diff --git a/build.sbt b/build.sbt
index 8b84a3e0..2d5d4952 100644
--- a/build.sbt
+++ b/build.sbt
@@ -27,7 +27,7 @@ lazy val V =
     val testcontainers = "0.39.3"
     val requests = "0.6.5"
     val minimalMillVersion = "0.10.0"
-    val millScipVersion = "0.3.5"
+    val millScipVersion = "0.3.6"
     val kotlinGradlePlugin = "1.5.31"
   }
 
diff --git a/docs/getting-started.md b/docs/getting-started.md
index a4b499a8..5d9ae9cd 100644
--- a/docs/getting-started.md
+++ b/docs/getting-started.md
@@ -26,7 +26,7 @@ after we renamed the "Docker container" section into "Docker image". -->
 Use the `sourcegraph/scip-java` Docker image to run `scip-java`.
 
 ```sh
-$ docker run -v $(pwd):/home/gradle --env JVM_VERSION=17 sourcegraph/scip-java:latest scip-java index
+$ docker run -v $(pwd):/sources --env JVM_VERSION=17 sourcegraph/scip-java:latest scip-java index
 $ src code-intel upload # (optional) upload index to Sourcegraph
 ```
 
@@ -47,13 +47,13 @@ Use the following commands to use a different JVM version:
 
 ```sh
 # Java 8
-docker run -v $(pwd):/home/gradle --env JVM_VERSION=8 sourcegraph/scip-java:latest scip-java index
+docker run -v $(pwd):/sources --env JVM_VERSION=8 sourcegraph/scip-java:latest scip-java index
 
 # Java 11
-docker run -v $(pwd):/home/gradle --env JVM_VERSION=11 sourcegraph/scip-java:latest scip-java index
+docker run -v $(pwd):/sources --env JVM_VERSION=11 sourcegraph/scip-java:latest scip-java index
 
 # Java 17 (default)
-docker run -v $(pwd):/home/gradle --env JVM_VERSION=17 sourcegraph/scip-java:latest scip-java index
+docker run -v $(pwd):/sources --env JVM_VERSION=17 sourcegraph/scip-java:latest scip-java index
 ```
 
 ### Java launcher
diff --git a/docs/manual-configuration.md b/docs/manual-configuration.md
index a9161608..3b1c1c03 100644
--- a/docs/manual-configuration.md
+++ b/docs/manual-configuration.md
@@ -163,6 +163,7 @@ one of the following files in the SemanticDB _targetroot_ directory (the path in
 
 - `javacopts.txt`: line-separated list of Java compiler options that got passed
   to the compiler. For example,
+
   ```sh
   $ cat $TARGETROOT/javacopts.txt
   -Xlint
@@ -172,22 +173,25 @@ one of the following files in the SemanticDB _targetroot_ directory (the path in
   /path/to/classes/directory
   /path/to/com/example/Main.java
   ```
+
   The `javacopts.txt` file format can only be used if the jars on the dependency
   classpath have sibling `.pom` files. In some build tools like Gradle, the POM
   files are not siblings to the jars on the classpath so the `javacopts.txt`
   format cannot be used.
+
 - `dependencies.txt`: a tab-separated values file where the columns are: group
   ID, artifact ID, version and jar path. For example,
+
   ```sh
   $ cat $TARGETROOT/dependencies.txt
   junit junit 4.13.2  /path/to/junit.jar
   org.hamcrest hamcrest-core 1.3  /path/to/hamcrest-core.jar
   ```
+
   The `dependencies.txt` format is used by scip-java to map symbols such as
-  `org.junit.Assert` to Maven co-ordinates like `junit:junit:4.13.2`. As long as
+  `org.junit.Assert` to Maven coordinates like `junit:junit:4.13.2`. As long as
   your Sourcegraph instance has another repository that defines that symbol, the
-  cross-repository navigation should succeed. Only jar files are supported at
-  the moment, classes directories are ignored.
+  cross-repository navigation should succeed. 
 
 Cross-repository navigation is a feature that allows "goto definition" and "find
 references" to show results from multiple repositories.
diff --git a/project/build.properties b/project/build.properties
index 52413ab7..e8a1e246 100644
--- a/project/build.properties
+++ b/project/build.properties
@@ -1 +1 @@
-sbt.version=1.9.3
+sbt.version=1.9.7
diff --git a/scip-java/src/main/scala/com/sourcegraph/scip_java/buildtools/SbtBuildTool.scala b/scip-java/src/main/scala/com/sourcegraph/scip_java/buildtools/SbtBuildTool.scala
index 8ac28d71..4633bc92 100644
--- a/scip-java/src/main/scala/com/sourcegraph/scip_java/buildtools/SbtBuildTool.scala
+++ b/scip-java/src/main/scala/com/sourcegraph/scip_java/buildtools/SbtBuildTool.scala
@@ -43,15 +43,19 @@ class SbtBuildTool(index: IndexCommand) extends BuildTool("sbt", index) {
 
   private def unconditionallyGenerateScip(): Int =
     Using.resource(sourcegraphSbtPluginFile()) { _ =>
+      val buildCommand = index.finalBuildCommand(List("sourcegraphScip"))
+
       val sourcegraphScip = index
-        .process(List("sbt", "sourcegraphEnable", "sourcegraphScip"))
+        .process(List("sbt", "sourcegraphEnable") ++ buildCommand)
+
       val inputDump = index
         .workingDirectory
         .resolve("target")
         .resolve("sbt-sourcegraph")
         .resolve("index.scip")
+
       if (sourcegraphScip.exitCode == 0 && Files.isRegularFile(inputDump)) {
-        val outputDump = index.workingDirectory.resolve("index.scip")
+        val outputDump = index.workingDirectory.resolve(index.output)
         Files.copy(inputDump, outputDump, StandardCopyOption.REPLACE_EXISTING)
         index.app.info(outputDump.toString)
       }
diff --git a/semanticdb-gradle-plugin/src/main/scala/SemanticdbGradlePlugin.scala b/semanticdb-gradle-plugin/src/main/scala/SemanticdbGradlePlugin.scala
index 6cc0924f..d11cf79e 100644
--- a/semanticdb-gradle-plugin/src/main/scala/SemanticdbGradlePlugin.scala
+++ b/semanticdb-gradle-plugin/src/main/scala/SemanticdbGradlePlugin.scala
@@ -5,7 +5,7 @@ import java.nio.file.Paths
 import java.{util => ju}
 
 import scala.jdk.CollectionConverters._
-import scala.util.control.NonFatal
+import scala.util._
 
 import com.sourcegraph.scip_java.BuildInfo
 import org.gradle.api.DefaultTask
@@ -416,42 +416,56 @@ class WriteDependencies extends DefaultTask {
     // List the project itself as a dependency so that we can assign project name/version to symbols that are defined in this project.
     // The code below is roughly equivalent to the following with Groovy:
     //   deps += "$publication.groupId $publication.artifactId $publication.version $sourceSets.main.output.classesDirectory"
-    try {
-      for {
-        classesDirectory <- project
-          .getExtensions()
-          .getByType(classOf[SourceSetContainer])
-          .getByName("main")
-          .getOutput()
-          .getClassesDirs()
-          .getFiles()
-          .asScala
-          .toList
-          .map(_.getAbsolutePath())
-          .sorted
-          .take(1)
-        publication <-
+
+    Try(
+      project
+        .getExtensions()
+        .findByType(classOf[PublishingExtension])
+        .getPublications()
+        .withType(classOf[MavenPublication])
+        .asScala
+    ) match {
+      case Failure(exception) =>
+        System
+          .err
+          .println(
+            s"""
+               |Failed to extract Maven publication from the project `${project
+              .getName()}`. 
+               |This will not prevent a SCIP index from being created, but the symbols 
+               |extracted from this project won't be available for cross-repository navigation,
+               |as this project doesn't define any Maven coordinates by which it can be referred back to.
+               |See here for more details: https://sourcegraph.github.io/scip-java/docs/manual-configuration.html#step-5-optional-enable-cross-repository-navigation
+               |Here's the raw error message:
+               |  "${exception.getMessage()}"
+               |Continuing without cross-repository support.
+          """.stripMargin.trim()
+          )
+
+      case Success(publications) =>
+        publications.foreach { publication =>
           project
             .getExtensions()
-            .findByType(classOf[PublishingExtension])
-            .getPublications()
-            .withType(classOf[MavenPublication])
+            .getByType(classOf[SourceSetContainer])
+            .getByName("main")
+            .getOutput()
+            .getClassesDirs()
+            .getFiles()
             .asScala
-      } {
-        deps +=
-          List(
-            publication.getGroupId(),
-            publication.getArtifactId(),
-            publication.getVersion(),
-            classesDirectory
-          ).mkString("\t")
-      }
-    } catch {
-      case NonFatal(ex) =>
-        println(
-          s"Failed to extract publication from project ${project.getName()}"
-        )
-        ex.printStackTrace()
+            .toList
+            .map(_.getAbsolutePath())
+            .sorted
+            .take(1)
+            .foreach { classesDirectory =>
+              deps +=
+                List(
+                  publication.getGroupId(),
+                  publication.getArtifactId(),
+                  publication.getVersion(),
+                  classesDirectory
+                ).mkString("\t")
+            }
+        }
     }
 
     project
diff --git a/tests/buildTools/src/test/scala/tests/SbtBuildToolSuite.scala b/tests/buildTools/src/test/scala/tests/SbtBuildToolSuite.scala
index 9eea1f6f..2f97a72f 100644
--- a/tests/buildTools/src/test/scala/tests/SbtBuildToolSuite.scala
+++ b/tests/buildTools/src/test/scala/tests/SbtBuildToolSuite.scala
@@ -1,15 +1,18 @@
 package tests
 
-abstract class SbtBuildToolSuite(sbtVersion: String)
+abstract class SbtBuildToolSuite(val sbtVersion: String)
     extends BaseBuildToolSuite {
-  List("2.11.9", "2.12.18", "2.13.11", "3.3.0").foreach { scalaVersion =>
+  val scala2Versions = List("2.11.9", "2.12.18", "2.13.11")
+  val scala3Versions = List("3.3.1")
+
+  (scala2Versions ++ scala3Versions).foreach { scalaVersion =>
     checkBuild(
       s"basic-sbt=$sbtVersion-scala=$scalaVersion",
       s"""|/build.sbt
           |scalaVersion := "$scalaVersion"
           |libraryDependencies += "junit" % "junit" % "4.13.2"
           |/project/build.properties
-          |sbt.version=1.5.2
+          |sbt.version=$sbtVersion
           |/src/main/java/example/ExampleJava.java
           |package example;
           |import org.junit.Assert;
@@ -29,8 +32,27 @@ abstract class SbtBuildToolSuite(sbtVersion: String)
       targetRoot = Some("target")
     )
   }
-
 }
 
-class Sbt_1_BuildToolSuite extends SbtBuildToolSuite("1.5.2")
-class Sbt_013_BuildToolSuite extends SbtBuildToolSuite("0.13.17")
+class Sbt_1_BuildToolSuite extends SbtBuildToolSuite("1.5.2") {
+  checkBuild(
+    s"custom-sbt-command=$sbtVersion",
+    s"""|/build.sbt
+        |lazy val bla = project.in(file("bla"))
+        |lazy val blaJS = project.in(file("bla-js")).enablePlugins(ScalaJSPlugin)
+        |/project/plugins.sbt
+        |addSbtPlugin("org.scala-js" % "sbt-scalajs" % "1.14.0")
+        |/project/build.properties
+        |sbt.version=$sbtVersion
+        |/bla/src/main/scala/example/ExampleScala.scala
+        |package example
+        |class ExampleScala()
+        |/bla-js/src/main/scala/example/ExampleScala.scala
+        |package example
+        |class ExampleScala!!!() // this file is intentionally broken
+        |""".stripMargin,
+    expectedSemanticdbFiles = 1,
+    extraArguments = List("--", "bla/compile"),
+    targetRoot = Some("bla/target")
+  )
+}
diff --git a/website/project/build.properties b/website/project/build.properties
index 52413ab7..e8a1e246 100644
--- a/website/project/build.properties
+++ b/website/project/build.properties
@@ -1 +1 @@
-sbt.version=1.9.3
+sbt.version=1.9.7