diff --git a/.eslintignore b/.eslintignore
index 3d6e61df24..8f826ff6b7 100644
--- a/.eslintignore
+++ b/.eslintignore
@@ -18,10 +18,10 @@ tools/catalog-remote.js
 tools/catalog.js
 tools/cleanup.js
 tools/colon-converter.js
-tools/commands-cordova.js
-tools/commands-packages-query.js
-tools/commands-packages.js
-tools/commands.js
+tools/cli/commands-cordova.js
+tools/cli/commands-packages-query.js
+tools/cli/commands-packages.js
+tools/cli/commands.js
 tools/config.js
 tools/console.js
 tools/deploy.js
@@ -33,7 +33,7 @@ tools/http-helpers.js
 tools/inspector.js
 tools/isopackets.js
 tools/main-transpile-wrapper.js
-tools/main.js
+tools/cli/main.js
 tools/mongo-exit-codes.js
 tools/package-client.js
 tools/package-map.js
diff --git a/tools/commands-cordova.js b/tools/cli/commands-cordova.js
similarity index 99%
rename from tools/commands-cordova.js
rename to tools/cli/commands-cordova.js
index 95115579d8..581a41dde7 100644
--- a/tools/commands-cordova.js
+++ b/tools/cli/commands-cordova.js
@@ -3,18 +3,18 @@ var _ = require('underscore');
 var util = require('util');
 var path = require('path');
 var chalk = require('chalk');
-var files = require('./files.js');
-var buildmessage = require('./buildmessage.js');
-var projectContextModule = require('./project-context.js');
+var files = require('../files.js');
+var buildmessage = require('../buildmessage.js');
+var projectContextModule = require('../project-context.js');
 var Future = require('fibers/future');
-var utils = require('./utils.js');
-var archinfo = require('./archinfo.js');
-var tropohouse = require('./tropohouse.js');
-var httpHelpers = require('./http-helpers.js');
-var Console = require('./console.js').Console;
-var processes = require('./processes.js');
-var catalog = require('./catalog.js');
-var release = require('./release.js');
+var utils = require('../utils.js');
+var archinfo = require('../archinfo.js');
+var tropohouse = require('../tropohouse.js');
+var httpHelpers = require('../http-helpers.js');
+var Console = require('../console.js').Console;
+var processes = require('../processes.js');
+var catalog = require('../catalog.js');
+var release = require('../release.js');
 
 // XXX hard-coded the use of default tropohouse
 var tropo = tropohouse.default;
@@ -212,7 +212,7 @@ var execFileAsyncOrThrow = function (file, args, opts, cb) {
                       process.env,
                       opts.env || {});
 
-  var execFileAsync = require('./utils.js').execFileAsync;
+  var execFileAsync = require('../utils.js').execFileAsync;
 
   var p = execFileAsync(file, args, opts);
   p.on('close', function (code) {
@@ -228,7 +228,7 @@ var execFileAsyncOrThrow = function (file, args, opts, cb) {
 };
 
 var execFileSyncOrThrow = function (file, args, opts) {
-  var execFileSync = require('./utils.js').execFileSync;
+  var execFileSync = require('../utils.js').execFileSync;
 
   verboseLog('Running synchronously: ', file, args);
 
@@ -277,7 +277,7 @@ var execFileSyncOrThrow = function (file, args, opts) {
 };
 
 var getLoadedPackages = function () {
-  var isopackets = require("./isopackets.js");
+  var isopackets = require("../isopackets.js");
   return isopackets.load('cordova-support');
 };
 
@@ -342,7 +342,7 @@ var generateCordovaBoilerplate = function (projectContext, clientDir, options) {
 // options
 //  - debug
 var getBundle = function (projectContext, bundlePath, options) {
-  var bundler = require('./isobuild/bundler.js');
+  var bundler = require('../isobuild/bundler.js');
 
   var bundleResult = bundler.bundle({
     projectContext: projectContext,
@@ -754,7 +754,7 @@ var fetchCordovaPluginFromShaUrl =
   var pluginPath = files.pathJoin(localPluginsDir, pluginName);
   var pluginTarballPath = pluginPath + '.tgz';
 
-  var execFileSync = require('./utils.js').execFileSync;
+  var execFileSync = require('../utils.js').execFileSync;
   var whichCurl = execFileSync('which', ['curl']);
 
   var downloadProcess = null;
@@ -2080,7 +2080,7 @@ _.extend(IOS.prototype, {
   },
 
   killSimulator: function () {
-    var execFileSync = require('./utils.js').execFileSync;
+    var execFileSync = require('../utils.js').execFileSync;
     execFileSync('killall', ['iOS Simulator']);
     execFileSync('killall', ['iPhone Simulator']);
   }
diff --git a/tools/commands-packages-query.js b/tools/cli/commands-packages-query.js
similarity index 99%
rename from tools/commands-packages-query.js
rename to tools/cli/commands-packages-query.js
index 2a5a8dfd02..0759468358 100644
--- a/tools/commands-packages-query.js
+++ b/tools/cli/commands-packages-query.js
@@ -2,17 +2,17 @@
 // contained in the Meteor Package Server. They also deal with presenting this
 // to the user in various human or machine-readable ways.
 var _ = require('underscore');
-var archinfo = require('./archinfo.js');
-var buildmessage = require('./buildmessage.js');
-var catalog = require('./catalog.js');
-var Console = require("./console.js").Console;
-var files = require('./files.js');
-var isopackets = require('./isopackets.js');
+var archinfo = require('../archinfo.js');
+var buildmessage = require('../buildmessage.js');
+var catalog = require('../catalog.js');
+var Console = require("../console.js").Console;
+var files = require('../files.js');
+var isopackets = require('../isopackets.js');
 var main = require('./main.js');
-var packageVersionParser = require('./package-version-parser.js');
-var projectContextModule = require('./project-context.js');
-var utils = require('./utils.js');
-var compiler = require('./isobuild/compiler.js');
+var packageVersionParser = require('../package-version-parser.js');
+var projectContextModule = require('../project-context.js');
+var utils = require('../utils.js');
+var compiler = require('../isobuild/compiler.js');
 
 // We want these queries to be relatively fast, so we will only refresh the
 // catalog if it is > 15 minutes old
diff --git a/tools/commands-packages.js b/tools/cli/commands-packages.js
similarity index 98%
rename from tools/commands-packages.js
rename to tools/cli/commands-packages.js
index ea7901e783..6c24c320f0 100644
--- a/tools/commands-packages.js
+++ b/tools/cli/commands-packages.js
@@ -1,33 +1,33 @@
 var main = require('./main.js');
 var _ = require('underscore');
-var files = require('./files.js');
-var deploy = require('./deploy.js');
-var buildmessage = require('./buildmessage.js');
-var warehouse = require('./warehouse.js');
-var auth = require('./auth.js');
-var config = require('./config.js');
-var release = require('./release.js');
+var files = require('../files.js');
+var deploy = require('../deploy.js');
+var buildmessage = require('../buildmessage.js');
+var warehouse = require('../warehouse.js');
+var auth = require('../auth.js');
+var config = require('../config.js');
+var release = require('../release.js');
 var Future = require('fibers/future');
-var runLog = require('./run-log.js');
-var packageClient = require('./package-client.js');
-var utils = require('./utils.js');
-var httpHelpers = require('./http-helpers.js');
-var archinfo = require('./archinfo.js');
-var tropohouse = require('./tropohouse.js');
-var PackageSource = require('./isobuild/package-source.js');
-var bundler = require('./isobuild/bundler.js');
-var compiler = require('./isobuild/compiler.js');
-var catalog = require('./catalog.js');
-var catalogRemote = require('./catalog-remote.js');
-var stats = require('./stats.js');
-var isopack = require('./isobuild/isopack.js');
-var updater = require('./updater.js');
+var runLog = require('../run-log.js');
+var packageClient = require('../package-client.js');
+var utils = require('../utils.js');
+var httpHelpers = require('../http-helpers.js');
+var archinfo = require('../archinfo.js');
+var tropohouse = require('../tropohouse.js');
+var PackageSource = require('../isobuild/package-source.js');
+var bundler = require('../isobuild/bundler.js');
+var compiler = require('../isobuild/compiler.js');
+var catalog = require('../catalog.js');
+var catalogRemote = require('../catalog-remote.js');
+var stats = require('../stats.js');
+var isopack = require('../isobuild/isopack.js');
+var updater = require('../updater.js');
 var cordova = require('./commands-cordova.js');
-var Console = require('./console.js').Console;
-var projectContextModule = require('./project-context.js');
-var packageMapModule = require('./package-map.js');
-var packageVersionParser = require('./package-version-parser.js');
-var colonConverter = require("./colon-converter.js");
+var Console = require('../console.js').Console;
+var projectContextModule = require('../project-context.js');
+var packageMapModule = require('../package-map.js');
+var packageVersionParser = require('../package-version-parser.js');
+var colonConverter = require("../colon-converter.js");
 
 // For each release (or package), we store a meta-record with its name,
 // maintainers, etc. This function takes in a name, figures out if
@@ -1477,7 +1477,7 @@ var maybeUpdateRelease = function (options) {
   // backward-compatibility code which knows how to deal with an older release,
   // but if we actually do that, we can change this code to add the extra
   // springboard at that time.
-  var upgraders = require('./upgraders.js');
+  var upgraders = require('../upgraders.js');
   var upgradersToRun = upgraders.upgradersToRun(projectContext);
 
   // Download and build packages and write the new versions to .meteor/versions.
@@ -1715,7 +1715,7 @@ main.registerCommand({
 
   var upgrader = options.args[0];
 
-  var upgraders = require("./upgraders.js");
+  var upgraders = require("../upgraders.js");
   console.log("%s: running upgrader %s.",
               files.pathBasename(options.appDir), upgrader);
   upgraders.runUpgrader(projectContext, upgrader);
diff --git a/tools/commands.js b/tools/cli/commands.js
similarity index 97%
rename from tools/commands.js
rename to tools/cli/commands.js
index 617332ad91..51ce610628 100644
--- a/tools/commands.js
+++ b/tools/cli/commands.js
@@ -1,29 +1,29 @@
 var main = require('./main.js');
 var _ = require('underscore');
-var files = require('./files.js');
-var deploy = require('./deploy.js');
-var buildmessage = require('./buildmessage.js');
-var warehouse = require('./warehouse.js');
-var auth = require('./auth.js');
-var authClient = require('./auth-client.js');
-var config = require('./config.js');
-var release = require('./release.js');
+var files = require('../files.js');
+var deploy = require('../deploy.js');
+var buildmessage = require('../buildmessage.js');
+var warehouse = require('../warehouse.js');
+var auth = require('../auth.js');
+var authClient = require('../auth-client.js');
+var config = require('../config.js');
+var release = require('../release.js');
 var Future = require('fibers/future');
-var runLog = require('./run-log.js');
-var packageClient = require('./package-client.js');
-var utils = require('./utils.js');
-var httpHelpers = require('./http-helpers.js');
-var archinfo = require('./archinfo.js');
-var tropohouse = require('./tropohouse.js');
-var catalog = require('./catalog.js');
-var stats = require('./stats.js');
-var isopack = require('./isobuild/isopack.js');
+var runLog = require('../run-log.js');
+var packageClient = require('../package-client.js');
+var utils = require('../utils.js');
+var httpHelpers = require('../http-helpers.js');
+var archinfo = require('../archinfo.js');
+var tropohouse = require('../tropohouse.js');
+var catalog = require('../catalog.js');
+var stats = require('../stats.js');
+var isopack = require('../isobuild/isopack.js');
 var cordova = require('./commands-cordova.js');
-var execFileSync = require('./utils.js').execFileSync;
-var Console = require('./console.js').Console;
-var projectContextModule = require('./project-context.js');
-var colonConverter = require('./colon-converter.js');
-var PackageSource = require('./isobuild/package-source.js');
+var execFileSync = require('../utils.js').execFileSync;
+var Console = require('../console.js').Console;
+var projectContextModule = require('../project-context.js');
+var colonConverter = require('../colon-converter.js');
+var PackageSource = require('../isobuild/package-source.js');
 
 // The architecture used by MDG's hosted servers; it's the architecture used by
 // 'meteor deploy'.
@@ -119,7 +119,7 @@ main.registerCommand({
   pretty: false,
   catalogRefresh: new catalog.Refresh.Never()
 }, function (options) {
-  var archinfo = require('./archinfo.js');
+  var archinfo = require('../archinfo.js');
   Console.rawInfo(archinfo.host() + "\n");
 });
 
@@ -383,7 +383,7 @@ function doRunCommand (options) {
     options.once = true;
     var serverUrl = "http://" + (parsedUrl.host || "localhost") +
           ":" + parsedUrl.port;
-    var velocity = require('./run-velocity.js');
+    var velocity = require('../run-velocity.js');
     velocity.runVelocity(serverUrl);
   }
 
@@ -392,7 +392,7 @@ function doRunCommand (options) {
     mobileServer = mobileServer + ":" + parsedMobileServer.port;
   }
 
-  var runAll = require('./run-all.js');
+  var runAll = require('../run-all.js');
   return runAll.run({
     projectContext: projectContext,
     proxyPort: parsedUrl.port,
@@ -450,7 +450,7 @@ main.registerCommand({
 
     // Convert to OS path here because shell/server.js doesn't know how to
     // convert paths, since it exists in the app and in the tool.
-    require('./shell-client.js').connect(
+    require('../shell-client.js').connect(
       files.convertToOSPath(projectContext.getMeteorShellDirectory())
     );
 
@@ -553,7 +553,7 @@ main.registerCommand({
     };
 
     try {
-      files.cp_r(files.pathJoin(__dirnameConverted, 'skel-pack'), packageDir, {
+      files.cp_r(files.pathJoin(__dirnameConverted, '..', 'skel-pack'), packageDir, {
         transformFilename: function (f) {
           return transform(f);
         },
@@ -600,7 +600,7 @@ main.registerCommand({
     }
   }
 
-  var exampleDir = files.pathJoin(__dirnameConverted, '..', 'examples');
+  var exampleDir = files.pathJoin(__dirnameConverted, '..', '..', 'examples');
   var examples = _.reject(files.readdir(exampleDir), function (e) {
     return (e === 'unfinished' || e === 'other'  || e[0] === '.');
   });
@@ -661,7 +661,7 @@ main.registerCommand({
       });
     }
   } else {
-    files.cp_r(files.pathJoin(__dirnameConverted, 'skel'), appPath, {
+    files.cp_r(files.pathJoin(__dirnameConverted, '..', 'skel'), appPath, {
       transformFilename: function (f) {
         return transform(f);
       },
@@ -698,7 +698,7 @@ main.registerCommand({
 
     // Any upgrader that is in this version of Meteor doesn't need to be run on
     // this project.
-    var upgraders = require('./upgraders.js');
+    var upgraders = require('../upgraders.js');
     projectContext.finishedUpgraders.appendUpgraders(upgraders.allUpgraders());
 
     projectContext.prepareProjectForBuild();
@@ -894,7 +894,7 @@ var buildCommand = function (options) {
     projectContext: projectContext
   });
 
-  var bundler = require('./isobuild/bundler.js');
+  var bundler = require('../isobuild/bundler.js');
   var bundleResult = bundler.bundle({
     projectContext: projectContext,
     outputPath: bundlePath,
@@ -1030,7 +1030,7 @@ main.registerCommand({
   });
 
   const bundlePath = projectContext.getProjectLocalDirectory('build');
-  const bundler = require('./isobuild/bundler.js');
+  const bundler = require('../isobuild/bundler.js');
   const bundle = bundler.bundle({
     projectContext: projectContext,
     outputPath: null,
@@ -1077,7 +1077,7 @@ main.registerCommand({
   if (options.args.length === 0) {
     // localhost mode
     var findMongoPort =
-      require('./run-mongo.js').findMongoPort;
+      require('../run-mongo.js').findMongoPort;
     var mongoPort = findMongoPort(options.appDir);
 
     // XXX detect the case where Meteor is running, but MONGO_URL was
@@ -1118,7 +1118,7 @@ main.registerCommand({
     if (usedMeteorAccount)
       auth.maybePrintRegistrationLink();
     process.stdin.pause();
-    var runMongo = require('./run-mongo.js');
+    var runMongo = require('../run-mongo.js');
     runMongo.runMongoShell(mongoUrl);
     throw new main.WaitForExit;
   }
@@ -1150,7 +1150,7 @@ main.registerCommand({
 
   // XXX detect the case where Meteor is running the app, but
   // MONGO_URL was set, so we don't see a Mongo process
-  var findMongoPort = require('./run-mongo.js').findMongoPort;
+  var findMongoPort = require('../run-mongo.js').findMongoPort;
   var isRunning = !! findMongoPort(options.appDir);
   if (isRunning) {
     Console.error("reset: Meteor is running.");
@@ -1582,7 +1582,7 @@ main.registerCommand({
   if (options.velocity) {
     var serverUrl = "http://" + (parsedUrl.host || "localhost") +
           ":" + parsedUrl.port;
-    var velocity = require('./run-velocity.js');
+    var velocity = require('../run-velocity.js');
     velocity.runVelocity(serverUrl);
   }
 
@@ -1667,7 +1667,7 @@ var runTestAppForPackages = function (projectContext, options) {
       recordPackageUsage: false
     });
   } else {
-    var runAll = require('./run-all.js');
+    var runAll = require('../run-all.js');
     return runAll.run({
       projectContext: projectContext,
       proxyPort: options.port,
@@ -1705,7 +1705,7 @@ main.registerCommand({
   catalogRefresh: new catalog.Refresh.Never(),
   'allow-incompatible-update': { type: Boolean }
 }, function (options) {
-  var projectContextModule = require('./project-context.js');
+  var projectContextModule = require('../project-context.js');
   var projectContext = new projectContextModule.ProjectContext({
     projectDir: options.appDir,
     forceRebuildPackages: options.args.length ? options.args : true,
@@ -1930,13 +1930,13 @@ main.registerCommand({
     return 1;
   }
 
-  var selftest = require('./selftest.js');
+  var selftest = require('../selftest.js');
 
   // Auto-detect whether to skip 'net' tests, unless --force-online is passed.
   var offline = false;
   if (!options['force-online']) {
     try {
-      require('./http-helpers.js').getUrl("http://www.google.com/");
+      require('../http-helpers.js').getUrl("http://www.google.com/");
     } catch (e) {
       if (e instanceof files.OfflineError)
         offline = true;
diff --git a/tools/help.txt b/tools/cli/help.txt
similarity index 100%
rename from tools/help.txt
rename to tools/cli/help.txt
diff --git a/tools/main.js b/tools/cli/main.js
similarity index 98%
rename from tools/main.js
rename to tools/cli/main.js
index 457a645b87..a2b42c625a 100644
--- a/tools/main.js
+++ b/tools/cli/main.js
@@ -1,20 +1,20 @@
 var showRequireProfile = ('METEOR_PROFILE_REQUIRE' in process.env);
 if (showRequireProfile)
-  require('./profile-require.js').start();
+  require('../profile-require.js').start();
 
 var assert = require("assert");
 var _ = require('underscore');
 var Fiber = require('fibers');
 var Future = require('fibers/future');
-var Console = require('./console.js').Console;
-var files = require('./files.js');
-var warehouse = require('./warehouse.js');
-var tropohouse = require('./tropohouse.js');
-var release = require('./release.js');
-var projectContextModule = require('./project-context.js');
-var catalog = require('./catalog.js');
-var buildmessage = require('./buildmessage.js');
-var httpHelpers = require('./http-helpers.js');
+var Console = require('../console.js').Console;
+var files = require('../files.js');
+var warehouse = require('../warehouse.js');
+var tropohouse = require('../tropohouse.js');
+var release = require('../release.js');
+var projectContextModule = require('../project-context.js');
+var catalog = require('../catalog.js');
+var buildmessage = require('../buildmessage.js');
+var httpHelpers = require('../http-helpers.js');
 
 var main = exports;
 
@@ -23,7 +23,7 @@ var main = exports;
 // Node 0.12, so when we upgrade let's remember to remove this clause, and the
 // file it requires. See https://github.com/joyent/node/issues/3584
 if (process.platform === "win32") {
-  require('./flush-buffers-on-exit-in-windows.js');
+  require('../flush-buffers-on-exit-in-windows.js');
 }
 
 // node (v8) defaults to only recording 10 lines of stack trace. This
@@ -400,12 +400,12 @@ var springboard = function (rel, options) {
   if (process.env.METEOR_DEBUG_SPRINGBOARD)
     console.log("WILL SPRINGBOARD TO", rel.getToolsPackageAtVersion());
 
-  var archinfo = require('./archinfo.js');
-  var isopack = require('./isobuild/isopack.js');
+  var archinfo = require('../archinfo.js');
+  var isopack = require('../isobuild/isopack.js');
 
   var toolsPkg = rel.getToolsPackage();
   var toolsVersion = rel.getToolsVersion();
-  var packageMapModule = require('./package-map.js');
+  var packageMapModule = require('../package-map.js');
   var versionMap = {};
   versionMap[toolsPkg] = toolsVersion;
   var packageMap = new packageMapModule.PackageMap(versionMap);
@@ -542,7 +542,7 @@ Fiber(function () {
 
   // Set up git hooks
   if (files.inCheckout()) {
-    var installGitHooks = require('./install-git-hooks.js');
+    var installGitHooks = require('../install-git-hooks.js');
     installGitHooks();
   }
 
@@ -745,7 +745,7 @@ Fiber(function () {
     appDir = files.pathResolve(appDir);
   }
 
-  require('./isopackets.js').ensureIsopacketsLoadable();
+  require('../isopackets.js').ensureIsopacketsLoadable();
 
   // Initialize the server catalog. Among other things, this is where we get
   // release information (used by springboarding). We do not at this point talk
@@ -974,7 +974,7 @@ Fiber(function () {
       // Let's do some processing here. If the user/release file specified a
       // track, we need to display that correctly, and if they didn't, we should
       // make it clear that we are talking about the default track.
-      var utils = require('./utils.js');
+      var utils = require('../utils.js');
       var trackAndVersion = utils.splitReleaseName(releaseName);
       var displayRelease = utils.displayRelease(
         trackAndVersion[0], trackAndVersion[1]);
@@ -1359,7 +1359,7 @@ Fiber(function () {
   // Now that we're ready to start executing the command, if we are in
   // startup time profiling mode, print the profile.
   if (showRequireProfile)
-    require('./profile-require.js').printReport();
+    require('../profile-require.js').printReport();
 
   Console.setPretty(command.evaluateOption('pretty', options));
   Console.enableProgressDisplay(true);
diff --git a/tools/main-transpile-wrapper.js b/tools/main-transpile-wrapper.js
index 8e299e07ed..068f5d898f 100644
--- a/tools/main-transpile-wrapper.js
+++ b/tools/main-transpile-wrapper.js
@@ -2,4 +2,4 @@
 require('./install-babel.js');
 
 // Run the Meteor command line tool
-require('./main.js');
+require('./cli/main.js');
diff --git a/tools/run-app.js b/tools/run-app.js
index dc0bf23556..038b252b9d 100644
--- a/tools/run-app.js
+++ b/tools/run-app.js
@@ -9,7 +9,7 @@ var release = require('./release.js');
 var buildmessage = require('./buildmessage.js');
 var runLog = require('./run-log.js');
 var stats = require('./stats.js');
-var cordova = require('./commands-cordova.js');
+var cordova = require('./cli/commands-cordova.js');
 var Console = require('./console.js').Console;
 var catalog = require('./catalog.js');
 var Profile = require('./profile.js').Profile;