diff --git a/.jscsrc b/.jscsrc
index 83287a3..8b12ca9 100644
--- a/.jscsrc
+++ b/.jscsrc
@@ -68,5 +68,7 @@
   "requireDotNotation": true,
   "disallowYodaConditions": true,
   "disallowNewlineBeforeBlockStatements": true,
-  "validateLineBreaks": "LF"
+  "validateLineBreaks": "LF",
+  "requireSpaceAfterLineComment": true,
+  "safeContextKeyword": "self"
 }
diff --git a/jsdox.js b/jsdox.js
index 1f746a5..61c096b 100644
--- a/jsdox.js
+++ b/jsdox.js
@@ -15,42 +15,16 @@ COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER I
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-var util = require('util');
 var fs = require('fs');
 var path = require('path');
 var q = require('q');
+var mkdirp = require('mkdirp');
+
 var packageJson = require('./package.json');
-var jsdocParser = require('jsdoc3-parser');
-var analyze = require('./lib/analyze');
+var generateForDir = require('./lib/generateForDir');
+var generateForFile = require('./lib/generateForFile');
 var generateMD = require('./lib/generateMD');
-var index = {
-  classes: [],
-  functions: []
-};
-
-/**
- * Whether or not to print debug information.
- * Global to this module.
- *
- * @type {Boolean}
- */
-var debug = false;
-
-/**
- * Cache of the optimist arguments list
- *
- * @type {Object}
- */
-var argv;
-
-/**
- * Pretty print utility
- * @param  {Object} ast [description]
- * @return {String}
- */
-function inspect(ast) {
-  return util.inspect(ast, false, 20);
-}
+var util = require('./lib/util');
 
 function printHelp() {
   console.log('Usage:\tjsdox [options] <file | directory>');
@@ -76,172 +50,11 @@ function printVersion() {
 }
 
 /**
- * @param  {String}   filename
- * @param  {String}   destination
- * @param  {String}   templateDir
- * @param  {Function} cb
- * @param  {Function} fileCb
- */
-function generateForDir(filename, destination, templateDir, cb, fileCb) {
-  var waiting = 0;
-  var touched = 0;
-  var error = null;
-
-  var readdirSyncRec = function(dir, filelist) {
-    var files = fs.readdirSync(dir);
-    filelist = filelist || [];
-    files.forEach(function(file) {
-      if (fs.statSync(path.join(dir, file)).isDirectory()) {
-        filelist = readdirSyncRec(path.join(dir, file), filelist);
-      } else {
-        filelist.push(path.join(dir, file));
-      }
-    });
-    return filelist;
-  };
-
-  function oneFile(directory, file, cb) {
-    var fullpath;
-    if (argv.rr) {
-      fullpath = path.join(path.join(destination, path.dirname(file)), path.basename(file));
-    } else {
-      fullpath = path.join(destination, file);
-    }
-    fullpath = fullpath.replace(/\.js$/, '.md');
-
-    if (debug) {
-      console.log('Generating', fullpath);
-    }
-
-    waiting++;
-
-    jsdocParser(path.join(directory, path.basename(file)), function(err, result) {
-      if (err) {
-        console.error('Error generating docs for file', file, err);
-        waiting--;
-        if (!waiting) {
-          return cb(err);
-        } else {
-          error = err;
-        }
-      }
-
-      if (debug) {
-        console.log(file + ' AST: ', util.inspect(result, false, 20));
-        console.log(file + ' Analyzed: ', util.inspect(analyze(result), false, 20));
-      }
-
-      var data = analyze(result, argv);
-      var output = generateMD(data, templateDir);
-
-      if (argv.index) {
-        for (var i = 0; i < data.functions.length; i++) {
-          if (data.functions[i].className === undefined) {
-            var toAddFct = data.functions[i];
-            toAddFct.file = path.relative(destination, fullpath);
-            toAddFct.sourcePath = path.relative(destination, path.join(directory, path.basename(file)));
-            index.functions.push(toAddFct);
-          }
-        }
-        for (var j = 0; j < data.classes.length; j++) {
-          if (data.functions[j].className === undefined) {
-            var toAddClass = data.classes[j];
-            toAddClass.file = path.relative(destination, fullpath);
-            toAddClass.sourcePath = path.relative(destination, path.join(directory, path.basename(file)));
-            index.classes.push(toAddClass);
-          }
-        }
-      }
-
-      if (output) {
-        fileCb && fileCb(file, data);
-        fs.writeFile(fullpath, output, function(err) {
-          waiting--;
-          if (err) {
-            console.error('Error generating docs for file', file, err);
-            error = err;
-          }
-          if (!waiting) {
-            return cb(error);
-          }
-        });
-
-      } else {
-        waiting--;
-        if (!waiting) {
-          return cb(error);
-        }
-      }
-    });
-  }
-
-  if (filename.match(/\.js$/)) {
-    oneFile(path.dirname(filename), path.basename(filename), cb);
-
-  } else {
-    if (argv.recursive || argv.rr) {
-      fs.stat(filename, function (err, s) {
-        if (!err && s.isDirectory()) {
-          var contentList = readdirSyncRec(filename);
-          contentList.forEach(function(fileFullPath) {
-            if (argv.rr) {
-              //create the sub-directories
-              try {
-                fs.mkdirSync(path.join(destination, path.dirname(fileFullPath)));
-              } catch(err) {} //lazy way: if the file already exists, everything is alright.
-              try {
-                oneFile(path.dirname(fileFullPath), fileFullPath, cb), touched++;
-              } catch(err) {
-                console.error('Error generating docs for files', path.basename(fileFullPath), err);
-                return cb(err);
-              }
-            } else {
-              try {
-                oneFile(path.dirname(fileFullPath), path.basename(fileFullPath), cb), touched++;
-              } catch(err) {
-                console.error('Error generating docs for files', path.basename(fileFullPath), err);
-                return cb(err);
-              }
-            }
-          });
-          if (!touched) {
-            cb();
-          }
-
-        } else {
-          cb();
-        }
-      });
-    } else {
-      fs.stat(filename, function (err, s) {
-        if (!err && s.isDirectory()) {
-          fs.readdir(filename, function (err, files) {
-            if (err) {
-              console.error('Error generating docs for files', filename, err);
-              return cb(err);
-            }
-            files.forEach(function (file) {
-              if (file.match(/\.js$/)) {
-                oneFile(filename, file, cb), touched++;
-              }
-            });
-            if (!touched) {
-              cb();
-            }
-          });
-        } else {
-          cb();
-        }
-      });
-    }
-  }
-}
-
-/**
- * @param  {String}   file
+ * @param  {Object}   argv
  * @param  {Function} callback
  */
-function loadConfigFile(file, argv, callback) {
+function loadConfigFile(argv, callback) {
+  var file = argv.config;
   var config;
 
   // Check to see if file exists
@@ -273,53 +86,51 @@ function loadConfigFile(file, argv, callback) {
 }
 
 function main(argv) {
-  if (typeof argv._[0] !== 'undefined') {
-    fs.mkdir(argv.output, function() {
-      q.all(argv._.map(function(file) {
-        var deferred = q.defer();
-
-        generateForDir(file, argv.output, argv.templateDir, function(err) {
-          if (err) {
-            console.error(err);
-            throw err;
-          }
 
-          deferred.resolve();
-        });
+  console.log(argv)
 
-        return deferred.promise;
-      }))
-        .then(function() {
-          //create index
-          if (argv.index) {
-            var fileName;
-            if (argv.index === true) {
-              fileName = 'index';
-            } else {
-              fileName = argv.index;
-            }
-            if (typeof argv.output === 'string') {
-              fileName = path.join(argv.output, fileName);
-            } else {
-              fileName = path.join('output', fileName);
-            }
-            fs.writeFileSync(fileName + '.md', generateMD(index, argv.templateDir, true));
-          }
-        })
-        .then(function () {
-          console.log('jsdox completed');
-        });
-    });
-  } else {
+  if (!argv._.length) {
     console.error('Error missing input file or directory.');
     printHelp();
+    return;
+  }
+
+  // @todo: support input being a directory and output being a directory
+  // @todo: support input being a file and output being a file
+
+  if (util.isDirectoryPath(argv.output)) {
+    try {
+      mkdirp.sync(argv.output);
+    } catch (err) {}
   }
-}
 
-function jsdox(args) {
-  argv = args;
-  debug = !!argv.debug;
+  q.all(argv._.map(function(filename) {
+    var options = {
+      filename: filename,
+      argv: argv
+    };
+
+    return util.isDirectory(filename) ?
+            generateForDir(options) :
+            generateForFile(options);
+  }))
+  .then(function() {
+    // Create index
+    if (argv.index) {
+      var fileName = argv.index === true ? 'index' : argv.index;
+      fileName = typeof argv.output === 'string' ?
+                  path.join(argv.output, fileName) :
+                  path.join('output', fileName);
+
+      fs.writeFileSync(fileName + '.md', generateMD(generateForDir.index, argv.templateDir, true));
+    }
+  })
+  .then(function () {
+    console.log('jsdox completed');
+  });
+}
 
+function jsdox(argv) {
   if (argv.help) {
     printHelp();
   }
@@ -329,14 +140,14 @@ function jsdox(args) {
   }
 
   if (argv.config) {
-    // @todo: refactor to not rely on argv
-    loadConfigFile(argv.config, argv, main);
+    loadConfigFile(argv, main);
   } else {
     main(argv);
   }
 }
 
-exports.analyze = analyze;
-exports.generateMD = generateMD;
-exports.generateForDir = generateForDir;
+exports.analyze = require('./lib/analyze');
+exports.generateMD = require('./lib/generateMD');
+exports.generateForDir = require('./lib/generateForDir');
+exports.generateForFile = require('./lib/generateForFile');
 exports.jsdox = jsdox;
diff --git a/lib/generateForDir.js b/lib/generateForDir.js
new file mode 100644
index 0000000..7ab4776
--- /dev/null
+++ b/lib/generateForDir.js
@@ -0,0 +1,83 @@
+var util = require('./util');
+var path = require('path');
+var fs = require('fs');
+var q = require('q');
+var dir = require('node-dir');
+var mkdirp = require('mkdirp');
+
+var generateForFile = require('./generateForFile');
+
+/**
+ * @param  {Object}   options
+ * @param  {String}   options.filename
+ * @param  {String}   options.destination
+ * @param  {String}   options.templateDir
+ * @param  {Function} options.fileCb
+ * @returns {Promise}
+ *
+ * @todo: Support options instead of separate params. Be sure to update grunt-jsdox
+ */
+module.exports = function(options) {
+  var deferred = q.defer();
+
+  var filename = options.filename;
+  var fileDir = path.dirname(filename);
+  var output = options.output;
+  var templateDir = options.templateDir;
+  var fileCb = options.fileCb;
+  var argv = options.argv;
+
+  var self = this;
+
+  // Aggregated index data about the directory
+  this.index = {
+    classes: [],
+    functions: []
+  };
+
+  var aggregateIndexData = function(file, data) {
+    var index;
+    if (argv.index) {
+      index = generateIndexData(data);
+      self.index.classes = self.index.classes.concat(index.classes);
+      self.index.functions = self.index.functions.concat(index.functions);
+    }
+  }
+
+  // If it's just a file and not a directory
+  if (filename.match(/\.js$/)) {
+    generateForFile({
+      directory: fileDir,
+      file: path.basename(filename),
+      argv: argv
+    })
+    .then(aggregateIndexData)
+    .then(deferred.resolve.bind(deferred));
+
+  } else {
+    dir.readFiles(directory,
+    {
+      match: /.js$/,
+      exclude: /^\./,
+    },
+    function (err, content, filename, next) {
+      next();
+    },
+    function(err, files) {
+      q.all(files.map(function(filename) {
+        mkdirp.sync(path.join(output, path.dirname(filename)));
+
+        return generateForFile({
+          directory: fileDir,
+          file: filename,
+          argv: argv,
+          templateDir: templateDir
+        }).then(aggregateIndexData);
+      }))
+      .then(deferred.resolve.bind(deferred));
+    });
+  }
+
+  return deferred.promise;
+};
+
diff --git a/lib/generateForFile.js b/lib/generateForFile.js
new file mode 100644
index 0000000..747c81d
--- /dev/null
+++ b/lib/generateForFile.js
@@ -0,0 +1,85 @@
+var path = require('path');
+var jsdocParser = require('jsdoc3-parser');
+var fs = require('fs');
+var q = require('q');
+
+var util = require('./util');
+var analyze = require('./analyze');
+var generateMD = require('./generateMD');
+
+/**
+ * Generates the markdown output for a single JS file
+ *
+ * @param  {Object} options
+ * @param  {String} options.directory
+ * @param  {String} options.file
+ * @param  {Object} options.argv
+ * @param  {String} options.templateDir
+ * @return {Promise} Resolves with the file {String} and the analyzed ast {Object}
+ */
+module.exports = function(options) {
+  console.log(options)
+
+  var deferred = q.defer();
+  var filename = options.filename;
+  var fileDir = path.dirname(filename);
+  var fileBase = path.basename(filename);
+  var argv = options.argv;
+  var outputPath;
+  var outputDir;
+
+  // Lazy way to check if it's a directory without
+  // hitting the filesystem, in case the output dir doesn't exist yet
+  if (path.dirname(argv.output) === argv.output) {
+    // Markdown should be in the proper subdirectory of the output dir
+    if (argv.recursive) {
+      outputPath = path.join(path.join(argv.output, fileDir), fileBase);
+
+    // Just dump the markdown into the output folder
+    } else {
+      outputPath = path.join(argv.output, fileBase);
+    }
+
+  // We're storing the markdown in a separate file
+  } else {
+    outputPath = argv.output;
+  }
+
+  console.log('fullpath: ', outputPath)
+  outputPath = outputPath.replace(/\.js$/, '.md');
+
+  if (argv.debug) {
+    console.log('Generating', outputPath);
+  }
+
+  jsdocParser(filename, function(err, result) {
+    if (err) {
+      console.error('Error generating docs for file', filename, err);
+      deferred.reject(err);
+      return;
+    }
+
+    if (options.debug) {
+      console.log(file + ' AST: ', util.inspect(result));
+      console.log(file + ' Analyzed: ', util.inspect(analyze(result)));
+    }
+
+    var data = analyze(result, argv);
+    var output = generateMD(data, options.templateDir);
+
+    try {
+      if (output) {
+        fs.writeFileSync(outputPath, output);
+      }
+
+      deferred.resolve(filename, data);
+      return;
+
+    } catch (err) {
+      console.error('Error generating docs for file', filename, err);
+      deferred.reject(err);
+    }
+  });
+
+  return deferred.promise;
+};
diff --git a/lib/generateIndex.js b/lib/generateIndex.js
new file mode 100644
index 0000000..381f4ec
--- /dev/null
+++ b/lib/generateIndex.js
@@ -0,0 +1,29 @@
+/**
+ * Aggregates functions and classes for an index page
+ * @param  {Object} data - Analyzed ast
+ * @return {Object} Index data
+ */
+module.exports = function(data) {
+  var index = {
+    classes: [],
+    functions: []
+  };
+
+  data.functions.forEach(function(toAddFct) {
+    if (toAddFct.className === undefined) {
+      toAddFct.file = path.relative(destination, fullpath);
+      toAddFct.sourcePath = path.relative(destination, path.join(directory, path.basename(file)));
+      index.functions.push(toAddFct);
+    }
+  });
+
+  data.classes.forEach(function(toAddClass) {
+    if (toAddClass.className === undefined) {
+      toAddClass.file = path.relative(destination, fullpath);
+      toAddClass.sourcePath = path.relative(destination, path.join(directory, path.basename(file)));
+      index.classes.push(toAddClass);
+    }
+  });
+
+  return index;
+};
diff --git a/lib/generateMD.js b/lib/generateMD.js
index cc63236..37e1def 100644
--- a/lib/generateMD.js
+++ b/lib/generateMD.js
@@ -1,6 +1,5 @@
 /**
  * Copyright (c) 2012-2014 Sutoiku
- *
  */
 
 var Mustache = require('mustache');
@@ -9,7 +8,7 @@ var path = require('path');
 
 /**
  * Renders markdown from the given analyzed AST
- * @param  {Object} ast - output from analyze()
+ * @param  {Object} ast
  * @param  {String} templateDir - templates directory (optional)
  * @return {String} Markdown output
  */
@@ -24,38 +23,33 @@ module.exports = function(ast, templateDir, isIndex) {
     templateDir = templateDir.replace(/\\/g, '/');
   }
 
-  //if ast is an index file, we need to sort the contents and to use the right templates;
+  // If ast is an index file, we need to sort the contents and to use the right templates
   if (isIndex) {
     console.log('Now generating index');
+
     ast.classes.sort(function(a, b) {
-      if (a.name < b.name) {
-        return -1;
-      } else {
-        return 1;
-      }
+      return a.name < b.name ? -1 : 1;
     });
+
     ast.functions.sort(function(a, b) {
-      if (a.name < b.name) {
-        return -1;
-      } else {
-        return 1;
-      }
+      return a.name < b.name ? -1 : 1;
     });
 
     templates = {
       index: fs.readFileSync(templateDir + '/index.mustache', 'utf8'),
-      class: fs.readFileSync(templateDir + '/overview.mustache', 'utf8'),//do we need different overview templates for functions or classes here ?
+      class: fs.readFileSync(templateDir + '/overview.mustache', 'utf8'),
       function: fs.readFileSync(templateDir + '/overview.mustache', 'utf8')
     };
-    return Mustache.render(templates.index, ast, templates);
-  }else {
 
+    return Mustache.render(templates.index, ast, templates);
 
+  } else {
     templates = {
       file: fs.readFileSync(templateDir + '/file.mustache', 'utf8'),
       class: fs.readFileSync(templateDir + '/class.mustache', 'utf8'),
       function: fs.readFileSync(templateDir + '/function.mustache', 'utf8')
     };
+
     return Mustache.render(templates.file, ast, templates);
   }
 };
diff --git a/lib/util.js b/lib/util.js
new file mode 100644
index 0000000..95723bb
--- /dev/null
+++ b/lib/util.js
@@ -0,0 +1,68 @@
+/**
+ * Copyright (c) 2012-2014 Sutoiku
+ */
+
+var fs = require('fs');
+var util = require('util');
+var path = require('path');
+
+/**
+ * Recursive readdirSync
+ * @param  {String} dir
+ * @param  {String[]} filelist
+ * @return {String[]}
+ */
+module.exports.readdirSyncRec = function(dir, filelist) {
+  var files = fs.readdirSync(dir);
+  var self = this;
+
+  filelist = filelist || [];
+  files.forEach(function(file) {
+    if (fs.statSync(path.join(dir, file)).isDirectory()) {
+      filelist = self.readdirSyncRec(path.join(dir, file), filelist);
+    } else {
+      filelist.push(path.join(dir, file));
+    }
+  });
+  return filelist;
+};
+
+/**
+ * Pretty print utility
+ *
+ * @param  {Object} ast [description]
+ * @return {String}
+ */
+module.exports.inspect = function(ast) {
+  return util.inspect(ast, false, 20);
+};
+
+/**
+ * Shallow copy
+ * @param  {Object} obj1
+ * @param  {Object} obj2
+ */
+module.exports.extend = function(obj1, obj2) {
+  Object.keys(obj2).forEach(function(prop) {
+    obj1[prop] = obj2[prop];
+  });
+};
+
+/**
+ * Whether or not the given path represents a directory name
+ * The directory name does not have to be of a directory on the filesystem
+ * @param  {String}  path
+ * @return {Boolean}
+ */
+module.exports.isDirectoryPath = function(path) {
+  return path.dirname(path) === path;
+};
+
+/**
+ * Whether or not the given resource is a directory on the filesystem
+ * @param  {String}  path
+ * @return {Boolean}
+ */
+module.exports.isDirectory = function(path) {
+  return fs.lstatSync(path).isDirectory();
+};
\ No newline at end of file
diff --git a/package.json b/package.json
index 6d05505..86488ce 100644
--- a/package.json
+++ b/package.json
@@ -44,7 +44,9 @@
     "jsdoc3-parser": "^1.0.0",
     "mustache": "^0.8.2",
     "optimist": "~0.3.4",
-    "q": "^1.0.1"
+    "q": "^1.0.1",
+    "node-dir": "^0.1.6",
+    "mkdirp": "^0.5.0"
   },
   "devDependencies": {
     "expect.js": "^0.3.1",
diff --git a/test/jsdox.js b/test/jsdox.js
index dfed0fe..eae0126 100644
--- a/test/jsdox.js
+++ b/test/jsdox.js
@@ -28,7 +28,7 @@ describe('jsdox', function() {
 
   it('generates non-empty output markdown files from the fixtures/ and the fixtures/under files', function(done) {
     var cmd = bin + ' fixtures/ -o sample_output -r';
-    //in case an old index.md is here
+    // In case an old index.md is here
     try {
       fs.unlinkSync('sample_output/index.md');
     } catch(err) {}
@@ -64,7 +64,7 @@ describe('jsdox', function() {
             var content = fs.readFileSync('sample_output/fixtures/' + outputFile).toString();
             expect(content).not.to.be.empty();
             nbFilesA += 1;
-            //clean for future tests
+            // Clean for future tests
             fs.unlinkSync('sample_output/fixtures/' + outputFile);
           }
         }
@@ -103,7 +103,7 @@ describe('jsdox', function() {
       });
       expect(nbFiles).to.be(7);
       expect(hasIndex).to.be(true);
-      //clean index for other tests
+      // Clean index for other tests
       fs.unlinkSync('sample_output/index.md');
 
       done();