Make package command handle directories in extra classpath

modules/cli/src/main/scala/scala/cli/commands/package0/Package.scala

@@ -856,26 +856,28 @@ object Package extends ScalaCommand[PackageOptions] with BuildCommandHelpers {
     alreadyExistsCheck: () => Either[BuildException, Unit],
     logger: Logger
   ): Either[BuildException, Unit] = either {
-    val byteCodeZipEntries = os.walk(build.output)
-      .filter(os.isFile(_))
-      .map { path =>
-        val name         = path.relativeTo(build.output).toString
-        val content      = os.read.bytes(path)
-        val lastModified = os.mtime(path)
-        val ent          = new ZipEntry(name)
-        ent.setLastModifiedTime(FileTime.fromMillis(lastModified))
-        ent.setSize(content.length)
-        (ent, content)
-      }
+    val compiledClasses = os.walk(build.output).filter(os.isFile(_))
+    val (extraClasseFolders, extraJars) =
+      build.options.classPathOptions.extraClassPath.partition(os.isDir(_))
+    val extraClasses = extraClasseFolders.flatMap(os.walk(_)).filter(os.isFile(_))
+
+    val byteCodeZipEntries = (compiledClasses ++ extraClasses).map { path =>
+      val name         = path.relativeTo(build.output).toString
+      val content      = os.read.bytes(path)
+      val lastModified = os.mtime(path)
+      val ent          = new ZipEntry(name)
+      ent.setLastModifiedTime(FileTime.fromMillis(lastModified))
+      ent.setSize(content.length)
+      (ent, content)
+    }
 
     val provided = build.options.notForBloopOptions.packageOptions.provided ++ extraProvided
-    val allFiles =
-      build.artifacts.runtimeArtifacts.map(_._2) ++ build.options.classPathOptions.extraClassPath
-    val files =
-      if (provided.isEmpty) allFiles
+    val allJars  = build.artifacts.runtimeArtifacts.map(_._2) ++ extraJars.filter(os.exists(_))
+    val jars =
+      if (provided.isEmpty) allJars
       else {
         val providedFilesSet = value(providedFiles(build, provided, logger)).toSet
-        allFiles.filterNot(providedFilesSet.contains)
+        allJars.filterNot(providedFilesSet.contains)
       }
 
     val preambleOpt =
@@ -889,7 +891,7 @@ object Package extends ScalaCommand[PackageOptions] with BuildCommandHelpers {
         None
     val params = Parameters.Assembly()
       .withExtraZipEntries(byteCodeZipEntries)
-      .withFiles(files.map(_.toIO))
+      .withFiles(jars.map(_.toIO))
       .withMainClass(mainClassOpt)
       .withPreambleOpt(preambleOpt)
     value(alreadyExistsCheck())

modules/integration/src/test/scala/scala/cli/integration/PackageTestDefinitions.scala

@@ -84,6 +84,7 @@ abstract class PackageTestDefinitions extends ScalaCliSuite with TestScalaVersio
       expect(output == message)
     }
   }
+
   test("resource directory for coursier bootstrap launcher") {
     val fileName = "hello.sc"
     val message  = "1,2,3"
@@ -285,6 +286,7 @@ abstract class PackageTestDefinitions extends ScalaCliSuite with TestScalaVersio
       expect(output == message)
     }
   }
+
   def smallModulesJsTest(jvm: Boolean): Unit = {
     val fileName = "Hello.scala"
     val message  = "Hello World from JS"
@@ -668,6 +670,72 @@ abstract class PackageTestDefinitions extends ScalaCliSuite with TestScalaVersio
     }
   }
 
+  test("assembly classpath") {
+    val lib = os.rel / "lib"
+    val app = os.rel / "app"
+    val inputs = TestInputs(
+      lib / "lib" / "Message.scala" ->
+        s"""package lib
+           |
+           |object Message {
+           |  def hello(name: String) = s"Hello $$name"
+           |}
+           |""".stripMargin,
+      app / "app" / "Hello.scala" ->
+        s"""package app
+           |
+           |import lib.Message.hello
+           |
+           |object Hello {
+           |  def main(args: Array[String]): Unit = println(hello("assembly"))
+           |}
+           |""".stripMargin
+    )
+    inputs.fromRoot { root =>
+      val classpath = os.proc(
+        TestUtil.cli,
+        "compile",
+        extraOptions,
+        "--print-classpath",
+        lib.toString
+      ).call(
+        cwd = root,
+        stdin = os.Inherit
+      ).out.text().trim
+
+      os.proc(
+        TestUtil.cli,
+        "--power",
+        "package",
+        extraOptions,
+        "--main-class",
+        "app.Hello",
+        "--assembly",
+        "-o",
+        "hello.jar",
+        s"--classpath=$classpath",
+        app.toString
+      ).call(
+        cwd = root,
+        stdin = os.Inherit,
+        stdout = os.Inherit
+      )
+
+      val launcher = root / "hello.jar"
+      expect(os.isFile(launcher))
+
+      Using.resource(new ZipFile(launcher.toIO)) { zf =>
+        val entries = zf.entries()
+          .asScala
+          .iterator
+          .map(_.getName)
+          .toVector
+        expect(entries.exists(_.endsWith("lib/Message.class")))
+        expect(entries.contains("app/Hello.class"))
+      }
+    }
+  }
+
   test("assembly provided") {
     val inputs = TestInputs(
       os.rel / "Hello.scala" ->