Add compiler pass 2 - run remaining functions

We're now back to where we started functionality-wise!

app/Engine/Cfnpp/Compiler.php

@@ -91,6 +91,7 @@ class Compiler implements \App\Engine\ICompile
 
 		$document = $this->pass_0($documents, $options);
 		$this->pass_1($document, $options);
+		$this->pass_2($document, $options);
 
 		return $document;
 
@@ -239,6 +240,19 @@ class Compiler implements \App\Engine\ICompile
 		return $variables;
 	}
 
+	/**
+	 * Compiler Pass 2 - Run all remaining functions in the resulting document,
+	 * mutating the passed in document as required.
+	 *
+	 * @param  Document $document
+	 * @param  IOptions $options
+	 * @return void
+	 */
+	protected function pass_2(Document $document, IOptions $options): void
+	{
+		$this->runFunctions($document);
+	}
+
 	/**
 	 * Performs a basic recursive merge of two dom trees with target overwriting
 	 * original.