Fix cleaning packed dir

`clean` should delete the packed dir. If it does not,
the next `compileIncremental`, which is a cache hit, will see that
the packed dir is already there and will not unpack it.

main/src/main/scala/sbt/Defaults.scala

@@ -919,9 +919,12 @@ object Defaults extends BuildCommon {
       compileOutputs := {
         import scala.jdk.CollectionConverters.*
         val c = fileConverter.value
-        val (_, vfDir, _) = compileIncremental.value
+        val (_, vfDir, packedDir) = compileIncremental.value
         val classFiles = compile.value.readStamps.getAllProductStamps.keySet.asScala
-        classFiles.toSeq.map(c.toPath) :+ compileAnalysisFile.value.toPath :+ c.toPath(vfDir)
+        classFiles.toSeq.map(c.toPath) :+
+          compileAnalysisFile.value.toPath :+
+          c.toPath(vfDir) :+
+          c.toPath(packedDir)
       },
       compileOutputs := compileOutputs.triggeredBy(compile).value,
       tastyFiles := Def.taskIf {

server-test/src/test/scala/testpkg/BuildServerTest.scala

@@ -377,7 +377,7 @@ class BuildServerTest extends AbstractServerTest {
     assertMessage(s""""id":"$id"""", """"class":"main.Main"""")(duration = 30.seconds)
   }
 
-  ignore("buildTarget/run") {
+  test("buildTarget/run") {
     val buildTarget = buildTargetUri("runAndTest", "Compile")
     val id = nextId()
     svr.sendJsonRpc(
@@ -388,7 +388,7 @@ class BuildServerTest extends AbstractServerTest {
          |} }""".stripMargin
     )
     assertProcessing("buildTarget/run")
-    assertMessage("build/logMessage", """"message":"Hello World!"""")(debug = true)
+    assertMessage("build/logMessage", """"message":"Hello World!"""")()
     assertMessage(s""""id":"$id"""", """"statusCode":1""")()
   }
 
@@ -412,7 +412,7 @@ class BuildServerTest extends AbstractServerTest {
     )()
   }
 
-  ignore("buildTarget/jvmTestEnvironment") {
+  test("buildTarget/jvmTestEnvironment") {
     val buildTarget = buildTargetUri("runAndTest", "Test")
     val id = nextId()
     svr.sendJsonRpc(
@@ -432,7 +432,7 @@ class BuildServerTest extends AbstractServerTest {
     )()
   }
 
-  ignore("buildTarget/scalaTestClasses") {
+  test("buildTarget/scalaTestClasses") {
     val buildTarget = buildTargetUri("runAndTest", "Test")
     val badBuildTarget = buildTargetUri("badBuildTarget", "Test")
     val id = nextId()
@@ -462,7 +462,7 @@ class BuildServerTest extends AbstractServerTest {
     assertMessage(s""""id":"$id"""", """"statusCode":2""")()
   }
 
-  ignore("buildTarget/test: run one test class") {
+  test("buildTarget/test: run one test class") {
     val buildTarget = buildTargetUri("runAndTest", "Test")
     val id = nextId()
     svr.sendJsonRpc(