gistfile1.txt

diff --git a/frontend/src/main/scala/bloop/data/Project.scala b/frontend/src/main/scala/bloop/data/Project.scala
index 3bf914d..7ae05fc 100644
--- a/frontend/src/main/scala/bloop/data/Project.scala
+++ b/frontend/src/main/scala/bloop/data/Project.scala
@@ -5,6 +5,7 @@ import bloop.logging.{DebugFilter, Logger}
 import bloop.ScalaInstance
 import bloop.bsp.ProjectUris
 import bloop.config.Config
+import bloop.data.Platform
 import bloop.engine.Dag
 import bloop.engine.caches.SemanticDBCache
 import bloop.engine.tasks.toolchains.{JvmToolchain, ScalaJsToolchain, ScalaNativeToolchain}
@@ -62,6 +63,19 @@ final case class Project(
     case Config.ScalaThenJava => CompileOrder.ScalaThenJava
   }
 
+  def workingDirectory: AbsolutePath = {
+    val customWorkingDirectory = platform match {
+      case Platform.Jvm(config, toolchain, userMainClass) =>
+        config.javaOptions.collectFirst {
+          case option if option.startsWith("-Duser.dir=") =>
+            AbsolutePath(option.stripPrefix("-Duser.dir="))
+        }
+      case _ =>
+        None
+    }
+    customWorkingDirectory.getOrElse(baseDirectory)
+  }
+
   val uniqueId = s"${origin.path.syntax}#${name}"
   override def toString: String = s"$name"
   override val hashCode: Int =
diff --git a/frontend/src/main/scala/bloop/engine/Interpreter.scala b/frontend/src/main/scala/bloop/engine/Interpreter.scala
index 13aef81..a463ea4 100644
--- a/frontend/src/main/scala/bloop/engine/Interpreter.scala
+++ b/frontend/src/main/scala/bloop/engine/Interpreter.scala
@@ -551,7 +551,7 @@ object Interpreter {
 
   private def run(cmd: Commands.Run, state: State): Task[State] = {
     def doRun(project: Project)(state: State): Task[State] = {
-      val cwd = project.baseDirectory
+      val cwd = project.workingDirectory
       compileAnd(cmd, state, List(project), false, cmd.cliOptions.noColor, "`run`") { state =>
         getMainClass(state, project, cmd.main) match {
           case Left(failedState) => Task.now(failedState)
diff --git a/frontend/src/main/scala/bloop/engine/tasks/Tasks.scala b/frontend/src/main/scala/bloop/engine/tasks/Tasks.scala
index 91f4ec3..7700c5d 100644
--- a/frontend/src/main/scala/bloop/engine/tasks/Tasks.scala
+++ b/frontend/src/main/scala/bloop/engine/tasks/Tasks.scala
@@ -113,7 +113,7 @@ object Tasks {
         }
       }
 
-      val cwd = project.baseDirectory
+      val cwd = project.workingDirectory
       TestTask.runTestSuites(
         state,
         project,