diff --git a/.arcconfig b/.arcconfig
deleted file mode 100644
index f54404245..000000000
--- a/.arcconfig
+++ /dev/null
@@ -1,8 +0,0 @@
-{
-  "project_id" : "edgehill",
-  "conduit_uri" : "https://phab.nylas.com/",
-  "load" : [
-    "arclib"
-  ],
-  "lint.engine": "ArcanistConfigurationDrivenLintEngine"
-}
diff --git a/.arclint b/.arclint
deleted file mode 100644
index f7b76ada9..000000000
--- a/.arclint
+++ /dev/null
@@ -1,10 +0,0 @@
-{
-  "linters": {
-    "coffeescript-linter": {
-      "type": "script-and-regex",
-      "script-and-regex.script": "script/grunt coffeelint:target --target",
-      "script-and-regex.regex": "/^  ((?P<error>✖)|(?P<warning>⚠)) *line (?P<line>\\d+) +(?P<message>.*)$/m",
-      "include": "{\\.(e?coffee|cjsx)}"
-    }
-  }
-}
\ No newline at end of file
diff --git a/.gitattributes b/.gitattributes
deleted file mode 100644
index 6eb1a23ae..000000000
--- a/.gitattributes
+++ /dev/null
@@ -1,14 +0,0 @@
-# Specs depend on character counts, if we don't specify the line endings the
-# fixtures will vary depending on platform
-spec/fixtures/**/*.js text eol=lf
-spec/fixtures/**/*.coffee text eol=lf
-spec/fixtures/**/*.less text eol=lf
-spec/fixtures/**/*.css text eol=lf
-spec/fixtures/**/*.txt text eol=lf
-spec/fixtures/dir/**/* text eol=lf
-
-# Git 1.7 does not support **/* patterns
-spec/fixtures/css.css text eol=lf
-spec/fixtures/sample.js text eol=lf
-spec/fixtures/sample.less text eol=lf
-spec/fixtures/sample.txt text eol=lf
diff --git a/.gitignore b/.gitignore
index 1abcd9ac1..1360a5a80 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,6 @@
+.arcconfig
+.arclint
+arclib
 *.swp
 *~
 .DS_Store
diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index e69de29bb..000000000
diff --git a/.node-version b/.node-version
deleted file mode 100644
index b58b2ff99..000000000
--- a/.node-version
+++ /dev/null
@@ -1 +0,0 @@
-v0.10.33
diff --git a/arclib/.phutil_module_cache b/arclib/.phutil_module_cache
deleted file mode 100644
index b7d92402c..000000000
--- a/arclib/.phutil_module_cache
+++ /dev/null
@@ -1 +0,0 @@
-{"__symbol_cache_version__":11}
\ No newline at end of file
diff --git a/arclib/__phutil_library_init__.php b/arclib/__phutil_library_init__.php
deleted file mode 100644
index 93cfbaabb..000000000
--- a/arclib/__phutil_library_init__.php
+++ /dev/null
@@ -1,3 +0,0 @@
-<?php
-
-phutil_register_library('customlib', __FILE__);
diff --git a/arclib/__phutil_library_map__.php b/arclib/__phutil_library_map__.php
deleted file mode 100644
index 1ebc28be0..000000000
--- a/arclib/__phutil_library_map__.php
+++ /dev/null
@@ -1,14 +0,0 @@
-<?php
-
-/**
- * This file is automatically generated. Use 'arc liberate' to rebuild it.
- *
- * @generated
- * @phutil-library-version 2
- */
-phutil_register_library_map(array(
-  '__library_version__' => 2,
-  'class' => array(),
-  'function' => array(),
-  'xmap' => array(),
-));
diff --git a/build/Gruntfile.coffee b/build/Gruntfile.coffee
index e186c59c9..eabee7333 100644
--- a/build/Gruntfile.coffee
+++ b/build/Gruntfile.coffee
@@ -215,7 +215,7 @@ module.exports = (grunt) ->
 
     coffeelint:
       options:
-        configFile: 'coffeelint.json'
+        configFile: 'build/config/coffeelint.json'
       src: [
         'internal_packages/**/*.cjsx'
         'internal_packages/**/*.coffee'
diff --git a/coffeelint.json b/build/config/coffeelint.json
similarity index 100%
rename from coffeelint.json
rename to build/config/coffeelint.json
diff --git a/build/tasks/build-task.coffee b/build/tasks/build-task.coffee
index e3f1b2b1d..afcf6285b 100644
--- a/build/tasks/build-task.coffee
+++ b/build/tasks/build-task.coffee
@@ -45,7 +45,6 @@ module.exports = (grunt) ->
     packageNames = []
     packageDirectories = []
     nonPackageDirectories = [
-      'benchmark'
       'dot-nylas'
       'vendor'
     ]
diff --git a/src/browser/application.coffee b/src/browser/application.coffee
index 64f34ebd9..f0d0f8849 100644
--- a/src/browser/application.coffee
+++ b/src/browser/application.coffee
@@ -231,9 +231,6 @@ class Application
           resourcePath: @resourcePath
           specDirectory: filenames[0]
 
-    @on 'application:run-benchmarks', ->
-      @runBenchmarks()
-
     @on 'application:reset-config-and-relaunch', @_resetConfigAndRelaunch
 
     @on 'application:quit', => app.quit()
@@ -484,15 +481,3 @@ class Application
     devMode = true
     safeMode ?= false
     new AtomWindow({bootstrapScript, resourcePath, exitWhenDone, isSpec, devMode, specDirectory, specFilePattern, logFile, safeMode})
-
-  runBenchmarks: ({exitWhenDone, specDirectory}={}) ->
-    try
-      bootstrapScript = require.resolve(path.resolve(global.devResourcePath, 'benchmark', 'benchmark-bootstrap'))
-    catch error
-      bootstrapScript = require.resolve(path.resolve(__dirname, '..', '..', 'benchmark', 'benchmark-bootstrap'))
-
-    specDirectory ?= path.dirname(bootstrapScript)
-
-    isSpec = true
-    devMode = true
-    new AtomWindow({bootstrapScript, @resourcePath, exitWhenDone, isSpec, specDirectory, devMode})
diff --git a/src/services/remove-thread-helper.coffee b/src/services/remove-thread-helper.coffee
index 814a80239..1817f1aa4 100644
--- a/src/services/remove-thread-helper.coffee
+++ b/src/services/remove-thread-helper.coffee
@@ -1,11 +1,11 @@
 _ = require 'underscore'
-CategoryStore = require '../stores/category-store'
+CategoryStore = require '../flux/stores/category-store'
 
-ChangeLabelsTask = require './change-labels-task'
-ChangeFolderTask = require './change-folder-task'
-Actions = require '../actions'
+ChangeLabelsTask = require '../flux/tasks/change-labels-task'
+ChangeFolderTask = require '../flux/tasks/change-folder-task'
+Actions = require '../flux/actions'
 
-AccountStore = require '../stores/account-store'
+AccountStore = require '../flux/stores/account-store'
 
 class RemoveThreadHelper