Eliminate a number of memory leaks in tests (#12414)

Memory usage has spin out of control recently when running our test-suite. Unnecessarily.
This change eliminates a number of leaks that haven't been properly cleaned up on test teardown.
Also closed a number of stale threads.

# Important Notes
Before:
![Screenshot from 2025-02-28 14-40-14](https://github.com/user-attachments/assets/25b084f9-a13d-4199-a7ab-5628d3ee421d)

After:
![Screenshot from 2025-03-04 17-43-23](https://github.com/user-attachments/assets/c5b3ee34-cea0-4774-953d-42cf54bbd94c)

Author: hubertp

engine/runtime-integration-tests/src/test/java/org/enso/compiler/dump/test/DocsGenerateTest.java

@@ -52,6 +52,7 @@ public static void initCtx() {
   public static void closeCtx() {
     ctx.close();
     ctx = null;
+    leak.shutdown();
     leak = null;
   }
 

engine/runtime-integration-tests/src/test/java/org/enso/compiler/test/ExecCompilerTest.java

@@ -22,6 +22,7 @@
 import org.graalvm.polyglot.Source;
 import org.graalvm.polyglot.io.IOAccess;
 import org.hamcrest.core.AllOf;
+import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Ignore;
@@ -55,6 +56,12 @@ public static void initEnsoContext() {
   @AfterClass
   public static void closeEnsoContext() throws Exception {
     ctx.close();
+    ctx = null;
+    out.close();
+  }
+
+  @After
+  public void cleanup() {
     out.reset();
   }
 

engine/runtime-integration-tests/src/test/java/org/enso/interpreter/runtime/ManagedResourceTest.java

@@ -53,7 +53,12 @@ Managed_Resource.register obj (_->0) system_resource
   @AfterClass
   public static void closeCtx() throws Exception {
     ctx.close();
+    ensoCtx.shutdown();
     ctx = null;
+    ensoCtx = null;
+    newResource = null;
+    createResource = null;
+    getResource = null;
   }
 
   @Test

engine/runtime-integration-tests/src/test/java/org/enso/interpreter/runtime/RefTest.java

@@ -35,6 +35,9 @@ public static void initCtx() throws Exception {
   public static void closeCtx() throws Exception {
     ctx.close();
     ctx = null;
+    refType = null;
+    ensoCtx.shutdown();
+    ensoCtx = null;
   }
 
   private static Value getRef(Value ref) {

engine/runtime-integration-tests/src/test/java/org/enso/interpreter/runtime/progress/ProgressTest.java

@@ -30,6 +30,8 @@ public static void initCtx() throws Exception {
   public static void closeCtx() throws Exception {
     ctx.close();
     ctx = null;
+    ensoCtx.shutdown();
+    ensoCtx = null;
   }
 
   public ProgressTest() {}

engine/runtime-integration-tests/src/test/java/org/enso/interpreter/test/AnyOrStaticTest.java

@@ -4,6 +4,7 @@
 import static org.junit.Assert.assertTrue;
 
 import java.io.ByteArrayOutputStream;
+import java.io.IOException;
 import org.enso.common.LanguageInfo;
 import org.enso.common.MethodNames;
 import org.enso.test.utils.ContextUtils;
@@ -24,8 +25,10 @@ public void prepareCtx() {
   }
 
   @After
-  public void disposeCtx() {
+  public void disposeCtx() throws IOException {
     ctx.close();
+    ctx = null;
+    out.close();
   }
 
   @Test

engine/runtime-integration-tests/src/test/java/org/enso/interpreter/test/AnyToTest.java

@@ -3,6 +3,7 @@
 import static org.junit.Assert.assertTrue;
 
 import java.io.ByteArrayOutputStream;
+import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import org.enso.interpreter.runtime.data.EnsoMultiValue;
 import org.enso.interpreter.runtime.data.Type;
@@ -27,9 +28,10 @@ public static void initCtx() {
   }
 
   @AfterClass
-  public static void disposeCtx() {
+  public static void disposeCtx() throws IOException {
     ctx.close();
     ctx = null;
+    out.close();
   }
 
   @Before

engine/runtime-integration-tests/src/test/java/org/enso/interpreter/test/AutoscopedConstructorTest.java

@@ -8,6 +8,7 @@
 import static org.junit.Assert.fail;
 
 import java.io.ByteArrayOutputStream;
+import java.io.IOException;
 import org.enso.common.MethodNames;
 import org.enso.test.utils.ContextUtils;
 import org.graalvm.polyglot.Context;
@@ -34,9 +35,10 @@ public void resetOut() {
   }
 
   @AfterClass
-  public static void disposeCtx() {
+  public static void disposeCtx() throws IOException {
     ctx.close();
     ctx = null;
+    out.close();
   }
 
   @Test

engine/runtime-integration-tests/src/test/java/org/enso/interpreter/test/BinaryOpFloatTest.java

@@ -90,6 +90,7 @@ public static void initContext() {
   public static void closeContext() {
     ctx.close();
     ctx = null;
+    wrapReal = null;
   }
 
   private final String operation;

engine/runtime-integration-tests/src/test/java/org/enso/interpreter/test/BinaryOpIntegerTest.java

@@ -109,6 +109,7 @@ public static void initContext() {
   public static void closeContext() {
     ctx.close();
     ctx = null;
+    wrapInt = null;
   }
 
   private final String operation;