diff --git a/lib/builder.js b/lib/builder.js
index 3cfd1e2..04e0dd8 100644
--- a/lib/builder.js
+++ b/lib/builder.js
@@ -574,9 +574,7 @@ Builder.prototype.bundle = function(expressionOrTree, outFile, opts) {
     .then(function(compiled) {
       return writeOutputs(compiled.outputs, self.loader.baseURL, outputOpts)
       .then(function(output) {
-        output.modules = Object.keys(tree).filter(function(moduleName) {
-          return tree[moduleName] && !tree[moduleName].conditional;
-        });
+        output.modules = compiled.modules;
         output.entryPoints = compiled.entryPoints;
         output.tree = tree;
         output.assetList = compiled.assetList;
@@ -662,9 +660,7 @@ Builder.prototype.buildStatic = function(expressionOrTree, outFile, opts) {
         if (inlineMap)
           output.inlineMap = inlineMap;
         output.assetList = compiled.assetList;
-        output.modules = Object.keys(tree).filter(function(moduleName) {
-          return tree[moduleName] && !tree[moduleName].conditional;
-        });
+        output.modules = compiled.modules;
         output.tree = tree;
         return output;        
       });
diff --git a/lib/compile.js b/lib/compile.js
index 48e0a4d..c094ef7 100644
--- a/lib/compile.js
+++ b/lib/compile.js
@@ -334,7 +334,8 @@ function compileTree(loader, tree, traceOpts, compileOpts, outputOpts, cache) {
     return {
       outputs: outputs,
       entryPoints: entryPoints,
-      assetList: assetList
+      assetList: assetList,
+      modules: modules.reverse()
     };
   });
 }