[release: nightly] Prune Versions when Verifying Modules Index (#1881)

clean module versions together with the module suggestions
2024-12-27 01:02:30 +03:00 · 2021-07-16 20:10:55 +03:00 · 2021-07-16 20:10:55 +03:00 · 4235d345aa
commit 4235d345aa
parent 214495ad56
24 changed files with 484 additions and 336 deletions
--- a/engine/language-server/src/main/scala/org/enso/languageserver/boot/MainModule.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/boot/MainModule.scala
@ -142,7 +142,7 @@ class MainModule(serverConfig: LanguageServerConfig, logLevel: LogLevel) {

  lazy val bufferRegistry =
    system.actorOf(
-      BufferRegistry.props(versionsRepo, fileManager, runtimeConnector),
+      BufferRegistry.props(fileManager, runtimeConnector),
      "buffer-registry"
    )

--- a/engine/language-server/src/main/scala/org/enso/languageserver/search/SuggestionsHandler.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/search/SuggestionsHandler.scala
@ -2,7 +2,7 @@ package org.enso.languageserver.search

 import java.util.UUID

-import akka.actor.{Actor, ActorRef, Props, Stash}
+import akka.actor.{Actor, ActorRef, Props, Stash, Status}
 import akka.pattern.{ask, pipe}
 import com.typesafe.scalalogging.LazyLogging
 import org.enso.languageserver.capability.CapabilityProtocol.{
@ -38,7 +38,7 @@ import org.enso.polyglot.Suggestion
 import org.enso.polyglot.data.TypeGraph
 import org.enso.polyglot.runtime.Runtime.Api
 import org.enso.searcher.data.QueryResult
-import org.enso.searcher.{FileVersionsRepo, SuggestionsRepo}
+import org.enso.searcher.{SuggestionsRepo, VersionsRepo}
 import org.enso.text.ContentVersion
 import org.enso.text.editing.model.Position

@ -80,6 +80,7 @@ import scala.util.{Failure, Success}
  * @param config the server configuration
  * @param contentRootManager the content root manager
  * @param suggestionsRepo the suggestions repo
+  * @param versionsRepo the versions repo
  * @param sessionRouter the session router
  * @param runtimeConnector the runtime connector
  */
@ -87,7 +88,7 @@ final class SuggestionsHandler(
  config: Config,
  contentRootManager: ContentRootManager,
  suggestionsRepo: SuggestionsRepo[Future],
-  fileVersionsRepo: FileVersionsRepo[Future],
+  versionsRepo: VersionsRepo[Future],
  sessionRouter: ActorRef,
  runtimeConnector: ActorRef
 ) extends Actor
@ -105,7 +106,7 @@ final class SuggestionsHandler(
      "Starting suggestions handler from [{}, {}, {}].",
      config,
      suggestionsRepo,
-      fileVersionsRepo
+      versionsRepo
    )
    context.system.eventStream
      .subscribe(self, classOf[Api.ExpressionUpdates])
@ -170,6 +171,13 @@ final class SuggestionsHandler(
      logger.info("Initializing: got type graph response.")
      tryInitialize(init.copy(typeGraph = Some(g)))

+    case Status.Failure(ex) =>
+      logger.error(
+        "Initialization failure [{}]. {}",
+        ex.getClass,
+        ex.getMessage
+      )
+
    case _ => stash()
  }

@ -179,16 +187,24 @@ final class SuggestionsHandler(
  ): Receive = {
    case Api.Response(_, Api.VerifyModulesIndexResponse(toRemove)) =>
      logger.info("Verifying: got verification response.")
-      suggestionsRepo
-        .removeModules(toRemove)
-        .map(_ => SuggestionsHandler.Verified)
-        .pipeTo(self)
+      val removeAction = for {
+        _ <- versionsRepo.remove(toRemove)
+        _ <- suggestionsRepo.removeModules(toRemove)
+      } yield SuggestionsHandler.Verified
+      removeAction.pipeTo(self)

    case SuggestionsHandler.Verified =>
      logger.info("Verified.")
      context.become(initialized(projectName, graph, Set()))
      unstashAll()

+    case Status.Failure(ex) =>
+      logger.error(
+        "Database verification failure [{}]. {}",
+        ex.getClass,
+        ex.getMessage
+      )
+
    case _ =>
      stash()
  }
@ -214,7 +230,7 @@ final class SuggestionsHandler(

    case msg: Api.SuggestionsDatabaseModuleUpdateNotification =>
      val isVersionChanged =
-        fileVersionsRepo.getVersion(msg.file).map { digestOpt =>
+        versionsRepo.getVersion(msg.module).map { digestOpt =>
          !digestOpt.map(ContentVersion(_)).contains(msg.version)
        }
      val applyUpdatesIfVersionChanged =
@ -234,7 +250,7 @@ final class SuggestionsHandler(
          case Failure(ex) =>
            logger.error(
              "Error applying suggestion database updates [{}, {}]. {}",
-              MaskedPath(msg.file.toPath),
+              msg.module,
              msg.version,
              ex.getMessage
            )
@ -366,7 +382,7 @@ final class SuggestionsHandler(
    case InvalidateSuggestionsDatabase =>
      val action = for {
        _ <- suggestionsRepo.clean
-        _ <- fileVersionsRepo.clean
+        _ <- versionsRepo.clean
      } yield SearchProtocol.InvalidateModulesIndex

      val runtimeFailureMapper = RuntimeFailureMapper(contentRootManager)
@ -468,7 +484,7 @@ final class SuggestionsHandler(
    for {
      actionResults      <- suggestionsRepo.applyActions(msg.actions)
      (version, results) <- suggestionsRepo.applyTree(msg.updates)
-      _                  <- fileVersionsRepo.setVersion(msg.file, msg.version.toDigest)
+      _                  <- versionsRepo.setVersion(msg.module, msg.version.toDigest)
    } yield {
      val actionUpdates = actionResults.flatMap {
        case QueryResult(ids, Api.SuggestionsDatabaseAction.Clean(_)) =>
@ -644,7 +660,7 @@ object SuggestionsHandler {
    config: Config,
    contentRootManager: ContentRootManager,
    suggestionsRepo: SuggestionsRepo[Future],
-    fileVersionsRepo: FileVersionsRepo[Future],
+    fileVersionsRepo: VersionsRepo[Future],
    sessionRouter: ActorRef,
    runtimeConnector: ActorRef
  ): Props =
--- a/engine/language-server/src/main/scala/org/enso/languageserver/text/BufferRegistry.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/text/BufferRegistry.scala
@ -20,11 +20,8 @@ import org.enso.languageserver.text.TextProtocol.{
  OpenFile,
  SaveFile
 }
-import org.enso.searcher.FileVersionsRepo
 import org.enso.text.ContentBasedVersioning

-import scala.concurrent.Future
-
 /** An actor that routes request regarding text editing to the right buffer.
  * It creates a buffer actor, if a buffer doesn't exists.
  *
@ -56,13 +53,11 @@ import scala.concurrent.Future
  *
  * }}}
  *
-  * @param versionsRepo a repo containing versions of indexed files
  * @param fileManager a file manager
  * @param runtimeConnector a gateway to the runtime
  * @param versionCalculator a content based version calculator
  */
 class BufferRegistry(
-  versionsRepo: FileVersionsRepo[Future],
  fileManager: ActorRef,
  runtimeConnector: ActorRef
 )(implicit
@ -102,7 +97,6 @@ class BufferRegistry(
          context.actorOf(
            CollaborativeBuffer.props(
              path,
-              versionsRepo,
              fileManager,
              runtimeConnector
            )
@ -157,19 +151,17 @@ object BufferRegistry {

  /** Creates a configuration object used to create a [[BufferRegistry]]
    *
-    * @param versionsRepo a repo containing versions of indexed files
    * @param fileManager a file manager actor
    * @param runtimeConnector a gateway to the runtime
    * @param versionCalculator a content based version calculator
    * @return a configuration object
    */
  def props(
-    versionsRepo: FileVersionsRepo[Future],
    fileManager: ActorRef,
    runtimeConnector: ActorRef
  )(implicit
    versionCalculator: ContentBasedVersioning
  ): Props =
-    Props(new BufferRegistry(versionsRepo, fileManager, runtimeConnector))
+    Props(new BufferRegistry(fileManager, runtimeConnector))

 }
--- a/engine/language-server/src/main/scala/org/enso/languageserver/text/CollaborativeBuffer.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/text/CollaborativeBuffer.scala
@ -1,7 +1,6 @@
 package org.enso.languageserver.text

 import akka.actor.{Actor, ActorRef, Cancellable, Props, Stash}
-import akka.pattern.pipe
 import cats.implicits._
 import com.typesafe.scalalogging.LazyLogging
 import org.enso.languageserver.capability.CapabilityProtocol._
@ -26,19 +25,16 @@ import org.enso.languageserver.text.CollaborativeBuffer.IOTimeout
 import org.enso.languageserver.text.TextProtocol._
 import org.enso.languageserver.util.UnhandledLogging
 import org.enso.polyglot.runtime.Runtime.Api
-import org.enso.searcher.FileVersionsRepo
 import org.enso.text.{ContentBasedVersioning, ContentVersion}
 import org.enso.text.editing._
 import org.enso.text.editing.model.TextEdit

-import scala.concurrent.Future
 import scala.concurrent.duration._
 import scala.language.postfixOps

 /** An actor enabling multiple users edit collaboratively a file.
  *
  * @param bufferPath a path to a file
-  * @param versionsRepo a repo containing versions of indexed files
  * @param fileManager a file manger actor
  * @param runtimeConnector a gateway to the runtime
  * @param timeout a request timeout
@ -46,7 +42,6 @@ import scala.language.postfixOps
  */
 class CollaborativeBuffer(
  bufferPath: Path,
-  versionsRepo: FileVersionsRepo[Future],
  fileManager: ActorRef,
  runtimeConnector: ActorRef,
  timeout: FiniteDuration
@ -304,17 +299,9 @@ class CollaborativeBuffer(
    originalSender ! OpenFileResponse(
      Right(OpenFileResult(buffer, Some(cap)))
    )
-    val currentVersion = versionCalculator.evalVersion(file.content)
-    versionsRepo
-      .setVersion(file.path, currentVersion.toDigest)
-      .map { prevDigestOpt =>
-        val prevVersionOpt = prevDigestOpt.map(ContentVersion(_))
-        val isIndexed      = prevVersionOpt.contains(currentVersion)
-        Api.Request(
-          Api.OpenFileNotification(file.path, file.content, isIndexed)
-        )
-      }
-      .pipeTo(runtimeConnector)
+    runtimeConnector ! Api.Request(
+      Api.OpenFileNotification(file.path, file.content)
+    )
    context.become(
      collaborativeEditing(
        buffer,
@ -425,7 +412,6 @@ object CollaborativeBuffer {
  /** Creates a configuration object used to create a [[CollaborativeBuffer]]
    *
    * @param bufferPath a path to a file
-    * @param versionsRepo a repo containing versions of indexed files
    * @param fileManager a file manager actor
    * @param runtimeConnector a gateway to the runtime
    * @param timeout a request timeout
@ -434,7 +420,6 @@ object CollaborativeBuffer {
    */
  def props(
    bufferPath: Path,
-    versionsRepo: FileVersionsRepo[Future],
    fileManager: ActorRef,
    runtimeConnector: ActorRef,
    timeout: FiniteDuration = 10 seconds
@ -442,7 +427,6 @@ object CollaborativeBuffer {
    Props(
      new CollaborativeBuffer(
        bufferPath,
-        versionsRepo,
        fileManager,
        runtimeConnector,
        timeout
--- a/engine/language-server/src/test/scala/org/enso/languageserver/search/SuggestionsHandlerSpec.scala
+++ b/engine/language-server/src/test/scala/org/enso/languageserver/search/SuggestionsHandlerSpec.scala
@ -18,7 +18,7 @@ import org.enso.polyglot.Suggestion
 import org.enso.polyglot.data.{Tree, TypeGraph}
 import org.enso.polyglot.runtime.Runtime.Api
 import org.enso.searcher.sql.{SqlDatabase, SqlSuggestionsRepo, SqlVersionsRepo}
-import org.enso.searcher.{FileVersionsRepo, SuggestionsRepo}
+import org.enso.searcher.{SuggestionsRepo, VersionsRepo}
 import org.enso.testkit.RetrySpec
 import org.enso.text.editing.model.Position
 import org.enso.text.{ContentVersion, Sha3_224VersionCalculator}
@ -26,7 +26,6 @@ import org.scalatest.BeforeAndAfterAll
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.wordspec.AnyWordSpecLike

-import java.io.File
 import java.nio.file.Files
 import java.util.UUID
 import scala.concurrent.duration._
@ -54,6 +53,60 @@ class SuggestionsHandlerSpec

  "SuggestionsHandler" should {

+    "prune stale modules" in withDbs { (config, suggestions, versions) =>
+      // setup database
+      val version1 = Array[Byte](1, 2, 3)
+      val version2 = Array[Byte](2, 3, 4)
+      val setupAction = for {
+        _ <- suggestions.insert(TestSuggestion.atom)
+        _ <- suggestions.insert(TestSuggestion.method)
+        _ <- versions.setVersion(TestSuggestion.atom.module, version1)
+        _ <- versions.setVersion(TestSuggestion.method.module, version2)
+      } yield ()
+      Await.ready(setupAction, Timeout)
+
+      withHandler(config, suggestions, versions) { (_, connector, handler) =>
+        // initialize
+        handler ! SuggestionsHandler.ProjectNameUpdated("Test")
+        handler ! InitializedEvent.TruffleContextInitialized
+        handler ! InitializedEvent.SuggestionsRepoInitialized
+        handler ! InitializedEvent.FileVersionsRepoInitialized
+        connector.receiveN(1)
+        handler ! Api.Response(
+          UUID.randomUUID(),
+          Api.GetTypeGraphResponse(buildTestTypeGraph)
+        )
+        connector.receiveN(1)
+        // prune atom module
+        handler ! Api.Response(
+          UUID.randomUUID(),
+          Api.VerifyModulesIndexResponse(Seq(TestSuggestion.atom.module))
+        )
+        // wait for initialization
+        handler ! AcquireCapability(
+          newJsonSession(UUID.randomUUID()),
+          CapabilityRegistration(ReceivesSuggestionsDatabaseUpdates())
+        )
+        expectMsg(CapabilityAcquired)
+        // check
+        val (_, entries) = Await.result(suggestions.getAll, Timeout)
+        entries.map(_.suggestion) should contain theSameElementsAs Seq(
+          TestSuggestion.method
+        )
+        val module1Version = Await.result(
+          versions.getVersion(TestSuggestion.atom.module),
+          Timeout
+        )
+        module1Version.isEmpty shouldBe true
+        val module2Version = Await.result(
+          versions.getVersion(TestSuggestion.method.module),
+          Timeout
+        )
+        module2Version.isEmpty shouldBe false
+        module2Version.get should contain theSameElementsInOrderAs version2
+      }
+    }
+
    "subscribe to notification updates" taggedAs Retry in withDb {
      (_, _, _, _, handler) =>
        val clientId = UUID.randomUUID()
@ -78,7 +131,7 @@ class SuggestionsHandlerSpec

        // receive updates
        handler ! Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          contentsVersion(""),
          Vector(),
          Tree.Root(Suggestions.all.toVector.map { suggestion =>
@ -123,7 +176,7 @@ class SuggestionsHandlerSpec

        // receive updates
        handler ! Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          contentsVersion(""),
          Vector(),
          Tree.Root(
@ -217,7 +270,7 @@ class SuggestionsHandlerSpec

        // add tree
        handler ! Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          contentsVersion(""),
          Vector(),
          tree1
@ -291,7 +344,7 @@ class SuggestionsHandlerSpec
        )
        // update tree
        handler ! Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          contentsVersion("1"),
          Vector(),
          tree2
@ -380,7 +433,7 @@ class SuggestionsHandlerSpec

        // add tree
        handler ! Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          contentsVersion(""),
          Vector(),
          tree
@ -458,7 +511,7 @@ class SuggestionsHandlerSpec

        // add tree
        handler ! Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          contentsVersion(""),
          Vector(),
          tree1
@ -482,7 +535,7 @@ class SuggestionsHandlerSpec

        // clean module
        handler ! Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          contentsVersion("1"),
          Vector(Api.SuggestionsDatabaseAction.Clean(Suggestions.atom.module)),
          Tree.Root(Vector())
@ -761,22 +814,38 @@ class SuggestionsHandlerSpec
    sessionRouter: TestProbe,
    runtimeConnector: TestProbe,
    suggestionsRepo: SuggestionsRepo[Future],
-    fileVersionsRepo: FileVersionsRepo[Future]
+    fileVersionsRepo: VersionsRepo[Future]
  ): ActorRef = {
    val contentRootManagerActor =
      system.actorOf(ContentRootManagerActor.props(config))
    val contentRootManagerWrapper: ContentRootManager =
      new ContentRootManagerWrapper(config, contentRootManagerActor)
+    system.actorOf(
+      SuggestionsHandler.props(
+        config,
+        contentRootManagerWrapper,
+        suggestionsRepo,
+        fileVersionsRepo,
+        sessionRouter.ref,
+        runtimeConnector.ref
+      )
+    )
+  }
+
+  def newInitializedSuggestionsHandler(
+    config: Config,
+    sessionRouter: TestProbe,
+    runtimeConnector: TestProbe,
+    suggestionsRepo: SuggestionsRepo[Future],
+    fileVersionsRepo: VersionsRepo[Future]
+  ): ActorRef = {
    val handler =
-      system.actorOf(
-        SuggestionsHandler.props(
-          config,
-          contentRootManagerWrapper,
-          suggestionsRepo,
-          fileVersionsRepo,
-          sessionRouter.ref,
-          runtimeConnector.ref
-        )
+      newSuggestionsHandler(
+        config,
+        sessionRouter,
+        runtimeConnector,
+        suggestionsRepo,
+        fileVersionsRepo
      )
    handler ! SuggestionsHandler.ProjectNameUpdated("Test")
    handler ! InitializedEvent.TruffleContextInitialized
@ -819,6 +888,69 @@ class SuggestionsHandlerSpec
  def newJsonSession(clientId: UUID): JsonSession =
    JsonSession(clientId, TestProbe().ref)

+  def withDbs(
+    test: (Config, SuggestionsRepo[Future], VersionsRepo[Future]) => Any
+  ): Unit = {
+    val testContentRoot = Files.createTempDirectory(null).toRealPath()
+    sys.addShutdownHook(FileUtils.deleteQuietly(testContentRoot.toFile))
+    val config = newConfig(
+      ContentRootWithFile(
+        ContentRoot.Project(UUID.randomUUID()),
+        testContentRoot.toFile
+      )
+    )
+    val sqlDatabase     = SqlDatabase(config.directories.suggestionsDatabaseFile)
+    val suggestionsRepo = new SqlSuggestionsRepo(sqlDatabase)
+    val versionsRepo    = new SqlVersionsRepo(sqlDatabase)
+
+    val suggestionsInit = suggestionsRepo.init
+    val versionsInit    = versionsRepo.init
+    suggestionsInit.onComplete {
+      case Success(()) =>
+        system.eventStream.publish(InitializedEvent.SuggestionsRepoInitialized)
+      case Failure(ex) =>
+        system.log.error(ex, "Failed to initialize Suggestions repo")
+    }
+    versionsInit.onComplete {
+      case Success(()) =>
+        system.eventStream.publish(InitializedEvent.FileVersionsRepoInitialized)
+      case Failure(ex) =>
+        system.log.error(ex, "Failed to initialize FileVersions repo")
+    }
+
+    Await.ready(suggestionsInit, Timeout)
+    Await.ready(versionsInit, Timeout)
+
+    try test(config, suggestionsRepo, versionsRepo)
+    finally {
+      versionsRepo.close()
+      suggestionsRepo.close()
+    }
+  }
+
+  def withHandler(
+    config: Config,
+    suggestionsRepo: SuggestionsRepo[Future],
+    versionsRepo: VersionsRepo[Future]
+  )(
+    test: (TestProbe, TestProbe, ActorRef) => Any
+  ): Unit = {
+    val router    = TestProbe("session-router")
+    val connector = TestProbe("runtime-connector")
+    val handler = newSuggestionsHandler(
+      config,
+      router,
+      connector,
+      suggestionsRepo,
+      versionsRepo
+    )
+
+    try test(router, connector, handler)
+    finally {
+      system.stop(handler)
+    }
+  }
+
  def withDb(
    test: (
      Config,
@ -836,9 +968,9 @@ class SuggestionsHandlerSpec
        testContentRoot.toFile
      )
    )
-    val router    = TestProbe("session-router")
-    val connector = TestProbe("runtime-connector")
-    val sqlDatabase = SqlDatabase( config.directories.suggestionsDatabaseFile)
+    val router          = TestProbe("session-router")
+    val connector       = TestProbe("runtime-connector")
+    val sqlDatabase     = SqlDatabase(config.directories.suggestionsDatabaseFile)
    val suggestionsRepo = new SqlSuggestionsRepo(sqlDatabase)
    val versionsRepo    = new SqlVersionsRepo(sqlDatabase)

@ -855,7 +987,7 @@ class SuggestionsHandlerSpec
        system.log.error(ex, "Failed to initialize FileVersions repo")
    }

-    val handler = newSuggestionsHandler(
+    val handler = newInitializedSuggestionsHandler(
      config,
      router,
      connector,
@ -870,4 +1002,33 @@ class SuggestionsHandlerSpec
    }
  }

+  object TestSuggestion {
+
+    val atom: Suggestion.Atom =
+      Suggestion.Atom(
+        externalId = None,
+        module     = "Test.Pair",
+        name       = "Pair",
+        arguments = Seq(
+          Suggestion.Argument("a", "Any", false, false, None),
+          Suggestion.Argument("b", "Any", false, false, None)
+        ),
+        returnType        = "Pair",
+        documentation     = Some("Awesome"),
+        documentationHtml = Some("")
+      )
+
+    val method: Suggestion.Method =
+      Suggestion.Method(
+        externalId        = Some(UUID.randomUUID()),
+        module            = "Test.Main",
+        name              = "main",
+        arguments         = Seq(),
+        selfType          = "Test.Main",
+        returnType        = "IO",
+        documentation     = None,
+        documentationHtml = None
+      )
+  }
+
 }
--- a/engine/language-server/src/test/scala/org/enso/languageserver/websocket/json/BaseServerTest.scala
+++ b/engine/language-server/src/test/scala/org/enso/languageserver/websocket/json/BaseServerTest.scala
@ -138,7 +138,6 @@ class BaseServerTest
    val bufferRegistry =
      system.actorOf(
        BufferRegistry.props(
-          versionsRepo,
          fileManager,
          runtimeConnectorProbe.ref
        )(
--- a/engine/language-server/src/test/scala/org/enso/languageserver/websocket/json/FileNotificationsTest.scala
+++ b/engine/language-server/src/test/scala/org/enso/languageserver/websocket/json/FileNotificationsTest.scala
@ -88,7 +88,7 @@ class FileNotificationsTest extends BaseServerTest with FlakySpec {
      // 4
      runtimeConnectorProbe.expectMsg(
        Api.Request(
-          Api.OpenFileNotification(file("foo.txt"), "123456789", false)
+          Api.OpenFileNotification(file("foo.txt"), "123456789")
        )
      )

--- a/engine/language-server/src/test/scala/org/enso/languageserver/websocket/json/SuggestionsHandlerEventsTest.scala
+++ b/engine/language-server/src/test/scala/org/enso/languageserver/websocket/json/SuggestionsHandlerEventsTest.scala
@ -1,7 +1,5 @@
 package org.enso.languageserver.websocket.json

-import java.io.File
-
 import io.circe.literal._
 import org.enso.languageserver.search.Suggestions
 import org.enso.languageserver.websocket.json.{SearchJsonMessages => json}
@ -22,7 +20,7 @@ class SuggestionsHandlerEventsTest extends BaseServerTest with FlakySpec {
      // add atom
      system.eventStream.publish(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          versionCalculator.evalVersion("1"),
          Vector(),
          Tree.Root(
@ -71,7 +69,7 @@ class SuggestionsHandlerEventsTest extends BaseServerTest with FlakySpec {
      // add method
      system.eventStream.publish(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          versionCalculator.evalVersion("2"),
          Vector(),
          Tree.Root(
@ -139,7 +137,7 @@ class SuggestionsHandlerEventsTest extends BaseServerTest with FlakySpec {
      // add function
      system.eventStream.publish(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          versionCalculator.evalVersion("3"),
          Vector(),
          Tree.Root(
@ -229,7 +227,7 @@ class SuggestionsHandlerEventsTest extends BaseServerTest with FlakySpec {
      // add local
      system.eventStream.publish(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          versionCalculator.evalVersion("4"),
          Vector(),
          Tree.Root(
@ -427,7 +425,7 @@ class SuggestionsHandlerEventsTest extends BaseServerTest with FlakySpec {
      // update items
      system.eventStream.publish(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          versionCalculator.evalVersion("5"),
          Vector(),
          Tree.Root(
@ -545,7 +543,7 @@ class SuggestionsHandlerEventsTest extends BaseServerTest with FlakySpec {
      // remove items
      system.eventStream.publish(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          new File("/tmp/foo"),
+          "Foo.Main",
          versionCalculator.evalVersion("6"),
          Vector(Api.SuggestionsDatabaseAction.Clean(Suggestions.atom.module)),
          Tree.Root(Vector())
--- 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
@ -1104,12 +1104,10 @@ object Runtime {
      *
      * @param path the file being moved to memory.
      * @param contents the current file contents.
-      * @param isIndexed the flag specifying whether the file is indexed
      */
    case class OpenFileNotification(
      path: File,
-      contents: String,
-      isIndexed: Boolean
+      contents: String
    ) extends ApiRequest
        with ToLogString {

@ -1118,7 +1116,6 @@ object Runtime {
        "OpenFileNotification(" +
        s"path=${MaskedPath(path.toPath).toLogString(shouldMask)}," +
        s"contents=${MaskedString(contents).toLogString(shouldMask)}," +
-        s"isIndexed=$isIndexed" +
        ")"
    }

@ -1260,13 +1257,13 @@ object Runtime {

    /** A notification about the changes in the suggestions database.
      *
-      * @param file the module file path
+      * @param module the module name
      * @param version the version of the module
      * @param actions the list of actions to apply to the suggestions database
      * @param updates the list of suggestions extracted from module
      */
    case class SuggestionsDatabaseModuleUpdateNotification(
-      file: File,
+      module: String,
      version: ContentVersion,
      actions: Vector[SuggestionsDatabaseAction],
      updates: Tree[SuggestionUpdate]
@ -1276,7 +1273,7 @@ object Runtime {
      /** @inheritdoc */
      override def toLogString(shouldMask: Boolean): String =
        "SuggestionsDatabaseModuleUpdateNotification(" +
-        s"file=${MaskedPath(file.toPath).toLogString(shouldMask)}," +
+        s"module=$module," +
        s"version=$version," +
        s"actions=$actions," +
        s"updates=${updates.map(_.toLogString(shouldMask))}" +
--- a/engine/runtime/src/main/java/org/enso/interpreter/service/ExecutionService.java
+++ b/engine/runtime/src/main/java/org/enso/interpreter/service/ExecutionService.java
@ -238,7 +238,7 @@ public class ExecutionService {
   * @param path the module path.
   * @param contents the sources to use for it.
   */
-  public void setModuleSources(File path, String contents, boolean isIndexed) {
+  public void setModuleSources(File path, String contents) {
    Optional<Module> module = context.getModuleForFile(path);
    if (module.isEmpty()) {
      module = context.createModuleForFile(path);
@ -246,7 +246,6 @@ public class ExecutionService {
    module.ifPresent(
        mod -> {
          mod.setLiteralSource(contents);
-          mod.setIndexed(isIndexed);
        });
  }

--- a/engine/runtime/src/main/scala/org/enso/interpreter/instrument/command/OpenFileCmd.scala
+++ b/engine/runtime/src/main/scala/org/enso/interpreter/instrument/command/OpenFileCmd.scala
@ -22,8 +22,7 @@ class OpenFileCmd(request: Api.OpenFileNotification) extends Command(None) {
      try {
        ctx.executionService.setModuleSources(
          request.path,
-          request.contents,
-          request.isIndexed
+          request.contents
        )
      } finally {
        ctx.locking.releaseReadCompilationLock()
--- 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
@ -157,7 +157,7 @@ class EnsureCompiledJob(protected val files: Iterable[File])
        .filter(isSuggestionGlobal)
      val version = ctx.versioning.evalVersion(module.getLiteralSource.toString)
      val notification = Api.SuggestionsDatabaseModuleUpdateNotification(
-        file    = getIndexingPath(module),
+        module  = moduleName.toString,
        version = version,
        actions =
          Vector(Api.SuggestionsDatabaseAction.Clean(moduleName.toString)),
@ -185,7 +185,7 @@ class EnsureCompiledJob(protected val files: Iterable[File])
      val diff = SuggestionDiff
        .compute(prevSuggestions, newSuggestions)
      val notification = Api.SuggestionsDatabaseModuleUpdateNotification(
-        file    = new File(module.getPath),
+        module  = moduleName.toString,
        version = version,
        actions = Vector(),
        updates = diff
@ -198,7 +198,7 @@ class EnsureCompiledJob(protected val files: Iterable[File])
        SuggestionBuilder(module.getLiteralSource)
          .build(moduleName, module.getIr)
      val notification = Api.SuggestionsDatabaseModuleUpdateNotification(
-        file    = new File(module.getPath),
+        module  = moduleName.toString,
        version = version,
        actions =
          Vector(Api.SuggestionsDatabaseAction.Clean(moduleName.toString)),
@ -441,17 +441,6 @@ class EnsureCompiledJob(protected val files: Iterable[File])
    ctx: RuntimeContext
  ): Iterable[Module] =
    ctx.executionService.getContext.getTopScope.getModules.asScala
-
-  /** Get the module path for suggestions database indexing.
-    *
-    * If the module is synthetic (i.e. Builtins), uses its name as a path.
-    */
-  private def getIndexingPath(module: Module): File =
-    if (module.getPath eq null) {
-      new File(s"/${module.getName}")
-    } else
-      new File(module.getPath)
-
 }

 object EnsureCompiledJob {
--- a/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeErrorsTest.scala
+++ b/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeErrorsTest.scala
@ -167,7 +167,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -251,7 +251,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -330,7 +330,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -397,7 +397,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -480,7 +480,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -554,7 +554,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -694,7 +694,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -783,7 +783,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -869,7 +869,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -968,7 +968,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1084,7 +1084,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1207,7 +1207,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1315,7 +1315,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1410,7 +1410,7 @@ class RuntimeErrorsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

--- a/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeInstrumentTest.scala
+++ b/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeInstrumentTest.scala
@ -152,7 +152,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -201,7 +201,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -258,7 +258,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -318,7 +318,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -377,7 +377,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -434,7 +434,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -493,7 +493,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -558,7 +558,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -618,7 +618,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -675,7 +675,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -737,7 +737,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -799,7 +799,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -859,7 +859,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -931,7 +931,7 @@ class RuntimeInstrumentTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

--- 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
@ -365,7 +365,7 @@ class RuntimeServerTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -473,7 +473,7 @@ class RuntimeServerTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -575,10 +575,10 @@ class RuntimeServerTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None
-    context.send(Api.Request(Api.OpenFileNotification(aFile, aCode, true)))
+    context.send(Api.Request(Api.OpenFileNotification(aFile, aCode)))
    context.receiveNone shouldEqual None

    // push main
@ -661,7 +661,7 @@ class RuntimeServerTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -720,7 +720,7 @@ class RuntimeServerTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -779,7 +779,7 @@ class RuntimeServerTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -840,7 +840,7 @@ class RuntimeServerTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -901,7 +901,7 @@ class RuntimeServerTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -969,7 +969,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1067,7 +1067,7 @@ class RuntimeServerTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1148,7 +1148,7 @@ class RuntimeServerTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1236,7 +1236,7 @@ class RuntimeServerTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1434,7 +1434,7 @@ class RuntimeServerTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1627,7 +1627,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1673,7 +1673,7 @@ class RuntimeServerTest
    val mainFile = context.writeMain(code)

    // Open the new file
-    context.send(Api.Request(Api.OpenFileNotification(mainFile, code, true)))
+    context.send(Api.Request(Api.OpenFileNotification(mainFile, code)))
    context.receiveNone shouldEqual None
    context.consumeOut shouldEqual List()

@ -1739,7 +1739,7 @@ class RuntimeServerTest
    val mainFile = context.writeMain(code)

    // Open the new file
-    context.send(Api.Request(Api.OpenFileNotification(mainFile, code, true)))
+    context.send(Api.Request(Api.OpenFileNotification(mainFile, code)))
    context.receiveNone shouldEqual None

    // Push new item on the stack to trigger the re-execution
@ -1798,7 +1798,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, context.Main.code, true))
+      Api.Request(Api.OpenFileNotification(mainFile, context.Main.code))
    )
    context.receiveNone shouldEqual None

@ -1874,7 +1874,7 @@ class RuntimeServerTest
    val mainFile = context.writeMain(code)

    // Open the new file
-    context.send(Api.Request(Api.OpenFileNotification(mainFile, code, true)))
+    context.send(Api.Request(Api.OpenFileNotification(mainFile, code)))
    context.receiveNone shouldEqual None
    context.consumeOut shouldEqual List()

@ -1951,7 +1951,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1997,7 +1997,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2049,7 +2049,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )

    context.receiveNone shouldEqual None
@ -2102,7 +2102,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )

    context.receiveNone shouldEqual None
@ -2146,7 +2146,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2197,7 +2197,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2255,7 +2255,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2323,7 +2323,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2399,7 +2399,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2477,7 +2477,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2556,7 +2556,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2650,7 +2650,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2711,7 +2711,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2771,7 +2771,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2835,7 +2835,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2899,7 +2899,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -2959,7 +2959,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -3008,7 +3008,7 @@ class RuntimeServerTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -3055,7 +3055,7 @@ class RuntimeServerTest
    // open file
    context.send(
      Api.Request(
-        Api.OpenFileNotification(mainFile, contents, isIndexed = true)
+        Api.OpenFileNotification(mainFile, contents)
      )
    )
    context.receiveNone shouldEqual None
--- a/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeStdlibTest.scala
+++ b/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeStdlibTest.scala
@ -165,7 +165,7 @@ class RuntimeStdlibTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveOne shouldEqual None

@ -208,8 +208,8 @@ class RuntimeStdlibTest
    val stdlibSuggestions = responses.collect {
      case Api.Response(
            None,
-            Api.SuggestionsDatabaseModuleUpdateNotification(file, _, as, xs)
-          ) if file.getPath.contains("Vector") =>
+            Api.SuggestionsDatabaseModuleUpdateNotification(module, _, as, xs)
+          ) if module.contains("Vector") =>
        (xs.nonEmpty || as.nonEmpty) shouldBe true
        xs.toVector.head.suggestion.module shouldEqual "Standard.Base.Data.Vector"
    }
@ -219,8 +219,8 @@ class RuntimeStdlibTest
    val builtinsSuggestions = responses.collect {
      case Api.Response(
            None,
-            Api.SuggestionsDatabaseModuleUpdateNotification(file, _, as, xs)
-          ) if file.getPath.contains("Builtins") =>
+            Api.SuggestionsDatabaseModuleUpdateNotification(module, _, as, xs)
+          ) if module.contains("Builtins") =>
        (xs.nonEmpty || as.nonEmpty) shouldBe true
    }
    builtinsSuggestions.length shouldBe 1
--- a/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeSuggestionUpdatesTest.scala
+++ b/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeSuggestionUpdatesTest.scala
@ -138,7 +138,7 @@ class RuntimeSuggestionUpdatesTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, code, false))
+      Api.Request(Api.OpenFileNotification(mainFile, code))
    )
    context.receiveNone shouldEqual None

@ -160,7 +160,7 @@ class RuntimeSuggestionUpdatesTest
      Api.Response(requestId, Api.PushContextResponse(contextId)),
      Api.Response(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          file    = mainFile,
+          module  = moduleName,
          version = version,
          actions = Vector(Api.SuggestionsDatabaseAction.Clean(moduleName)),
          updates = Tree.Root(
@ -230,7 +230,7 @@ class RuntimeSuggestionUpdatesTest
    context.receive(2) should contain theSameElementsAs Seq(
      Api.Response(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          file = mainFile,
+          module = moduleName,
          version = contentsVersion(
            """from Standard.Builtins import all
              |
@ -313,7 +313,7 @@ class RuntimeSuggestionUpdatesTest
    context.receive(2) should contain theSameElementsAs Seq(
      Api.Response(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          file = mainFile,
+          module = moduleName,
          version = contentsVersion(
            """from Standard.Builtins import all
              |
@ -416,7 +416,7 @@ class RuntimeSuggestionUpdatesTest
    context.receive(2) should contain theSameElementsAs Seq(
      Api.Response(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          file = mainFile,
+          module = moduleName,
          version = contentsVersion(
            """from Standard.Builtins import all
              |
@ -528,7 +528,7 @@ class RuntimeSuggestionUpdatesTest
    context.receive(2) should contain theSameElementsAs Seq(
      Api.Response(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          file = mainFile,
+          module = moduleName,
          version = contentsVersion(
            """from Standard.Builtins import all
              |
@ -668,7 +668,7 @@ class RuntimeSuggestionUpdatesTest
    context.receive(2) should contain theSameElementsAs Seq(
      Api.Response(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          file = mainFile,
+          module = moduleName,
          version = contentsVersion(
            """from Standard.Builtins import all
              |
@ -764,7 +764,7 @@ class RuntimeSuggestionUpdatesTest

    // open file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, false))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -786,7 +786,7 @@ class RuntimeSuggestionUpdatesTest
      Api.Response(requestId, Api.PushContextResponse(contextId)),
      Api.Response(
        Api.SuggestionsDatabaseModuleUpdateNotification(
-          file    = mainFile,
+          module  = moduleName,
          version = version,
          actions = Vector(Api.SuggestionsDatabaseAction.Clean(moduleName)),
          updates = Tree.Root(
--- a/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeVisualisationsTest.scala
+++ b/engine/runtime/src/test/scala/org/enso/interpreter/test/instrument/RuntimeVisualisationsTest.scala
@ -288,8 +288,7 @@ class RuntimeVisualisationsTest
      Api.Request(
        Api.OpenFileNotification(
          visualisationFile,
-          context.Visualisation.code,
-          true
+          context.Visualisation.code
        )
      )
    )
@ -306,7 +305,7 @@ class RuntimeVisualisationsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -402,8 +401,7 @@ class RuntimeVisualisationsTest
      Api.Request(
        Api.OpenFileNotification(
          visualisationFile,
-          context.Visualisation.code,
-          true
+          context.Visualisation.code
        )
      )
    )
@ -420,7 +418,7 @@ class RuntimeVisualisationsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -536,14 +534,13 @@ class RuntimeVisualisationsTest
      Api.Request(
        Api.OpenFileNotification(
          visualisationFile,
-          context.Visualisation.code,
-          true
+          context.Visualisation.code
        )
      )
    )
    context.receiveNone shouldEqual None
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -659,14 +656,13 @@ class RuntimeVisualisationsTest
      Api.Request(
        Api.OpenFileNotification(
          visualisationFile,
-          context.Visualisation.code,
-          true
+          context.Visualisation.code
        )
      )
    )
    context.receiveNone shouldEqual None
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -774,15 +770,14 @@ class RuntimeVisualisationsTest

    // open files
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None
    context.send(
      Api.Request(
        Api.OpenFileNotification(
          visualisationFile,
-          context.Visualisation.code,
-          true
+          context.Visualisation.code
        )
      )
    )
@ -896,15 +891,14 @@ class RuntimeVisualisationsTest

    // open files
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None
    context.send(
      Api.Request(
        Api.OpenFileNotification(
          visualisationFile,
-          context.Visualisation.code,
-          true
+          context.Visualisation.code
        )
      )
    )
@ -1038,14 +1032,13 @@ class RuntimeVisualisationsTest
      Api.Request(
        Api.OpenFileNotification(
          visualisationFile,
-          context.Visualisation.code,
-          true
+          context.Visualisation.code
        )
      )
    )
    context.receiveNone shouldEqual None
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1137,15 +1130,14 @@ class RuntimeVisualisationsTest

    // open files
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None
    context.send(
      Api.Request(
        Api.OpenFileNotification(
          visualisationFile,
-          context.Visualisation.code,
-          true
+          context.Visualisation.code
        )
      )
    )
@ -1281,7 +1273,7 @@ class RuntimeVisualisationsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1341,7 +1333,7 @@ class RuntimeVisualisationsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1429,7 +1421,7 @@ class RuntimeVisualisationsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1503,7 +1495,7 @@ class RuntimeVisualisationsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

@ -1591,8 +1583,7 @@ class RuntimeVisualisationsTest
      Api.Request(
        Api.OpenFileNotification(
          visualisationFile,
-          visualisationCode,
-          true
+          visualisationCode
        )
      )
    )
@ -1609,7 +1600,7 @@ class RuntimeVisualisationsTest

    // Open the new file
    context.send(
-      Api.Request(Api.OpenFileNotification(mainFile, contents, true))
+      Api.Request(Api.OpenFileNotification(mainFile, contents))
    )
    context.receiveNone shouldEqual None

--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/FileVersionsRepo.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/FileVersionsRepo.scala
@ -1,48 +0,0 @@
-package org.enso.searcher
-
-import java.io.File
-
-/** The object for accessing the database containing the file versions. */
-trait FileVersionsRepo[F[_]] {
-
-  /** Initialize the repo. */
-  def init: F[Unit]
-
-  /** Get the file version.
-    *
-    * @param file the file path
-    * @return the version digest
-    */
-  def getVersion(file: File): F[Option[Array[Byte]]]
-
-  /** Set the file version.
-    *
-    * @param file the file path
-    * @param digest the version digest
-    * @return previously recorded file version
-    */
-  def setVersion(file: File, digest: Array[Byte]): F[Option[Array[Byte]]]
-
-  /** Update the version if it differs from the recorded version.
-    *
-    * @param file the file path
-    * @param digest the version digest
-    * @return `true` if the version has been updated
-    */
-  def updateVersion(file: File, digest: Array[Byte]): F[Boolean]
-
-  /** Update the versions in batch.
-    *
-    * @param versions files with corresponding digests
-    */
-  def updateVersions(versions: Seq[(File, Array[Byte])]): F[Unit]
-
-  /** Remove the version record.
-    *
-    * @param file the file path
-    */
-  def remove(file: File): F[Unit]
-
-  /** Clean the repo. */
-  def clean: F[Unit]
-}
--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/VersionsRepo.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/VersionsRepo.scala
@ -0,0 +1,52 @@
+package org.enso.searcher
+
+/** The object for accessing the database containing the module versions. */
+trait VersionsRepo[F[_]] {
+
+  /** Initialize the repo. */
+  def init: F[Unit]
+
+  /** Get the module version.
+    *
+    * @param module the module name
+    * @return the version digest
+    */
+  def getVersion(module: String): F[Option[Array[Byte]]]
+
+  /** Set the module version.
+    *
+    * @param module the module name
+    * @param digest the version digest
+    * @return previously recorded version
+    */
+  def setVersion(module: String, digest: Array[Byte]): F[Option[Array[Byte]]]
+
+  /** Update the version if it differs from the recorded version.
+    *
+    * @param module the module name
+    * @param digest the version digest
+    * @return `true` if the version has been updated
+    */
+  def updateVersion(module: String, digest: Array[Byte]): F[Boolean]
+
+  /** Update the versions in batch.
+    *
+    * @param versions files with corresponding digests
+    */
+  def updateVersions(versions: Seq[(String, Array[Byte])]): F[Unit]
+
+  /** Remove the version record.
+    *
+    * @param module the module name
+    */
+  def remove(module: String): F[Unit]
+
+  /** Remove a list of version records.
+    *
+    * @param modules the list of modules to remove
+    */
+  def remove(modules: Seq[String]): F[Unit]
+
+  /** Clean the repo. */
+  def clean: F[Unit]
+}
--- 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
@ -202,7 +202,7 @@ final class SqlSuggestionsRepo(val db: SqlDatabase)(implicit
      } yield ()

    val tables: Seq[TableQuery[RelationalTable[_]]] =
-      Seq(Suggestions, Arguments, SuggestionsVersions, SchemaVersion)
+      Seq(Suggestions, Arguments, SuggestionsVersion, SchemaVersion)
        .asInstanceOf[Seq[TableQuery[RelationalTable[_]]]]
    val initSchemas =
      for {
@ -222,7 +222,7 @@ final class SqlSuggestionsRepo(val db: SqlDatabase)(implicit
    for {
      _ <- Suggestions.delete
      _ <- Arguments.delete
-      _ <- SuggestionsVersions.delete
+      _ <- SuggestionsVersion.delete
    } yield ()
  }

@ -758,17 +758,17 @@ final class SqlSuggestionsRepo(val db: SqlDatabase)(implicit
  /** The query to get current version of the repo. */
  private def currentVersionQuery: DBIO[Long] = {
    for {
-      versionOpt <- SuggestionsVersions.result.headOption
+      versionOpt <- SuggestionsVersion.result.headOption
    } yield versionOpt.flatMap(_.id).getOrElse(0L)
  }

  /** The query to increment the current version of the repo. */
  private def incrementVersionQuery: DBIO[Long] = {
    val incrementQuery = for {
-      version <- SuggestionsVersions.returning(
-        SuggestionsVersions.map(_.id)
+      version <- SuggestionsVersion.returning(
+        SuggestionsVersion.map(_.id)
      ) += SuggestionsVersionRow(None)
-      _ <- SuggestionsVersions.filterNot(_.id === version).delete
+      _ <- SuggestionsVersion.filterNot(_.id === version).delete
    } yield version
    incrementQuery
  }
--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlVersionsRepo.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlVersionsRepo.scala
@ -1,45 +1,51 @@
 package org.enso.searcher.sql

-import java.io.File
 import java.util

-import org.enso.searcher.FileVersionsRepo
+import org.enso.searcher.VersionsRepo
 import slick.jdbc.SQLiteProfile.api._
 import slick.jdbc.meta.MTable

 import scala.concurrent.{ExecutionContext, Future}

 final class SqlVersionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
-    extends FileVersionsRepo[Future] {
+    extends VersionsRepo[Future] {

  /** Initialize the repo. */
  override def init: Future[Unit] =
    db.run(initQuery)

  /** @inheritdoc */
-  override def getVersion(file: File): Future[Option[Array[Byte]]] =
-    db.run(getVersionQuery(file))
+  override def getVersion(module: String): Future[Option[Array[Byte]]] =
+    db.run(getVersionQuery(module))

  /** @inheritdoc */
  override def setVersion(
-    file: File,
+    module: String,
    digest: Array[Byte]
  ): Future[Option[Array[Byte]]] =
-    db.run(setVersionQuery(file, digest))
+    db.run(setVersionQuery(module, digest))

  /** @inheritdoc */
-  override def updateVersion(file: File, digest: Array[Byte]): Future[Boolean] =
-    db.run(updateVersionQuery(file, digest))
+  override def updateVersion(
+    module: String,
+    digest: Array[Byte]
+  ): Future[Boolean] =
+    db.run(updateVersionQuery(module, digest))

  /** @inheritdoc */
  override def updateVersions(
-    versions: Seq[(File, Array[Byte])]
+    versions: Seq[(String, Array[Byte])]
  ): Future[Unit] =
    db.run(updateVersionsQuery(versions))

  /** @inheritdoc */
-  override def remove(file: File): Future[Unit] =
-    db.run(removeQuery(file))
+  override def remove(module: String): Future[Unit] =
+    db.run(removeQuery(module))
+
+  /** @inheritdoc */
+  override def remove(modules: Seq[String]): Future[Unit] =
+    db.run(removeModulesQuery(modules))

  /** @inheritdoc */
  override def clean: Future[Unit] =
@ -51,7 +57,7 @@ final class SqlVersionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)

  /** The query to initialize the repo. */
  private def initQuery: DBIO[Unit] = {
-    val table = FileVersions
+    val table = ModuleVersions
    for {
      tables <- MTable.getTables(table.shaped.value.tableName)
      _      <- if (tables.isEmpty) table.schema.create else DBIO.successful(())
@ -60,54 +66,54 @@ final class SqlVersionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)

  /** The query to clean the repo. */
  private def cleanQuery: DBIO[Unit] =
-    FileVersions.delete >> DBIO.successful(())
+    ModuleVersions.delete >> DBIO.successful(())

  /** The query to get the version digest of the file.
    *
-    * @param file the file path
+    * @param module the module name
    * @return the version digest
    */
-  private def getVersionQuery(file: File): DBIO[Option[Array[Byte]]] = {
+  private def getVersionQuery(module: String): DBIO[Option[Array[Byte]]] = {
    val query = for {
-      row <- FileVersions
-      if row.path === file.toString
+      row <- ModuleVersions
+      if row.module === module
    } yield row.digest
    query.result.headOption
  }

  /** The query to set the version digest of the file.
    *
-    * @param file the file path
+    * @param module the module name
    * @param version the version digest
    * @return the previously recorded vile version
    */
  private def setVersionQuery(
-    file: File,
+    module: String,
    version: Array[Byte]
  ): DBIO[Option[Array[Byte]]] = {
-    val upsertQuery = FileVersions
-      .insertOrUpdate(FileVersionRow(file.toString, version))
+    val upsertQuery =
+      ModuleVersions.insertOrUpdate(ModuleVersionRow(module, version))
    for {
-      version <- getVersionQuery(file)
+      version <- getVersionQuery(module)
      _       <- upsertQuery
    } yield version
  }

  /** The query to update the version if it differs from the recorded version.
    *
-    * @param file the file path
+    * @param module the module name
    * @param version the version digest
    * @return `true` if the version has been updated
    */
  private def updateVersionQuery(
-    file: File,
+    module: String,
    version: Array[Byte]
  ): DBIO[Boolean] =
    for {
-      repoVersion <- getVersionQuery(file)
-      versionsEquals = repoVersion.fold(false)(compareVersions(_, version))
+      moduleVersion <- getVersionQuery(module)
+      versionsEquals = moduleVersion.fold(false)(compareVersions(_, version))
      _ <-
-        if (!versionsEquals) setVersionQuery(file, version)
+        if (!versionsEquals) setVersionQuery(module, version)
        else DBIO.successful(None)
    } yield !versionsEquals

@ -116,11 +122,11 @@ final class SqlVersionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
    * @param versions files with corresponding digests
    */
  private def updateVersionsQuery(
-    versions: Seq[(File, Array[Byte])]
+    versions: Seq[(String, Array[Byte])]
  ): DBIO[Unit] =
    if (versions.nonEmpty) {
-      def upsertQuery(file: File, version: Array[Byte]) = FileVersions
-        .insertOrUpdate(FileVersionRow(file.toString, version))
+      def upsertQuery(module: String, version: Array[Byte]) =
+        ModuleVersions.insertOrUpdate(ModuleVersionRow(module, version))
      DBIO.sequence(versions.map(Function.tupled(upsertQuery))) >>
      DBIO.successful(())
    } else {
@ -129,16 +135,29 @@ final class SqlVersionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)

  /** The query to remove the version record.
    *
-    * @param file the file path
+    * @param module the module name
    */
-  private def removeQuery(file: File): DBIO[Unit] = {
+  private def removeQuery(module: String): DBIO[Unit] = {
    val query = for {
-      row <- FileVersions
-      if row.path === file.toString
+      row <- ModuleVersions
+      if row.module === module
    } yield row
    query.delete >> DBIO.successful(())
  }

+  /** The query to remove multiple module versions.
+    *
+    * @param modules the list of module names
+    */
+  private def removeModulesQuery(modules: Seq[String]): DBIO[Unit] = {
+    val deleteQuery = ModuleVersions
+      .filter(_.module.inSet(modules))
+      .delete
+    for {
+      _ <- deleteQuery
+    } yield ()
+  }
+
  private def compareVersions(v1: Array[Byte], v2: Array[Byte]): Boolean =
    util.Arrays.equals(v1, v2)

--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/Tables.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/Tables.scala
@ -74,10 +74,10 @@ case class SchemaVersionRow(id: Option[Long])

 /** A row in the file_versions table
  *
-  * @param path the file path
+  * @param module the module name
  * @param digest the file version
  */
-case class FileVersionRow(path: String, digest: Array[Byte])
+case class ModuleVersionRow(module: String, digest: Array[Byte])

 /** The type of a suggestion. */
 object SuggestionKind {
@ -215,15 +215,16 @@ final class SuggestionsTable(tag: Tag)
    )
 }

-/** The schema of the file_versions table. */
+/** The schema of the module_versions table. */
@nowarn("msg=multiarg infix syntax")
-final class FileVersionsTable(tag: Tag)
-    extends Table[FileVersionRow](tag, "file_versions") {
+final class ModuleVersionsTable(tag: Tag)
+    extends Table[ModuleVersionRow](tag, "module_versions") {

-  def path   = column[String]("path", O.PrimaryKey)
+  def module = column[String]("module", O.PrimaryKey)
  def digest = column[Array[Byte]]("digest")

-  def * = (path, digest) <> (FileVersionRow.tupled, FileVersionRow.unapply)
+  def * =
+    (module, digest) <> (ModuleVersionRow.tupled, ModuleVersionRow.unapply)
 }

 /** The schema of the suggestions_version table. */
@ -250,12 +251,12 @@ object Arguments extends TableQuery(new ArgumentsTable(_))

 object Suggestions extends TableQuery(new SuggestionsTable(_))

-object FileVersions extends TableQuery(new FileVersionsTable(_))
+object ModuleVersions extends TableQuery(new ModuleVersionsTable(_))

-object SuggestionsVersions extends TableQuery(new SuggestionsVersionTable(_))
+object SuggestionsVersion extends TableQuery(new SuggestionsVersionTable(_))

 object SchemaVersion extends TableQuery(new SchemaVersionTable(_)) {

  /** The current schema version. */
-  val CurrentVersion: Long = 2
+  val CurrentVersion: Long = 3
 }
--- a/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/FileVersionsRepoTest.scala
+++ b/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/FileVersionsRepoTest.scala
@ -1,6 +1,5 @@
 package org.enso.searcher.sql

-import java.io.File
 import java.nio.file.{Files, Path}
 import java.util

@ -13,7 +12,7 @@ import scala.concurrent.ExecutionContext.Implicits.global
 import scala.concurrent.duration._
 import scala.util.Random

-class FileVersionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {
+class VersionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {

  val Timeout: FiniteDuration = 20.seconds

@ -49,12 +48,12 @@ class FileVersionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {
    }

    "insert digest" taggedAs Retry in withRepo { repo =>
-      val file   = new File("/foo/bar")
+      val module = "Foo.Bar"
      val digest = nextDigest()
      val action =
        for {
-          v1 <- repo.setVersion(file, digest)
-          v2 <- repo.getVersion(file)
+          v1 <- repo.setVersion(module, digest)
+          v2 <- repo.getVersion(module)
        } yield (v1, v2)

      val (v1, v2) = Await.result(action, Timeout)
@ -64,14 +63,14 @@ class FileVersionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {
    }

    "set digest" taggedAs Retry in withRepo { repo =>
-      val file    = new File("/foo/bar")
+      val module  = "Foo.Bar"
      val digest1 = nextDigest()
      val digest2 = nextDigest()
      val action =
        for {
-          v1 <- repo.setVersion(file, digest1)
-          v2 <- repo.setVersion(file, digest2)
-          v3 <- repo.getVersion(file)
+          v1 <- repo.setVersion(module, digest1)
+          v2 <- repo.setVersion(module, digest2)
+          v3 <- repo.getVersion(module)
        } yield (v1, v2, v3)

      val (v1, v2, v3) = Await.result(action, Timeout)
@ -83,18 +82,18 @@ class FileVersionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {
    }

    "update digest" taggedAs Retry in withRepo { repo =>
-      val file    = new File("/foo/bazz")
+      val module  = "Foo.Bar"
      val digest1 = nextDigest()
      val digest2 = nextDigest()
      val digest3 = nextDigest()
      val action =
        for {
-          b1 <- repo.updateVersion(file, digest1)
-          v2 <- repo.setVersion(file, digest2)
-          b2 <- repo.updateVersion(file, digest2)
-          b3 <- repo.updateVersion(file, digest3)
-          b4 <- repo.updateVersion(file, digest3)
-          v3 <- repo.getVersion(file)
+          b1 <- repo.updateVersion(module, digest1)
+          v2 <- repo.setVersion(module, digest2)
+          b2 <- repo.updateVersion(module, digest2)
+          b3 <- repo.updateVersion(module, digest3)
+          b4 <- repo.updateVersion(module, digest3)
+          v3 <- repo.getVersion(module)
        } yield (v2, v3, b1, b2, b3, b4)

      val (v2, v3, b1, b2, b3, b4) = Await.result(action, Timeout)
@ -109,18 +108,18 @@ class FileVersionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {
    }

    "batch update digest" taggedAs Retry in withRepo { repo =>
-      val file1   = new File("/foo/1")
-      val file2   = new File("/foo/2")
+      val module1 = "Foo.Bar"
+      val module2 = "Foo.Baz"
      val digest0 = nextDigest()
      val digest1 = nextDigest()
      val digest2 = nextDigest()
-      val input   = Seq(file1 -> digest1, file2 -> digest2)
+      val input   = Seq(module1 -> digest1, module2 -> digest2)
      val action =
        for {
-          _  <- repo.setVersion(file1, digest0)
+          _  <- repo.setVersion(module1, digest0)
          _  <- repo.updateVersions(input)
-          v1 <- repo.getVersion(file1)
-          v2 <- repo.getVersion(file2)
+          v1 <- repo.getVersion(module1)
+          v2 <- repo.getVersion(module2)
        } yield (v1, v2)

      val (v1, v2) = Await.result(action, Timeout)
@ -131,13 +130,13 @@ class FileVersionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {
    }

    "delete digest" taggedAs Retry in withRepo { repo =>
-      val file   = new File("/foo/bar")
+      val module = "Foo.Bar"
      val digest = nextDigest()
      val action =
        for {
-          v1 <- repo.setVersion(file, digest)
-          _  <- repo.remove(file)
-          v2 <- repo.getVersion(file)
+          v1 <- repo.setVersion(module, digest)
+          _  <- repo.remove(module)
+          v2 <- repo.getVersion(module)
        } yield (v1, v2)

      val (v1, v2) = Await.result(action, Timeout)