server/src/main/scala/org/enso/languageserver/runtime/ExpressionValueUpdate.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/runtime/ExpressionValueUpdate.scala
@@ -6,6 +6,11 @@ import org.enso.languageserver.runtime.ExecutionApi.ExpressionId
   * An update containing information about expression.
   *
   * @param expressionId the id of updated expression
-  * @param suggestionId the updated suggestion id
+  * @param `type` the updated type of expression
+  * @param methodPointer the suggestion id of the updated method pointer
   */
-case class ExpressionValueUpdate(expressionId: ExpressionId, suggestionId: Long)
+case class ExpressionValueUpdate(
+  expressionId: ExpressionId,
+  `type`: Option[String],
+  methodPointer: Option[Long]
+)
diff --git a/engine/language-server/src/main/scala/org/enso/languageserver/runtime/MethodPointer.scala b/engine/language-server/src/main/scala/org/enso/languageserver/runtime/MethodPointer.scala
index a619da7821..7ea0e8f534 100644
--- a/engine/language-server/src/main/scala/org/enso/languageserver/runtime/MethodPointer.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/runtime/MethodPointer.scala
@@ -1,12 +1,10 @@
 package org.enso.languageserver.runtime
 
-import org.enso.languageserver.filemanager.Path
-
 /**
   * An object pointing to a method definition.
   *
-  * @param file path to the method file
+  * @param module the module of the method file
   * @param definedOnType method type
   * @param name method name
   */
-case class MethodPointer(file: Path, definedOnType: String, name: String)
+case class MethodPointer(module: String, definedOnType: String, name: String)
diff --git a/engine/language-server/src/test/scala/org/enso/languageserver/runtime/ContextEventsListenerSpec.scala b/engine/language-server/src/test/scala/org/enso/languageserver/runtime/ContextEventsListenerSpec.scala
index ba19fa48f2..264f864e8e 100644
--- a/engine/language-server/src/test/scala/org/enso/languageserver/runtime/ContextEventsListenerSpec.scala
+++ b/engine/language-server/src/test/scala/org/enso/languageserver/runtime/ContextEventsListenerSpec.scala
@@ -74,8 +74,14 @@ class ContextEventsListenerSpec
           Vector(
             Api.ExpressionValueUpdate(
               Suggestions.method.externalId.get,
-              None,
-              None
+              Some(Suggestions.method.returnType),
+              Some(
+                Api.MethodPointer(
+                  Suggestions.method.module,
+                  Suggestions.method.selfType,
+                  Suggestions.method.name
+                )
+              )
             )
           )
         )
@@ -88,7 +94,8 @@ class ContextEventsListenerSpec
               Vector(
                 ExpressionValueUpdate(
                   Suggestions.method.externalId.get,
-                  suggestionIds(1).get
+                  Some(Suggestions.method.returnType),
+                  Some(suggestionIds(1).get)
                 )
               )
             )
@@ -98,7 +105,7 @@ class ContextEventsListenerSpec
 
     "send expression updates grouped" taggedAs Retry in withDb(0.seconds) {
       (clientId, contextId, repo, router, listener) =>
-        val (_, suggestionIds) = Await.result(
+        Await.result(
           repo.insertAll(
             Seq(
               Suggestions.atom,
@@ -142,11 +149,13 @@ class ContextEventsListenerSpec
               Vector(
                 ExpressionValueUpdate(
                   Suggestions.method.externalId.get,
-                  suggestionIds(1).get
+                  None,
+                  None
                 ),
                 ExpressionValueUpdate(
                   Suggestions.local.externalId.get,
-                  suggestionIds(3).get
+                  None,
+                  None
                 )
               )
             )
diff --git a/engine/polyglot-api/src/main/scala/org/enso/polyglot/runtime/Runtime.scala b/engine/polyglot-api/src/main/scala/org/enso/polyglot/runtime/Runtime.scala
index 28b9be501b..00c07edc90 100644
--- a/engine/polyglot-api/src/main/scala/org/enso/polyglot/runtime/Runtime.scala
+++ b/engine/polyglot-api/src/main/scala/org/enso/polyglot/runtime/Runtime.scala
@@ -198,7 +198,11 @@ object Runtime {
     /**
       * A representation of a pointer to a method definition.
       */
-    case class MethodPointer(file: File, definedOnType: String, name: String)
+    case class MethodPointer(
+      module: String,
+      definedOnType: String,
+      name: String
+    )
 
     /**
       * A representation of an executable position in code.
diff --git a/engine/runtime/src/main/java/org/enso/interpreter/service/ExecutionService.java b/engine/runtime/src/main/java/org/enso/interpreter/service/ExecutionService.java
index c8cc43437b..92ef77c59c 100644
--- a/engine/runtime/src/main/java/org/enso/interpreter/service/ExecutionService.java
+++ b/engine/runtime/src/main/java/org/enso/interpreter/service/ExecutionService.java
@@ -119,7 +119,7 @@ public class ExecutionService {
    * Executes a method described by its name, constructor it's defined on and the module it's
    * defined in.
    *
-   * @param modulePath the path to the module where the method is defined.
+   * @param moduleName the module where the method is defined.
    * @param consName the name of the constructor the method is defined on.
    * @param methodName the method name.
    * @param cache the precomputed expression values.
@@ -129,7 +129,7 @@ public class ExecutionService {
    * @param funCallCallback the consumer for function call events.
    */
   public void execute(
-      File modulePath,
+      String moduleName,
       String consName,
       String methodName,
       RuntimeCache cache,
@@ -140,7 +140,7 @@ public class ExecutionService {
       throws UnsupportedMessageException, ArityException, UnsupportedTypeException {
     Optional<FunctionCallInstrumentationNode.FunctionCall> callMay =
         context
-            .getModuleForFile(modulePath)
+            .findModule(moduleName)
             .flatMap(module -> prepareFunctionCall(module, consName, methodName));
     if (!callMay.isPresent()) {
       return;
diff --git a/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/EnsureCompiledJob.scala b/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/EnsureCompiledJob.scala
index 7efa7a0156..2cd09bc30f 100644
--- a/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/EnsureCompiledJob.scala
+++ b/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/EnsureCompiledJob.scala
@@ -21,7 +21,7 @@ import scala.jdk.OptionConverters._
   *
   * @param files a files to compile
   */
-class EnsureCompiledJob(protected val files: List[File])
+class EnsureCompiledJob(protected val files: Iterable[File])
     extends Job[Unit](List.empty, true, false) {
 
   /**
diff --git a/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/EnsureCompiledStackJob.scala b/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/EnsureCompiledStackJob.scala
index 58a0c5f801..3d4a126630 100644
--- a/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/EnsureCompiledStackJob.scala
+++ b/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/EnsureCompiledStackJob.scala
@@ -14,8 +14,9 @@ import scala.jdk.OptionConverters._
   *
   * @param stack a call stack
   */
-class EnsureCompiledStackJob(stack: Iterable[InstrumentFrame])
-    extends EnsureCompiledJob(EnsureCompiledStackJob.extractFiles(stack)) {
+class EnsureCompiledStackJob(stack: Iterable[InstrumentFrame])(implicit
+  ctx: RuntimeContext
+) extends EnsureCompiledJob(EnsureCompiledStackJob.extractFiles(stack)) {
 
   /** @inheritdoc */
   override def ensureCompiled(
@@ -38,7 +39,7 @@ class EnsureCompiledStackJob(stack: Iterable[InstrumentFrame])
   )(implicit ctx: RuntimeContext): Option[CachePreferenceAnalysis.Metadata] =
     stack.lastOption flatMap {
       case InstrumentFrame(Api.StackItem.ExplicitCall(ptr, _, _), _) =>
-        ctx.executionService.getContext.getModuleForFile(ptr.file).toScala.map {
+        ctx.executionService.getContext.findModule(ptr.module).toScala.map {
           module =>
             module.getIr
               .unsafeGetMetadata(
@@ -58,12 +59,19 @@ object EnsureCompiledStackJob {
     * @param stack a call stack
     * @return a list of files to compile
     */
-  private def extractFiles(stack: Iterable[InstrumentFrame]): List[File] =
+  private def extractFiles(stack: Iterable[InstrumentFrame])(implicit
+    ctx: RuntimeContext
+  ): Iterable[File] =
     stack
       .map(_.item)
-      .collect {
+      .flatMap {
         case Api.StackItem.ExplicitCall(methodPointer, _, _) =>
-          methodPointer.file
+          ctx.executionService.getContext
+            .findModule(methodPointer.module)
+            .flatMap(module => java.util.Optional.ofNullable(module.getPath))
+            .map(path => new File(path))
+            .toScala
+        case _ =>
+          None
       }
-      .toList
 }
diff --git a/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/ProgramExecutionSupport.scala b/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/ProgramExecutionSupport.scala
index b00e3dab8b..d203aa7fbe 100644
--- a/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/ProgramExecutionSupport.scala
+++ b/engine/runtime/src/main/scala/org/enso/interpreter/instrument/job/ProgramExecutionSupport.scala
@@ -1,6 +1,5 @@
 package org.enso.interpreter.instrument.job
 
-import java.io.File
 import java.util.{Objects, UUID}
 import java.util.function.Consumer
 import java.util.logging.Level
@@ -25,8 +24,6 @@ import org.enso.interpreter.node.callable.FunctionCallInstrumentationNode.Functi
 import org.enso.polyglot.runtime.Runtime.Api
 import org.enso.polyglot.runtime.Runtime.Api.ContextId
 
-import scala.jdk.javaapi.OptionConverters
-
 /**
   * Provides support for executing Enso code. Adds convenient methods to
   * run Enso programs in a Truffle context.
@@ -56,9 +53,12 @@ trait ProgramExecutionSupport {
         enterables += fun.getExpressionId -> fun.getCall
       }
     executionFrame match {
-      case ExecutionFrame(ExecutionItem.Method(file, cons, function), cache) =>
+      case ExecutionFrame(
+            ExecutionItem.Method(module, cons, function),
+            cache
+          ) =>
         ctx.executionService.execute(
-          file,
+          module,
           cons,
           function,
           cache,
@@ -250,21 +250,15 @@ trait ProgramExecutionSupport {
 
   private def toMethodPointer(
     value: ExpressionValue
-  )(implicit ctx: RuntimeContext): Option[Api.MethodPointer] =
+  ): Option[Api.MethodPointer] =
     for {
       call       <- Option(value.getCallInfo)
       moduleName <- Option(call.getModuleName)
-      functionName = call.getFunctionName
-      typeName <- Option(call.getTypeName).map(_.item)
-      module <- OptionConverters.toScala(
-        ctx.executionService.getContext.getTopScope
-          .getModule(moduleName.toString)
-      )
-      modulePath <- Option(module.getPath)
+      typeName   <- Option(call.getTypeName).map(_.item)
     } yield Api.MethodPointer(
-      new File(modulePath),
+      moduleName.toString,
       typeName,
-      functionName
+      call.getFunctionName
     )
 }
 
@@ -296,11 +290,11 @@ object ProgramExecutionSupport {
 
     /** The explicit method call.
       *
-      * @param file the file containing the method
+      * @param module the module containing the method
       * @param constructor the type on which the method is defined
       * @param function the method name
       */
-    case class Method(file: File, constructor: String, function: String)
+    case class Method(module: String, constructor: String, function: String)
         extends ExecutionItem
 
     object Method {
@@ -312,7 +306,7 @@ object ProgramExecutionSupport {
         */
       def apply(call: Api.StackItem.ExplicitCall): Method =
         Method(
-          call.methodPointer.file,
+          call.methodPointer.module,
           call.methodPointer.definedOnType,
           call.methodPointer.name
         )
diff --git a/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerTest.scala b/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerTest.scala
index d939d09620..c3c3fb20cd 100644
--- a/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerTest.scala
+++ b/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeServerTest.scala
@@ -144,7 +144,7 @@ class RuntimeServerTest
                 Api.ExpressionValueUpdate(
                   Main.idMainY,
                   Some("Number"),
-                  Some(Api.MethodPointer(pkg.mainFile, "Number", "foo"))
+                  Some(Api.MethodPointer("Test.Main", "Number", "foo"))
                 )
               )
             )
@@ -228,7 +228,7 @@ class RuntimeServerTest
                 Api.ExpressionValueUpdate(
                   idMainY,
                   Some("Number"),
-                  Some(Api.MethodPointer(pkg.mainFile, "Main", "foo"))
+                  Some(Api.MethodPointer("Test.Main", "Main", "foo"))
                 )
               )
             )
@@ -242,7 +242,7 @@ class RuntimeServerTest
                 Api.ExpressionValueUpdate(
                   idMainZ,
                   Some("Number"),
-                  Some(Api.MethodPointer(pkg.mainFile, "Main", "bar"))
+                  Some(Api.MethodPointer("Test.Main", "Main", "bar"))
                 )
               )
             )
@@ -284,7 +284,7 @@ class RuntimeServerTest
   }
 
   "RuntimeServer" should "push and pop functions on the stack" in {
-    val mainFile  = context.writeMain(context.Main.code)
+    context.writeMain(context.Main.code)
     val contextId = UUID.randomUUID()
     val requestId = UUID.randomUUID()
 
@@ -306,7 +306,7 @@ class RuntimeServerTest
 
     // push main
     val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(mainFile, "Main", "main"),
+      Api.MethodPointer("Test.Main", "Main", "main"),
       None,
       Vector()
     )
@@ -333,7 +333,7 @@ class RuntimeServerTest
 
     // push method pointer on top of the non-empty stack
     val invalidExplicitCall = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(mainFile, "Main", "main"),
+      Api.MethodPointer("Test.Main", "Main", "main"),
       None,
       Vector()
     )
@@ -402,7 +402,7 @@ class RuntimeServerTest
         Api.PushContextRequest(
           contextId,
           Api.StackItem.ExplicitCall(
-            Api.MethodPointer(mainFile, "Main", "main"),
+            Api.MethodPointer(moduleName, "Main", "main"),
             None,
             Vector()
           )
@@ -521,7 +521,7 @@ class RuntimeServerTest
         Api.PushContextRequest(
           contextId,
           Api.StackItem.ExplicitCall(
-            Api.MethodPointer(mainFile, "Main", "main"),
+            Api.MethodPointer(moduleName, "Main", "main"),
             None,
             Vector()
           )
@@ -689,7 +689,7 @@ class RuntimeServerTest
         Api.PushContextRequest(
           contextId,
           Api.StackItem.ExplicitCall(
-            Api.MethodPointer(mainFile, "Main", "main"),
+            Api.MethodPointer(moduleName, "Main", "main"),
             None,
             Vector()
           )
@@ -818,7 +818,7 @@ class RuntimeServerTest
             Api.ExpressionValueUpdate(
               idMainA,
               Some("Number"),
-              Some(Api.MethodPointer(mainFile, "Number", "x"))
+              Some(Api.MethodPointer(moduleName, "Number", "x"))
             )
           )
         )
@@ -865,7 +865,7 @@ class RuntimeServerTest
             Api.ExpressionValueUpdate(
               idMainA,
               Some("Number"),
-              Some(Api.MethodPointer(mainFile, "Main", "pie"))
+              Some(Api.MethodPointer(moduleName, "Main", "pie"))
             )
           )
         )
@@ -895,7 +895,7 @@ class RuntimeServerTest
             Api.ExpressionValueUpdate(
               idMainA,
               Some("Number"),
-              Some(Api.MethodPointer(mainFile, "Main", "uwu"))
+              Some(Api.MethodPointer(moduleName, "Main", "uwu"))
             )
           )
         )
@@ -925,7 +925,7 @@ class RuntimeServerTest
             Api.ExpressionValueUpdate(
               idMainA,
               Some("Text"),
-              Some(Api.MethodPointer(mainFile, "Main", "hie"))
+              Some(Api.MethodPointer(moduleName, "Main", "hie"))
             )
           )
         )
@@ -992,7 +992,7 @@ class RuntimeServerTest
           contextId,
           Api.StackItem
             .ExplicitCall(
-              Api.MethodPointer(fooFile, "Foo", "main"),
+              Api.MethodPointer("Test.Foo", "Foo", "main"),
               None,
               Vector()
             )
@@ -1080,7 +1080,7 @@ class RuntimeServerTest
           contextId,
           Api.StackItem
             .ExplicitCall(
-              Api.MethodPointer(fooFile, "Foo", "main"),
+              Api.MethodPointer("Test.Foo", "Foo", "main"),
               None,
               Vector()
             )
@@ -1168,7 +1168,7 @@ class RuntimeServerTest
 
     // push main
     val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(mainFile, "Main", "main"),
+      Api.MethodPointer("Test.Main", "Main", "main"),
       None,
       Vector()
     )
@@ -1329,7 +1329,7 @@ class RuntimeServerTest
           contextId,
           Api.StackItem
             .ExplicitCall(
-              Api.MethodPointer(fooFile, "Foo", "main"),
+              Api.MethodPointer("Test.Foo", "Foo", "main"),
               None,
               Vector()
             )
@@ -1405,7 +1405,7 @@ class RuntimeServerTest
   }
 
   it should "recompute expressions without invalidation" in {
-    val mainFile  = context.writeMain(context.Main.code)
+    context.writeMain(context.Main.code)
     val contextId = UUID.randomUUID()
     val requestId = UUID.randomUUID()
 
@@ -1417,7 +1417,7 @@ class RuntimeServerTest
 
     // push main
     val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(mainFile, "Main", "main"),
+      Api.MethodPointer("Test.Main", "Main", "main"),
       None,
       Vector()
     )
@@ -1441,7 +1441,7 @@ class RuntimeServerTest
   }
 
   it should "recompute expressions invalidating all" in {
-    val mainFile  = context.writeMain(context.Main.code)
+    context.writeMain(context.Main.code)
     val contextId = UUID.randomUUID()
     val requestId = UUID.randomUUID()
 
@@ -1453,7 +1453,7 @@ class RuntimeServerTest
 
     // push main
     val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(mainFile, "Main", "main"),
+      Api.MethodPointer("Test.Main", "Main", "main"),
       None,
       Vector()
     )
@@ -1483,7 +1483,7 @@ class RuntimeServerTest
   }
 
   it should "recompute expressions invalidating some" in {
-    val mainFile  = context.writeMain(context.Main.code)
+    context.writeMain(context.Main.code)
     val contextId = UUID.randomUUID()
     val requestId = UUID.randomUUID()
 
@@ -1495,7 +1495,7 @@ class RuntimeServerTest
 
     // push main
     val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(mainFile, "Main", "main"),
+      Api.MethodPointer("Test.Main", "Main", "main"),
       None,
       Vector()
     )
@@ -1527,7 +1527,7 @@ class RuntimeServerTest
   }
 
   it should "return error when computing erroneous code" in {
-    val mainFile  = context.writeMain(context.MainWithError.code)
+    context.writeMain(context.MainWithError.code)
     val contextId = UUID.randomUUID()
     val requestId = UUID.randomUUID()
 
@@ -1539,7 +1539,7 @@ class RuntimeServerTest
 
     // push main
     val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(mainFile, "Main", "main"),
+      Api.MethodPointer("Test.Main", "Main", "main"),
       None,
       Vector()
     )
@@ -1562,7 +1562,7 @@ class RuntimeServerTest
   }
 
   it should "skip side effects when evaluating cached expression" in {
-    val file      = context.writeMain(context.Main2.code)
+    context.writeMain(context.Main2.code)
     val contextId = UUID.randomUUID()
     val requestId = UUID.randomUUID()
 
@@ -1574,7 +1574,7 @@ class RuntimeServerTest
 
     // push main
     val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(file, "Main", "main"),
+      Api.MethodPointer("Test.Main", "Main", "main"),
       None,
       Vector()
     )
@@ -1601,7 +1601,7 @@ class RuntimeServerTest
   }
 
   it should "emit visualisation update when expression is evaluated" in {
-    val mainFile = context.writeMain(context.Main.code)
+    context.writeMain(context.Main.code)
     val visualisationFile =
       context.writeInSrcDir("Visualisation", context.Visualisation.code)
 
@@ -1627,7 +1627,7 @@ class RuntimeServerTest
 
     // push main
     val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(mainFile, "Main", "main"),
+      Api.MethodPointer("Test.Main", "Main", "main"),
       None,
       Vector()
     )
@@ -1752,7 +1752,7 @@ class RuntimeServerTest
 
     // push main
     val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(mainFile, "Main", "main"),
+      Api.MethodPointer(moduleName, "Main", "main"),
       None,
       Vector()
     )
@@ -1918,7 +1918,7 @@ class RuntimeServerTest
   }
 
   it should "be able to modify visualisations" in {
-    val mainFile = context.writeMain(context.Main.code)
+    context.writeMain(context.Main.code)
     val visualisationFile =
       context.writeInSrcDir("Visualisation", context.Visualisation.code)
 
@@ -1944,7 +1944,7 @@ class RuntimeServerTest
 
     // push main
     val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(mainFile, "Main", "main"),
+      Api.MethodPointer("Test.Main", "Main", "main"),
       None,
       Vector()
     )
@@ -2031,7 +2031,7 @@ class RuntimeServerTest
   }
 
   it should "not emit visualisation updates when visualisation is detached" in {
-    val mainFile = context.writeMain(context.Main.code)
+    context.writeMain(context.Main.code)
     val visualisationFile =
       context.writeInSrcDir("Visualisation", context.Visualisation.code)
 
@@ -2075,7 +2075,7 @@ class RuntimeServerTest
     )
     // push main
     val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(mainFile, "Main", "main"),
+      Api.MethodPointer("Test.Main", "Main", "main"),
       None,
       Vector()
     )
@@ -2130,7 +2130,7 @@ class RuntimeServerTest
   }
 
   it should "rename a project" in {
-    val mainFile  = context.writeMain(context.Main.code)
+    context.writeMain(context.Main.code)
     val contextId = UUID.randomUUID()
     val requestId = UUID.randomUUID()
 
@@ -2142,7 +2142,7 @@ class RuntimeServerTest
 
     // push main
     val item1 = Api.StackItem.ExplicitCall(
-      Api.MethodPointer(mainFile, "Main", "main"),
+      Api.MethodPointer("Test.Main", "Main", "main"),
       None,
       Vector()
     )
diff --git a/lib/scala/searcher/src/bench/java/org/enso/searcher/sql/SuggestionsRepoBenchmark.java b/lib/scala/searcher/src/bench/java/org/enso/searcher/sql/SuggestionsRepoBenchmark.java
index fdaa8d2d15..9f2dc60207 100644
--- a/lib/scala/searcher/src/bench/java/org/enso/searcher/sql/SuggestionsRepoBenchmark.java
+++ b/lib/scala/searcher/src/bench/java/org/enso/searcher/sql/SuggestionsRepoBenchmark.java
@@ -32,7 +32,8 @@ public class SuggestionsRepoBenchmark {
   final Path dbfile = Path.of(System.getProperty("java.io.tmpdir"), "bench-suggestions.db");
   final Seq<Suggestion.Kind> kinds = SuggestionRandom.nextKinds();
   final Seq<scala.Tuple2<UUID, String>> updateInput = SuggestionRandom.nextUpdateAllInput();
-  final Seq<UUID> getAllByExternalIdsInput = SuggestionRandom.nextGetByExternalIdsInput();
+  final Seq<scala.Tuple3<String, String, String>> getAllMethodsInput =
+      SuggestionRandom.nextGetAllMethodsInput();
 
   SqlSuggestionsRepo repo;
 
@@ -104,8 +105,8 @@ public class SuggestionsRepoBenchmark {
   }
 
   @Benchmark
-  public Object searchByExternalIds() throws TimeoutException, InterruptedException {
-    return Await.result(repo.getAllByExternalIds(getAllByExternalIdsInput), TIMEOUT);
+  public Object getAllMethods() throws TimeoutException, InterruptedException {
+    return Await.result(repo.getAllMethods(getAllMethodsInput), TIMEOUT);
   }
 
   @Benchmark
diff --git a/lib/scala/searcher/src/bench/scala/org/enso/searcher/sql/SuggestionRandom.scala b/lib/scala/searcher/src/bench/scala/org/enso/searcher/sql/SuggestionRandom.scala
index 17a829fb55..aa771eed69 100644
--- a/lib/scala/searcher/src/bench/scala/org/enso/searcher/sql/SuggestionRandom.scala
+++ b/lib/scala/searcher/src/bench/scala/org/enso/searcher/sql/SuggestionRandom.scala
@@ -11,8 +11,11 @@ object SuggestionRandom {
   def nextUpdateAllInput(): Seq[(UUID, String)] =
     Seq(UUID.randomUUID() -> nextString())
 
-  def nextGetByExternalIdsInput(): Seq[UUID] =
-    Seq(UUID.randomUUID(), UUID.randomUUID(), UUID.randomUUID())
+  def nextGetAllMethodsInput(): Seq[(String, String, String)] =
+    Seq(
+      (nextString(), nextString(), nextString()),
+      (nextString(), nextString(), nextString())
+    )
 
   def nextKinds(): Seq[Suggestion.Kind] =
     Set.fill(1)(nextKind()).toSeq
diff --git a/lib/scala/searcher/src/main/scala/org/enso/searcher/SuggestionsRepo.scala b/lib/scala/searcher/src/main/scala/org/enso/searcher/SuggestionsRepo.scala
index e9c575aeea..e6e6011ef7 100644
--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/SuggestionsRepo.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/SuggestionsRepo.scala
@@ -14,12 +14,12 @@ trait SuggestionsRepo[F[_]] {
     */
   def getAll: F[(Long, Seq[SuggestionEntry])]
 
-  /** Get suggestions by external ids.
+  /** Get suggestions by the method call info.
     *
-    * @param ids the list of external ids
+    * @param calls the list of triples: module, self type and method name
     * @return the list of found suggestion ids
     */
-  def getAllByExternalIds(ids: Seq[Suggestion.ExternalId]): F[Seq[Option[Long]]]
+  def getAllMethods(calls: Seq[(String, String, String)]): F[Seq[Option[Long]]]
 
   /** Search suggestion by various parameters.
     *
diff --git a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlSuggestionsRepo.scala b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlSuggestionsRepo.scala
index 06e8971411..4b6b1a8c93 100644
--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlSuggestionsRepo.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlSuggestionsRepo.scala
@@ -40,10 +40,10 @@ final class SqlSuggestionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
     db.run(getAllQuery)
 
   /** @inheritdoc */
-  override def getAllByExternalIds(
-    ids: Seq[Suggestion.ExternalId]
+  override def getAllMethods(
+    calls: Seq[(String, String, String)]
   ): Future[Seq[Option[Long]]] =
-    db.run(getAllByExternalIdsQuery(ids))
+    db.run(getAllMethodsQuery(calls))
 
   /** @inheritdoc */
   override def search(
@@ -140,34 +140,32 @@ final class SqlSuggestionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
     query.transactionally
   }
 
-  /** The query to get suggestions by external ids.
+  /** The query to get the suggestions by the method call info.
     *
-    * @param ids the list of external ids
+    * @param calls the triples containing module name, self type, method name
     * @return the list of found suggestion ids
     */
-  private def getAllByExternalIdsQuery(
-    ids: Seq[Suggestion.ExternalId]
+  def getAllMethodsQuery(
+    calls: Seq[(String, String, String)]
   ): DBIO[Seq[Option[Long]]] =
-    if (ids.isEmpty) {
+    if (calls.isEmpty) {
       DBIO.successful(Seq())
     } else {
-      val bits =
-        ids.map(id => (id.getLeastSignificantBits, id.getMostSignificantBits))
       val query = Suggestions
         .filter { row =>
-          bits
+          calls
             .map {
-              case (least, most) =>
-                row.externalIdLeast === least && row.externalIdMost === most
+              case (module, selfType, name) =>
+                row.module === module && row.selfType === selfType && row.name === name
             }
             .reduce(_ || _)
         }
-        .map(row => (row.id, row.externalIdLeast, row.externalIdMost))
-      query.result.map { triples =>
-        val result = triples.flatMap {
-          case (id, least, most) => toUUID(least, most).map(_ -> id)
+        .map(row => (row.id, row.module, row.selfType, row.name))
+      query.result.map { tuples =>
+        val result = tuples.map {
+          case (id, module, selfType, name) => (module, selfType, name) -> id
         }.toMap
-        ids.map(result.get)
+        calls.map(result.get)
       }
     }
 
diff --git a/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/SuggestionsRepoTest.scala b/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/SuggestionsRepoTest.scala
index 16159de0f7..129b11834a 100644
--- a/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/SuggestionsRepoTest.scala
+++ b/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/SuggestionsRepoTest.scala
@@ -63,7 +63,7 @@ class SuggestionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {
       )
     }
 
-    "get suggestions by external ids" taggedAs Retry in withRepo { repo =>
+    "get suggestions by method call info" taggedAs Retry in withRepo { repo =>
       val action = for {
         (_, ids) <- repo.insertAll(
           Seq(
@@ -73,30 +73,31 @@ class SuggestionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {
             suggestion.local
           )
         )
-        results <- repo.getAllByExternalIds(
-          Seq(suggestion.method.externalId.get, suggestion.local.externalId.get)
+        results <- repo.getAllMethods(
+          Seq(("Test.Main", "Main", "main"), ("Test.Main", "Main", "foo"))
         )
       } yield (ids, results)
 
       val (ids, results) = Await.result(action, Timeout)
-      results should contain theSameElementsAs Seq(ids(1), ids(3))
+      results should contain theSameElementsInOrderAs Seq(ids(1), None)
     }
 
-    "get suggestions by empty external ids" taggedAs Retry in withRepo { repo =>
-      val action = for {
-        _ <- repo.insertAll(
-          Seq(
-            suggestion.atom,
-            suggestion.method,
-            suggestion.function,
-            suggestion.local
+    "get suggestions by empty method call info" taggedAs Retry in withRepo {
+      repo =>
+        val action = for {
+          _ <- repo.insertAll(
+            Seq(
+              suggestion.atom,
+              suggestion.method,
+              suggestion.function,
+              suggestion.local
+            )
           )
-        )
-        results <- repo.getAllByExternalIds(Seq())
-      } yield results
+          results <- repo.getAllMethods(Seq())
+        } yield results
 
-      val results = Await.result(action, Timeout)
-      results.isEmpty shouldEqual true
+        val results = Await.result(action, Timeout)
+        results.isEmpty shouldEqual true
     }
 
     "fail to insert duplicate suggestion" taggedAs Retry in withRepo { repo =>