Let paper be an instance of Base, and use its #extend() function to create scopes that inherit from paper but do not directly modify it.

src/paper.js

@@ -1,4 +1,4 @@
-var paper = {
+var paper = new Base().inject({
 	document: null,
 	documents: [],
 
@@ -7,4 +7,4 @@ var paper = {
 			scope[i] = paper[i];
 		}
 	}
-};
+});

src/util/PaperScript.js

@@ -4,7 +4,9 @@ var PaperScript = new function() {
 	}
 
 	function run(code) {
-		with (paper) {
+		// Use paper.extend() to create a paper scope within which the code is
+		// evaluated.
+		with (paper.extend()) {
 			return eval(compile(code));
 		}
 	}