diff --git a/jsdoc.js b/jsdoc.js
index f234804a..39d0443e 100644
--- a/jsdoc.js
+++ b/jsdoc.js
@@ -160,10 +160,14 @@ function main() {
     if (env.conf.opts) {
         for (var opt in env.conf.opts) {
             // arguments passed in command are more important
-            if (!(opt in env.opts) || opt=='_' && env.opts['_'] && env.opts['_'].length<1) {
+            if (!(opt in env.opts)) {
                 env.opts[opt] = env.conf.opts[opt];
             }
         }
+        // command file list is concatenated after conf list
+        if( env.conf.opts._ ){
+            env.opts._ = env.conf.opts._.concat( env.opts._ );
+        }
     }
     
     if (env.opts.query) {