Merging in .coffee.md support alongside .litcoffee ... I think we'll keep .litcoffee as the canonical, however.

src/coffee-script.coffee

@@ -10,19 +10,17 @@ fs        = require 'fs'
 path      = require 'path'
 {Lexer}   = require './lexer'
 {parser}  = require './parser'
+helpers   = require './helpers'
 vm        = require 'vm'
 
-# The file extensions that are considered to be CoffeeScript.
-extensions = ['.coffee', '.litcoffee']
-
 # Load and run a CoffeeScript file for Node, stripping any `BOM`s.
 loadFile = (module, filename) ->
   raw = fs.readFileSync filename, 'utf8'
   stripped = if raw.charCodeAt(0) is 0xFEFF then raw.substring 1 else raw
-  module._compile compile(stripped, {filename}), filename
+  module._compile compile(stripped, {filename, literate: helpers.isLiterate filename}), filename
 
 if require.extensions
-  for ext in extensions
+  for ext in ['.coffee', '.litcoffee', '.md', '.coffee.md']
     require.extensions[ext] = loadFile
 
 # The current CoffeeScript version number.
@@ -73,7 +71,7 @@ exports.run = (code, options = {}) ->
   mainModule.paths = require('module')._nodeModulePaths path.dirname fs.realpathSync options.filename
 
   # Compile.
-  if (path.extname(mainModule.filename) not in extensions) or require.extensions
+  if not helpers.isCoffee(mainModule.filename) or require.extensions
     mainModule._compile compile(code, options), mainModule.filename
   else
     mainModule._compile code, mainModule.filename

src/command.coffee

@@ -56,7 +56,6 @@ sourceCode   = []
 notSources   = {}
 watchers     = {}
 optionParser = null
-coffee_exts  = ['.coffee', '.litcoffee']
 
 # Run `coffee` by parsing passed options and determining what action to take.
 # Many flags cause us to divert before compiling anything. Flags passed after
@@ -79,8 +78,8 @@ exports.run = ->
     compilePath source, yes, path.normalize source
 
 # Compile a path, which could be a script or a directory. If a directory
-# is passed, recursively compile all '.coffee' and '.litcoffee' extension source
-# files in it and all subdirectories.
+# is passed, recursively compile all '.coffee', '.litcoffee', and '.coffee.md'
+# extension source files in it and all subdirectories.
 compilePath = (source, topLevel, base) ->
   fs.stat source, (err, stats) ->
     throw err if err and err.code isnt 'ENOENT'
@@ -98,7 +97,7 @@ compilePath = (source, topLevel, base) ->
         sourceCode[index..index] = files.map -> null
         files.forEach (file) ->
           compilePath (path.join source, file), no, base
-    else if topLevel or path.extname(source) in coffee_exts
+    else if topLevel or helpers.isCoffee source
       watch source, base if opts.watch
       fs.readFile source, (err, code) ->
         throw err if err and err.code isnt 'ENOENT'
@@ -243,7 +242,7 @@ removeSource = (source, base, removeJs) ->
 
 # Get the corresponding output JavaScript path for a source file.
 outputPath = (source, base) ->
-  filename  = path.basename(source, path.extname(source)) + '.js'
+  filename  = helpers.getBasename(source) + '.js'
   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
@@ -306,8 +305,7 @@ parseOptions = ->
 
 # The compile-time options to pass to the CoffeeScript compiler.
 compileOptions = (filename) ->
-  literate = path.extname(filename) is '.litcoffee'
-  {filename, literate, bare: opts.bare, header: opts.compile}
+  {filename, literate: helpers.isLiterate(filename), bare: opts.bare, header: opts.compile}
 
 # Start up a new Node.js instance with the arguments in `--nodejs` passed to
 # the `node` binary, preserving the other options.

src/helpers.coffee

@@ -2,6 +2,8 @@
 # the **Lexer**, **Rewriter**, and the **Nodes**. Merge objects, flatten
 # arrays, count characters, that sort of thing.
 
+path = require 'path'
+
 # Peek at the beginning of a given string to see if it matches a sequence.
 exports.starts = (string, literal, start) ->
   literal is string.substr start, literal.length
@@ -92,4 +94,14 @@ exports.locationDataToString = (obj) ->
     else
       "No location data"
 
+# Determine if a filename represents a CoffeeScript file.
+exports.isCoffee = (file) -> /\.((lit)?coffee|coffee\.md)$/.test file
+
+# Determine if a filename represents a Literate CoffeeScript file.
+exports.isLiterate = (file) -> /\.(litcoffee|coffee\.md)$/.test file
+
+# Extract the basename from a source file name, accounting for all possible
+# CoffeeScript extensions.
+exports.getBasename = (file) -> path.basename file, file?.match?(/\.((lit)?coffee|coffee\.md)$/)?[0] or path.extname(file)
+