diff --git a/lib/coffee-script/coffee-script.js b/lib/coffee-script/coffee-script.js
index 66f4acc5..d7e13699 100644
--- a/lib/coffee-script/coffee-script.js
+++ b/lib/coffee-script/coffee-script.js
@@ -1,6 +1,6 @@
 // Generated by CoffeeScript 1.6.0
 (function() {
-  var Lexer, baseFileName, compile, ext, fs, helpers, lexer, loadFile, parser, path, sourcemap, vm, _i, _len, _ref,
+  var Lexer, compile, ext, fs, helpers, lexer, loadFile, parser, path, sourcemap, vm, _i, _len, _ref,
     __hasProp = {}.hasOwnProperty;
 
   fs = require('fs');
@@ -37,13 +37,7 @@
 
   exports.VERSION = '1.6.0';
 
-  exports.helpers = require('./helpers');
-
-  baseFileName = function(fileName) {
-    var extension;
-    extension = path.extname(fileName);
-    return path.basename(fileName, extension);
-  };
+  exports.helpers = helpers;
 
   exports.compile = compile = function(code, options) {
     var answer, coffeeFile, currentColumn, currentLine, fragment, fragments, header, js, jsFile, merge, newLines, sourceMap, _j, _len1;
@@ -54,7 +48,7 @@
     try {
       if (options.sourceMap) {
         coffeeFile = path.basename(options.filename);
-        jsFile = baseFileName(options.filename) + ".js";
+        jsFile = helpers.baseFileName(options.filename) + ".js";
         sourceMap = new sourcemap.SourceMap();
       }
       fragments = (parser.parse(lexer.tokenize(code, options))).compileToFragments(options);
diff --git a/lib/coffee-script/command.js b/lib/coffee-script/command.js
index beb55d8a..308646da 100644
--- a/lib/coffee-script/command.js
+++ b/lib/coffee-script/command.js
@@ -170,7 +170,7 @@
       } else {
         compiled = CoffeeScript.compile(t.input, t.options);
         t.output = compiled;
-        if (o.sourceMap) {
+        if (o.map) {
           t.output = compiled.js;
           t.sourceMap = compiled.v3SourceMap;
         }
@@ -370,11 +370,11 @@
   };
 
   outputPath = function(source, base, extension) {
-    var baseDir, basename, dir, srcDir, _ref1;
+    var baseDir, basename, dir, srcDir;
     if (extension == null) {
       extension = ".js";
     }
-    basename = path.basename(source, ((_ref1 = source.match(/\.((lit)?coffee|coffee\.md)$/)) != null ? _ref1[0] : void 0) || path.extname(source));
+    basename = helpers.baseFileName(source);
     srcDir = path.dirname(source);
     baseDir = base === '.' ? srcDir : srcDir.substring(base.length);
     dir = opts.output ? path.join(opts.output, baseDir) : srcDir;
diff --git a/lib/coffee-script/helpers.js b/lib/coffee-script/helpers.js
index 10f5e352..54d060e4 100644
--- a/lib/coffee-script/helpers.js
+++ b/lib/coffee-script/helpers.js
@@ -121,6 +121,18 @@
     }
   };
 
+  exports.baseFileName = function(file) {
+    var parts;
+    parts = file.split('/');
+    file = parts[parts.length - 1];
+    parts = file.split('.');
+    parts.pop();
+    if (parts[parts.length - 1] === 'coffee') {
+      parts.pop();
+    }
+    return parts.join('.');
+  };
+
   exports.isCoffee = function(file) {
     return /\.((lit)?coffee|coffee\.md)$/.test(file);
   };
diff --git a/src/coffee-script.coffee b/src/coffee-script.coffee
index 6d749437..3fc124e4 100644
--- a/src/coffee-script.coffee
+++ b/src/coffee-script.coffee
@@ -12,7 +12,7 @@ path      = require 'path'
 {parser}  = require './parser'
 helpers   = require './helpers'
 vm        = require 'vm'
-sourcemap   = require './sourcemap'
+sourcemap = require './sourcemap'
 
 # Load and run a CoffeeScript file for Node, stripping any `BOM`s.
 loadFile = (module, filename) ->
@@ -28,11 +28,7 @@ if require.extensions
 exports.VERSION = '1.6.0'
 
 # Expose helpers for testing.
-exports.helpers = require './helpers'
-
-baseFileName = (fileName) ->
-  extension = path.extname(fileName)
-  return path.basename fileName, extension
+exports.helpers = helpers
 
 # Compile CoffeeScript code to JavaScript, using the Coffee/Jison compiler.
 #
@@ -48,7 +44,7 @@ exports.compile = compile = (code, options = {}) ->
 
     if options.sourceMap
       coffeeFile = path.basename options.filename
-      jsFile = baseFileName(options.filename) + ".js"
+      jsFile = helpers.baseFileName(options.filename) + ".js"
       sourceMap = new sourcemap.SourceMap()
 
     fragments = (parser.parse lexer.tokenize(code, options)).compileToFragments options
diff --git a/src/command.coffee b/src/command.coffee
index 00fd4cc6..126ebe7d 100644
--- a/src/command.coffee
+++ b/src/command.coffee
@@ -127,7 +127,7 @@ compileScript = (file, input, base) ->
     else
       compiled = CoffeeScript.compile t.input, t.options
       t.output = compiled
-      if o.sourceMap
+      if o.map
         t.output = compiled.js
         t.sourceMap = compiled.v3SourceMap
 
@@ -251,7 +251,7 @@ removeSource = (source, base, removeJs) ->
 
 # Get the corresponding output JavaScript path for a source file.
 outputPath = (source, base, extension=".js") ->
-  basename  = path.basename source, source.match(/\.((lit)?coffee|coffee\.md)$/)?[0] or path.extname(source)
+  basename  = helpers.baseFileName source
   srcDir    = path.dirname source
   baseDir   = if base is '.' then srcDir else srcDir.substring base.length
   dir       = if opts.output then path.join opts.output, baseDir else srcDir
diff --git a/src/helpers.coffee b/src/helpers.coffee
index 5c1dfab4..a496b234 100644
--- a/src/helpers.coffee
+++ b/src/helpers.coffee
@@ -92,6 +92,15 @@ exports.locationDataToString = (obj) ->
     else
       "No location data"
 
+# A `.coffee.md` compatible version of `basename`, that returns the file sans-extension.
+exports.baseFileName = (file) ->
+  parts = file.split('/')
+  file = parts[parts.length - 1]
+  parts = file.split('.')
+  parts.pop()
+  parts.pop() if parts[parts.length - 1] is 'coffee'
+  parts.join('.')
+
 # Determine if a filename represents a CoffeeScript file.
 exports.isCoffee = (file) -> /\.((lit)?coffee|coffee\.md)$/.test file