diff --git a/package.json b/package.json
index 84ca82304..a70ee36c1 100644
--- a/package.json
+++ b/package.json
@@ -24,8 +24,9 @@
     "atom-keymap": "^3.1.2",
     "bootstrap": "git+https://github.com/atom/bootstrap.git#6af81906189f1747fd6c93479e3d998ebe041372",
     "clear-cut": "0.4.0",
+    "coffee-cash": "0.7.0",
     "coffee-script": "1.8.0",
-    "coffeestack": "0.8.0",
+    "coffeestack": "^1.1",
     "color": "^0.7.3",
     "delegato": "^1",
     "emissary": "^1.3.1",
@@ -35,10 +36,10 @@
     "fstream": "0.1.24",
     "fuzzaldrin": "^2.1",
     "git-utils": "^3.0.0",
-    "grim": "1.1.1",
+    "grim": "1.1.2",
     "guid": "0.0.10",
     "jasmine-json": "~0.0",
-    "jasmine-tagged": "^1.1.3",
+    "jasmine-tagged": "^1.1.4",
     "jquery": "^2.1.1",
     "less-cache": "0.21",
     "marked": "^0.3",
@@ -57,7 +58,7 @@
     "scandal": "2.0.0",
     "scoped-property-store": "^0.16.2",
     "scrollbar-style": "^2.0.0",
-    "season": "^5.1.2",
+    "season": "^5.1.4",
     "semver": "~4.2",
     "serializable": "^1",
     "service-hub": "^0.4.0",
@@ -93,7 +94,7 @@
     "deprecation-cop": "0.36.0",
     "dev-live-reload": "0.41.0",
     "encoding-selector": "0.18.0",
-    "exception-reporting": "0.23.0",
+    "exception-reporting": "0.24.0",
     "find-and-replace": "0.157.0",
     "fuzzy-finder": "0.66.0",
     "git-diff": "0.52.0",
diff --git a/spec/compile-cache-spec.coffee b/spec/compile-cache-spec.coffee
new file mode 100644
index 000000000..0cae70434
--- /dev/null
+++ b/spec/compile-cache-spec.coffee
@@ -0,0 +1,28 @@
+path = require 'path'
+CSON = require 'season'
+CoffeeCache = require 'coffee-cash'
+
+to5 = require '../src/6to5'
+CompileCache = require '../src/compile-cache'
+
+describe "Compile Cache", ->
+  describe ".addPathToCache(filePath)", ->
+    it "adds the path to the correct CSON, CoffeeScript, or 6to5 cache", ->
+      spyOn(CSON, 'readFileSync').andCallThrough()
+      spyOn(CoffeeCache, 'addPathToCache').andCallThrough()
+      spyOn(to5, 'addPathToCache').andCallThrough()
+
+      CompileCache.addPathToCache(path.join(__dirname, 'fixtures', 'cson.cson'))
+      expect(CSON.readFileSync.callCount).toBe 1
+      expect(CoffeeCache.addPathToCache.callCount).toBe 0
+      expect(to5.addPathToCache.callCount).toBe 0
+
+      CompileCache.addPathToCache(path.join(__dirname, 'fixtures', 'coffee.coffee'))
+      expect(CSON.readFileSync.callCount).toBe 1
+      expect(CoffeeCache.addPathToCache.callCount).toBe 1
+      expect(to5.addPathToCache.callCount).toBe 0
+
+      CompileCache.addPathToCache(path.join(__dirname, 'fixtures', '6to5', 'double-quotes.js'))
+      expect(CSON.readFileSync.callCount).toBe 1
+      expect(CoffeeCache.addPathToCache.callCount).toBe 1
+      expect(to5.addPathToCache.callCount).toBe 1
diff --git a/spec/fixtures/cson.cson b/spec/fixtures/cson.cson
new file mode 100644
index 000000000..6fe1e8a01
--- /dev/null
+++ b/spec/fixtures/cson.cson
@@ -0,0 +1 @@
+a: 4
diff --git a/src/6to5.coffee b/src/6to5.coffee
index 15059ad62..9d67efcf8 100644
--- a/src/6to5.coffee
+++ b/src/6to5.coffee
@@ -89,6 +89,7 @@ create6to5VersionAndOptionsDigest = (version, options) ->
   updateDigestForJsonValue(shasum, options)
   shasum.digest('hex')
 
+cacheDir = null
 jsCacheDir = null
 
 getCachePath = (sourceCode) ->
@@ -96,8 +97,7 @@ getCachePath = (sourceCode) ->
 
   unless jsCacheDir?
     to5Version = require('6to5-core/package.json').version
-    cacheDir = path.join(process.env.ATOM_HOME, 'compile-cache')
-    jsCacheDir = path.join(cacheDir, 'js', '6to5', create6to5VersionAndOptionsDigest(to5Version, defaultOptions))
+    jsCacheDir = path.join(cacheDir, create6to5VersionAndOptionsDigest(to5Version, defaultOptions))
 
   path.join(jsCacheDir, "#{digest}.js")
 
@@ -141,12 +141,19 @@ loadFile = (module, filePath) ->
 
 register = ->
   Object.defineProperty(require.extensions, '.js', {
+    enumerable: true
     writable: false
     value: loadFile
   })
 
+setCacheDirectory = (newCacheDir) ->
+  if cacheDir isnt newCacheDir
+    cacheDir = newCacheDir
+    jsCacheDir = null
+
 module.exports =
   register: register
+  setCacheDirectory: setCacheDirectory
   getCacheMisses: -> stats.misses
   getCacheHits: -> stats.hits
 
diff --git a/src/browser/main.coffee b/src/browser/main.coffee
index 22360a076..3b6018d5b 100644
--- a/src/browser/main.coffee
+++ b/src/browser/main.coffee
@@ -15,6 +15,8 @@ process.on 'uncaughtException', (error={}) ->
 
 start = ->
   setupAtomHome()
+  setupCoffeeCache()
+
   if process.platform is 'win32'
     SquirrelUpdate = require './squirrel-update'
     squirrelCommand = process.argv[1]
@@ -49,9 +51,7 @@ start = ->
       else
         path.resolve(pathToOpen)
 
-    setupCoffeeScript()
     if args.devMode
-      require(path.join(args.resourcePath, 'src', 'coffee-cache')).register()
       AtomApplication = require path.join(args.resourcePath, 'src', 'browser', 'atom-application')
     else
       AtomApplication = require './atom-application'
@@ -66,15 +66,6 @@ global.devResourcePath = path.normalize(global.devResourcePath) if global.devRes
 setupCrashReporter = ->
   crashReporter.start(productName: 'Atom', companyName: 'GitHub')
 
-setupCoffeeScript = ->
-  CoffeeScript = null
-
-  require.extensions['.coffee'] = (module, filePath) ->
-    CoffeeScript ?= require('coffee-script')
-    coffee = fs.readFileSync(filePath, 'utf8')
-    js = CoffeeScript.compile(coffee, filename: filePath)
-    module._compile(js, filePath)
-
 setupAtomHome = ->
   return if process.env.ATOM_HOME
 
@@ -83,6 +74,15 @@ setupAtomHome = ->
     atomHome = fs.realpathSync(atomHome)
   process.env.ATOM_HOME = atomHome
 
+setupCoffeeCache = ->
+  CoffeeCache = require 'coffee-cash'
+  cacheDir = path.join(process.env.ATOM_HOME, 'compile-cache')
+  # Use separate compile cache when sudo'ing as root to avoid permission issues
+  if process.env.USER is 'root' and process.env.SUDO_USER and process.env.SUDO_USER isnt process.env.USER
+    cacheDir = path.join(cacheDir, 'root')
+  CoffeeCache.setCacheDirectory(path.join(cacheDir, 'coffee'))
+  CoffeeCache.register()
+
 parseCommandLine = ->
   version = app.getVersion()
   options = optimist(process.argv[1..])
diff --git a/src/coffee-cache.coffee b/src/coffee-cache.coffee
deleted file mode 100644
index 1e06fd4d5..000000000
--- a/src/coffee-cache.coffee
+++ /dev/null
@@ -1,76 +0,0 @@
-crypto = require 'crypto'
-path = require 'path'
-
-CoffeeScript = require 'coffee-script'
-CSON = require 'season'
-fs = require 'fs-plus'
-
-cacheDir = path.join(process.env.ATOM_HOME, 'compile-cache')
-
-stats =
-  hits: 0
-  misses: 0
-
-# Use separate compile cache when sudo'ing as root to avoid permission issues
-if process.env.USER is 'root' and process.env.SUDO_USER and process.env.SUDO_USER isnt process.env.USER
-  cacheDir = path.join(cacheDir, 'root')
-
-coffeeCacheDir = path.join(cacheDir, 'coffee')
-CSON.setCacheDir(path.join(cacheDir, 'cson'))
-
-getCachePath = (coffee) ->
-  digest = crypto.createHash('sha1').update(coffee, 'utf8').digest('hex')
-  path.join(coffeeCacheDir, "#{digest}.js")
-
-getCachedJavaScript = (cachePath) ->
-  if fs.isFileSync(cachePath)
-    try
-      cachedJavaScript = fs.readFileSync(cachePath, 'utf8')
-      stats.hits++
-      return cachedJavaScript
-  return
-
-convertFilePath = (filePath) ->
-  if process.platform is 'win32'
-    filePath = "/#{path.resolve(filePath).replace(/\\/g, '/')}"
-  encodeURI(filePath)
-
-compileCoffeeScript = (coffee, filePath, cachePath) ->
-  {js, v3SourceMap} = CoffeeScript.compile(coffee, filename: filePath, sourceMap: true)
-  stats.misses++
-  # Include source map in the web page environment.
-  if btoa? and JSON? and unescape? and encodeURIComponent?
-    js = "#{js}\n//# sourceMappingURL=data:application/json;base64,#{btoa unescape encodeURIComponent v3SourceMap}\n//# sourceURL=#{convertFilePath(filePath)}"
-  try
-    fs.writeFileSync(cachePath, js)
-  js
-
-requireCoffeeScript = (module, filePath) ->
-  coffee = fs.readFileSync(filePath, 'utf8')
-  cachePath = getCachePath(coffee)
-  js = getCachedJavaScript(cachePath) ? compileCoffeeScript(coffee, filePath, cachePath)
-  module._compile(js, filePath)
-
-module.exports =
-  cacheDir: cacheDir
-
-  register: ->
-    Object.defineProperty(require.extensions, '.coffee', {
-      writable: false
-      value: requireCoffeeScript
-    })
-
-  addPathToCache: (filePath) ->
-    switch path.extname(filePath)
-      when '.coffee'
-        content = fs.readFileSync(filePath, 'utf8')
-        cachePath = getCachePath(coffee)
-        compileCoffeeScript(coffee, filePath, cachePath)
-      when '.cson'
-        CSON.readFileSync(filePath)
-      when '.js'
-        require('./6to5').addPathToCache(filePath)
-
-  getCacheMisses: -> stats.misses
-
-  getCacheHits: -> stats.hits
diff --git a/src/compile-cache.coffee b/src/compile-cache.coffee
new file mode 100644
index 000000000..ec85ae674
--- /dev/null
+++ b/src/compile-cache.coffee
@@ -0,0 +1,26 @@
+path = require 'path'
+CSON = require 'season'
+CoffeeCache = require 'coffee-cash'
+to5 = require './6to5'
+
+# This file is required directly by apm so that files can be cached during
+# package install so that the first package load in Atom doesn't have to
+# compile anything.
+exports.addPathToCache = (filePath, atomHome) ->
+  atomHome ?= process.env.ATOM_HOME
+  cacheDir = path.join(atomHome, 'compile-cache')
+  # Use separate compile cache when sudo'ing as root to avoid permission issues
+  if process.env.USER is 'root' and process.env.SUDO_USER and process.env.SUDO_USER isnt process.env.USER
+    cacheDir = path.join(cacheDir, 'root')
+
+  CoffeeCache.setCacheDirectory(path.join(cacheDir, 'coffee'))
+  CSON.setCacheDir(path.join(cacheDir, 'cson'))
+  to5.setCacheDirectory(path.join(cacheDir, 'js'))
+
+  switch path.extname(filePath)
+    when '.coffee'
+      CoffeeCache.addPathToCache(filePath)
+    when '.cson'
+      CSON.readFileSync(filePath)
+    when '.js'
+      to5.addPathToCache(filePath)
diff --git a/src/task.coffee b/src/task.coffee
index 42b744b6d..6fe055ca6 100644
--- a/src/task.coffee
+++ b/src/task.coffee
@@ -65,12 +65,15 @@ class Task
   # * `taskPath` The {String} path to the CoffeeScript/JavaScript file that
   #   exports a single {Function} to execute.
   constructor: (taskPath) ->
-    coffeeCacheRequire = "require('#{require.resolve('./coffee-cache')}').register();"
-    coffeeScriptRequire = "require('#{require.resolve('coffee-script')}').register();"
+    coffeeCacheRequire = "require('#{require.resolve('coffee-cash')}')"
+    coffeeCachePath = require('coffee-cash').getCacheDirectory()
+    coffeeStackRequire = "require('#{require.resolve('coffeestack')}')"
+    stackCachePath = require('coffeestack').getCacheDirectory()
     taskBootstrapRequire = "require('#{require.resolve('./task-bootstrap')}');"
     bootstrap = """
-      #{coffeeScriptRequire}
-      #{coffeeCacheRequire}
+      #{coffeeCacheRequire}.setCacheDirectory('#{coffeeCachePath}');
+      #{coffeeCacheRequire}.register();
+      #{coffeeStackRequire}.setCacheDirectory('#{stackCachePath}');
       #{taskBootstrapRequire}
     """
     bootstrap = bootstrap.replace(/\\/g, "\\\\")
diff --git a/static/index.js b/static/index.js
index e5f84f794..fb56a84bd 100644
--- a/static/index.js
+++ b/static/index.js
@@ -1,33 +1,17 @@
-function registerRuntimeTranspilers() {
-  // This sets require.extensions['.coffee'].
-  require('coffee-script').register();
-
-  // This redefines require.extensions['.js'].
-  require('../src/6to5').register();
-}
+var fs = require('fs');
+var path = require('path');
 
 window.onload = function() {
   try {
     var startTime = Date.now();
 
-    var fs = require('fs');
-    var path = require('path');
-
     // Ensure ATOM_HOME is always set before anything else is required
-    if (!process.env.ATOM_HOME) {
-      var home;
-      if (process.platform === 'win32') {
-        home = process.env.USERPROFILE;
-      } else {
-        home = process.env.HOME;
-      }
-      var atomHome = path.join(home, '.atom');
-      try {
-        atomHome = fs.realpathSync(atomHome);
-      } catch (error) {
-        // Ignore since the path might just not exist yet.
-      }
-      process.env.ATOM_HOME = atomHome;
+    setupAtomHome();
+
+    var cacheDir = path.join(process.env.ATOM_HOME, 'compile-cache');
+    // Use separate compile cache when sudo'ing as root to avoid permission issues
+    if (process.env.USER === 'root' && process.env.SUDO_USER && process.env.SUDO_USER !== process.env.USER) {
+      cacheDir = path.join(cacheDir, 'root');
     }
 
     // Skip "?loadSettings=".
@@ -45,10 +29,7 @@ window.onload = function() {
 
     var devMode = loadSettings.devMode || !loadSettings.resourcePath.startsWith(process.resourcesPath + path.sep);
 
-    // Require before the module cache in dev mode
-    if (devMode) {
-      registerRuntimeTranspilers();
-    }
+    setupCoffeeCache(cacheDir);
 
     ModuleCache = require('../src/module-cache');
     ModuleCache.register(loadSettings);
@@ -65,11 +46,9 @@ window.onload = function() {
 
     require('vm-compatibility-layer');
 
-    if (!devMode) {
-      registerRuntimeTranspilers();
-    }
-
-    require('../src/coffee-cache').register();
+    setupCsonCache(cacheDir);
+    setupSourceMapCache(cacheDir);
+    setup6to5(cacheDir);
 
     require(loadSettings.bootstrapScript);
     require('ipc').sendChannel('window-command', 'window:loaded');
@@ -78,8 +57,7 @@ window.onload = function() {
       global.atom.loadTime = Date.now() - startTime;
       console.log('Window load time: ' + global.atom.getWindowLoadTime() + 'ms');
     }
-  }
-  catch (error) {
+  } catch (error) {
     var currentWindow = require('remote').getCurrentWindow();
     currentWindow.setSize(800, 600);
     currentWindow.center();
@@ -88,3 +66,41 @@ window.onload = function() {
     console.error(error.stack || error);
   }
 }
+
+var setupCoffeeCache = function(cacheDir) {
+  var CoffeeCache = require('coffee-cash');
+  CoffeeCache.setCacheDirectory(path.join(cacheDir, 'coffee'));
+  CoffeeCache.register();
+}
+
+var setupAtomHome = function() {
+  if (!process.env.ATOM_HOME) {
+    var home;
+    if (process.platform === 'win32') {
+      home = process.env.USERPROFILE;
+    } else {
+      home = process.env.HOME;
+    }
+    var atomHome = path.join(home, '.atom');
+    try {
+      atomHome = fs.realpathSync(atomHome);
+    } catch (error) {
+      // Ignore since the path might just not exist yet.
+    }
+    process.env.ATOM_HOME = atomHome;
+  }
+}
+
+var setup6to5 = function(cacheDir) {
+  var to5 = require('../src/6to5');
+  to5.setCacheDirectory(path.join(cacheDir, 'js', '6to5'));
+  to5.register();
+}
+
+var setupCsonCache = function(cacheDir) {
+  require('season').setCacheDir(path.join(cacheDir, 'cson'));
+}
+
+var setupSourceMapCache = function(cacheDir) {
+  require('coffeestack').setCacheDirectory(path.join(cacheDir, 'coffee', 'source-maps'));
+}