Add VM.clear method

Use it before loading projects so targets don't accumulate when multiple projects are loaded on the same instance.

Move check to see if the clone is the original clone onto the block implementation so all clones can be removed.

Fixes #274

src/engine/runtime.js

@@ -368,18 +368,26 @@ Runtime.prototype.startHats = function (requestedHatOpcode,
     return newThreads;
 };
 
+/**
+ * Dispose all targets. Return to clean state.
+ */
+Runtime.prototype.dispose = function () {
+    this.stopAll();
+    this.targets.map(this.disposeTarget, this);
+};
+
 /**
  * Dispose of a target.
  * @param {!Target} target Target to dispose of.
  */
-Runtime.prototype.disposeTarget = function (target) {
-    // Allow target to do dispose actions.
-    target.dispose();
-    // Remove from list of targets.
-    var index = this.targets.indexOf(target);
-    if (index > -1) {
-        this.targets.splice(index, 1);
-    }
+Runtime.prototype.disposeTarget = function (disposingTarget) {
+    this.targets = this.targets.filter(function (target) {
+        if (disposingTarget !== target) return true;
+        // Allow target to do dispose actions.
+        target.dispose();
+        // Remove from list of targets.
+        return false;
+    });
 };
 
 /**