diff --git a/jsdoc.js b/jsdoc.js
index fb44a411..d1314f3f 100644
--- a/jsdoc.js
+++ b/jsdoc.js
@@ -156,6 +156,7 @@ function main() {
     var filter;
     var i;
     var info;
+    var isFile;
     var l;
     var packageDocs;
     var packageJson;
@@ -178,7 +179,14 @@ function main() {
     env.opts = jsdoc.opts.args.parse(env.args);
 
     confPath = env.opts.configure || path.join(__dirname, 'conf.json');
-    if ( !fs.statSync(confPath).isFile() && !env.opts.configure ) {
+    try {
+        isFile = fs.statSync(confPath).isFile();
+    }
+    catch(e) {
+        isFile = false;
+    }
+
+    if ( !isFile && !env.opts.configure ) {
         confPath = path.join(__dirname, 'conf.json.EXAMPLE');
     }
 
diff --git a/lib/jsdoc/fs.js b/lib/jsdoc/fs.js
index 1993807a..00cbcd90 100644
--- a/lib/jsdoc/fs.js
+++ b/lib/jsdoc/fs.js
@@ -2,10 +2,68 @@
  * Extended version of the standard `fs` module.
  * @module jsdoc/fs
  */
-
-var fs = exports.fs = require('fs');
+var fs = require('fs');
+var path = require('path');
 var runtime = require('jsdoc/util/runtime');
 
+var ls = exports.ls = function(dir, recurse, _allFiles, _path) {
+    var file;
+    var files;
+    var isFile;
+
+    // first pass
+    if (_path === undefined) {
+        _allFiles = [];
+        _path = [dir];
+    }
+
+    if (!_path.length) {
+        return _allFiles;
+    }
+
+    if (recurse === undefined) {
+        recurse = 1;
+    }
+
+    try {
+        isFile = fs.statSync(dir).isFile();
+    }
+    catch (e) {
+        isFile = false;
+    }
+    if (isFile) {
+        files = [dir];
+    }
+    else {
+        files = fs.readdirSync(dir);
+    }
+
+    for (var i = 0, l = files.length; i < l; i++) {
+        file = String(files[i]);
+
+        // skip dot files
+        if (file.match(/^\.[^\.\/\\]/)) {
+            continue;
+        }
+
+        if ( fs.statSync(path.join(_path.join('/'), file)).isDirectory() ) {
+            // it's a directory
+            _path.push(file);
+
+            if (_path.length - 1 < recurse) {
+                ls(_path.join('/'), recurse, _allFiles, _path);
+            }
+            _path.pop();
+        }
+        else {
+            // it's a file
+            _allFiles.push( path.normalize(path.join(_path.join('/'), file)) );
+        }
+    }
+
+    return _allFiles;
+};
+
 // export the VM-specific implementations of the extra methods
 // TODO: document extra methods here
 var extras = require( runtime.getModulePath('fs') );
diff --git a/lib/jsdoc/src/scanner.js b/lib/jsdoc/src/scanner.js
index 914cf7fe..f3b23519 100644
--- a/lib/jsdoc/src/scanner.js
+++ b/lib/jsdoc/src/scanner.js
@@ -24,16 +24,26 @@ exports.Scanner.prototype = Object.create( require('events').EventEmitter.protot
     @fires sourceFileFound
  */
 exports.Scanner.prototype.scan = function(searchPaths, depth, filter) {
-    var cwd = process.cwd(),
-        filePaths = [],
-        self = this;
+    var isFile;
+
+    var cwd = process.cwd();
+    var filePaths = [];
+    var self = this;
 
     searchPaths = searchPaths || [];
     depth = depth || 1;
 
     searchPaths.forEach(function($) {
         var filepath = decodeURIComponent($);
-        if ( fs.statSync(filepath).isFile() ) {
+
+        try {
+            isFile = fs.statSync(filepath).isFile();
+        }
+        catch(e) {
+            isFile = false;
+        }
+
+        if (isFile) {
             filePaths.push( path.resolve(cwd, filepath) );
         }
         else {
diff --git a/rhino/fs.js b/rhino/fs.js
index eeb29c6f..c452428a 100644
--- a/rhino/fs.js
+++ b/rhino/fs.js
@@ -6,6 +6,7 @@
  */
 
 var path = require('path');
+var util = require('util');
 
 var asyncify = path._asyncify;
 
@@ -24,6 +25,11 @@ function checkEncoding(enc, name) {
     return enc;
 }
 
+// provide an error that's consistent with Node.js
+function errorFactory(filepath) {
+    return new Error( util.format("ENOENT, no such file or directory '%s'", filepath) );
+}
+
 exports.readFileSync = function(filename, encoding) {
     encoding = checkEncoding(encoding, 'fs.readFile[Sync]');
 
@@ -37,6 +43,10 @@ exports.exists = path.exists;
 
 var statSync = exports.statSync = function(_path) {
     var f = new java.io.File(_path);
+    if (!f) {
+        throw errorFactory(_path);
+    }
+
     return {
         isFile: function() {
             return f.isFile();
@@ -54,7 +64,7 @@ var readdirSync = exports.readdirSync = function(_path) {
 
     dir = new java.io.File(_path);
     if (!dir.directory) {
-        throw new Error("ENOENT, no such file or directory '" + _path + "'");
+        throw errorFactory(_path);
     }
 
     files = dir.list();
@@ -68,49 +78,6 @@ var readdirSync = exports.readdirSync = function(_path) {
 };
 exports.readdir = asyncify(readdirSync);
 
-// JSDoc extension to `fs` module
-var ls = exports.ls = function(dir, recurse, _allFiles, _path) {
-    var files,
-        file;
-
-    if (typeof _path === 'undefined') { // initially
-        _allFiles = [];
-        _path = [dir];
-    }
-
-    if (_path.length === 0) { return _allFiles; }
-    if (typeof recurse === 'undefined') { recurse = 1; }
-
-    if ( statSync(dir).isFile(dir) ) {
-        files = [dir];
-    }
-    else {
-        files = readdirSync(dir);
-    }
-
-    for (var f = 0, lenf = files.length; f < lenf; f++) {
-        file = String(files[f]);
-
-        if (file.match(/^\.[^\.\/\\]/)) { continue; } // skip dot files
-
-        if ((new java.io.File(_path.join('/') + '/' + file)).list()) { // it's a directory
-            _path.push(file);
-
-            if (_path.length - 1 < recurse) {
-                ls(_path.join('/'), recurse, _allFiles, _path);
-            }
-            _path.pop();
-        }
-        else { // it's a file
-            _allFiles.push(
-                path.normalize(_path.join('/') + '/' + file)
-            );
-        }
-    }
-
-    return _allFiles;
-};
-
 // JSDoc extension to `fs` module
 var toDir = exports.toDir = function(_path) {
     var f = new java.io.File(_path);
diff --git a/templates/default/publish.js b/templates/default/publish.js
index 63a62f96..aaf6e171 100644
--- a/templates/default/publish.js
+++ b/templates/default/publish.js
@@ -409,8 +409,7 @@ exports.publish = function(taffyData, opts, tutorials) {
             var extraStaticFiles = staticFileScanner.scan([filePath], 10, staticFileFilter);
 
             extraStaticFiles.forEach(function(fileName) {
-                var sourcePath = fs.statSync(filePath).isDirectory() ? filePath :
-                    path.dirname(filePath);
+                var sourcePath = fs.toDir(filePath);
                 var toDir = fs.toDir( fileName.replace(sourcePath, outdir) );
                 fs.mkPath(toDir);
                 fs.copyFileSync(fileName, toDir);