diff --git a/src/Pure/Tools/scala_project.scala b/src/Pure/Tools/scala_project.scala
--- a/src/Pure/Tools/scala_project.scala
+++ b/src/Pure/Tools/scala_project.scala
@@ -1,193 +1,187 @@
 /*  Title:      Pure/Tools/scala_project.scala
     Author:     Makarius
 
 Setup Gradle project for Isabelle/Scala/jEdit.
 */
 
 package isabelle
 
 
 object Scala_Project
 {
   /* groovy syntax */
 
   def groovy_string(s: String): String =
   {
     s.map(c =>
       c match {
         case '\t' | '\b' | '\n' | '\r' | '\f' | '\\' | '\'' | '"' => "\\" + c
         case _ => c.toString
       }).mkString("'", "", "'")
   }
 
 
   /* file and directories */
 
   lazy val isabelle_files: List[String] =
   {
     val files1 =
     {
       val isabelle_home = Path.ISABELLE_HOME.canonical
       Path.split(Isabelle_System.getenv("ISABELLE_CLASSPATH")).
         map(path => File.relative_path(isabelle_home, path).getOrElse(path).implode)
     }
 
     val files2 =
       (for {
         path <-
           List(
             Path.explode("~~/lib/classes/Pure.shasum"),
             Path.explode("~~/src/Tools/jEdit/dist/Isabelle-jEdit.shasum"))
         if path.is_file
         line <- Library.trim_split_lines(File.read(path))
         name =
           if (line.length > 42 && line(41) == '*') line.substring(42)
           else error("Bad shasum entry: " + quote(line))
         if name != "lib/classes/Pure.jar" &&
           name != "src/Tools/jEdit/dist/jedit.jar" &&
           name != "src/Tools/jEdit/dist/jars/Isabelle-jEdit-base.jar" &&
           name != "src/Tools/jEdit/dist/jars/Isabelle-jEdit.jar"
       } yield name)
 
     files1 ::: files2
   }
 
   lazy val isabelle_scala_files: Map[String, Path] =
     isabelle_files.foldLeft(Map.empty[String, Path]) {
       case (map, name) =>
         if (!name.startsWith("src/Tools/jEdit/") && name.endsWith(".scala")) {
           val path = Path.explode("~~/" + name)
           val base = path.base.implode
           map.get(base) match {
             case None => map + (base -> path)
             case Some(path1) => error("Conflicting base names: " + path + " vs. " + path1)
           }
         }
         else map
     }
 
-  val isabelle_dirs: List[(String, Path)] =
-    List(
-      "src/Pure/" -> Path.explode("isabelle"),
-      "src/Tools/Graphview/" -> Path.explode("isabelle.graphview"),
-      "src/Tools/VSCode/" -> Path.explode("isabelle.vscode"),
-      "src/Tools/jEdit/src-base/" -> Path.explode("isabelle.jedit_base"),
-      "src/Tools/jEdit/src/" -> Path.explode("isabelle.jedit"),
-      "src/HOL/SPARK/Tools" -> Path.explode("isabelle.spark"),
-      "src/HOL/Tools/ATP" -> Path.explode("isabelle.atp"),
-      "src/HOL/Tools/Nitpick" -> Path.explode("isabelle.nitpick"))
+  private def guess_package(path: Path): String =
+  {
+    val lines = split_lines(File.read(path))
+    val Package = """\bpackage\b +(?:object +)?\b((?:\w|\.)+)\b""".r
+
+    lines.collectFirst({ case Package(name) => name }) getOrElse
+      error("Failed to guess package from " + path)
+  }
 
 
   /* compile-time position */
 
   def here: Here =
   {
     val exn = new Exception
     exn.getStackTrace.toList match {
       case _ :: caller :: _ =>
         val name = proper_string(caller.getFileName).getOrElse("")
         val line = caller.getLineNumber
         new Here(name, line)
       case _ => new Here("", 0)
     }
   }
 
   class Here private[Scala_Project](name: String, line: Int)
   {
     override def toString: String = name + ":" + line
     def position: Position.T =
       isabelle_scala_files.get(name) match {
         case Some(path) => Position.Line_File(line, path.implode)
         case None => Position.none
       }
   }
 
 
   /* scala project */
 
   def scala_project(project_dir: Path, symlinks: Boolean = false): Unit =
   {
     if (symlinks && Platform.is_windows)
       error("Cannot create symlinks on Windows")
 
     if (project_dir.is_file || project_dir.is_dir)
       error("Project directory already exists: " + project_dir)
 
     val src_dir = project_dir + Path.explode("src/main/scala")
     val java_src_dir = project_dir + Path.explode("src/main/java")
     val scala_src_dir = Isabelle_System.make_directory(project_dir + Path.explode("src/main/scala"))
 
     Isabelle_System.copy_dir(Path.explode("~~/src/Tools/jEdit/dist/jEdit"), java_src_dir)
 
     val files = isabelle_files
     isabelle_scala_files
 
     for (file <- files if file.endsWith(".scala")) {
-      val (path, target) =
-        isabelle_dirs.collectFirst({
-          case (prfx, p) if file.startsWith(prfx) =>
-            (Path.ISABELLE_HOME + Path.explode(file), scala_src_dir + p)
-        }).getOrElse(error("Unknown directory prefix for " + quote(file)))
-
+      val path = Path.ISABELLE_HOME + Path.explode(file)
+      val target = scala_src_dir + Path.basic(guess_package(path))
       Isabelle_System.make_directory(target)
       if (symlinks) Isabelle_System.symlink(path, target)
       else Isabelle_System.copy_file(path, target)
     }
 
     val jars =
       for (file <- files if file.endsWith(".jar"))
       yield {
         if (file.startsWith("/")) file
         else Isabelle_System.getenv("ISABELLE_HOME") + "/" + file
       }
 
     File.write(project_dir + Path.explode("settings.gradle"), "rootProject.name = 'Isabelle'\n")
     File.write(project_dir + Path.explode("build.gradle"),
 """plugins {
   id 'scala'
 }
 
 repositories {
   mavenCentral()
 }
 
 dependencies {
   implementation 'org.scala-lang:scala-library:""" + scala.util.Properties.versionNumberString + """'
   compile files(
     """ + jars.map(jar => groovy_string(File.platform_path(jar))).mkString("", ",\n    ", ")") +
 """
 }
 """)
   }
 
 
   /* Isabelle tool wrapper */
 
   val isabelle_tool =
     Isabelle_Tool("scala_project", "setup Gradle project for Isabelle/Scala/jEdit",
       Scala_Project.here, args =>
     {
       var symlinks = false
 
       val getopts = Getopts("""
 Usage: isabelle scala_project [OPTIONS] PROJECT_DIR
 
   Options are:
     -L           make symlinks to original scala files
 
   Setup Gradle project for Isabelle/Scala/jEdit --- to support Scala IDEs
   such as IntelliJ IDEA.
 """,
         "L" -> (_ => symlinks = true))
 
       val more_args = getopts(args)
 
       val project_dir =
         more_args match {
           case List(dir) => Path.explode(dir)
           case _ => getopts.usage()
         }
 
       scala_project(project_dir, symlinks = symlinks)
     })
 }