diff --git a/dot-nylas/config.json b/dot-nylas/config.json
index 8997f2ed7..5701cf243 100644
--- a/dot-nylas/config.json
+++ b/dot-nylas/config.json
@@ -6,6 +6,11 @@
         "ui-light"
       ],
       "disabledPackages": [
+        "message-view-on-github",
+        "personal-level-indicators",
+        "phishing-detection",
+        "github-contact-card",
+        "keybase"
       ]
     }
   }
diff --git a/src/browser/application.es6 b/src/browser/application.es6
index 8503bbb78..0e3c7be2f 100644
--- a/src/browser/application.es6
+++ b/src/browser/application.es6
@@ -7,6 +7,7 @@ import ApplicationMenu from './application-menu';
 import AutoUpdateManager from './auto-update-manager';
 import PerformanceMonitor from './performance-monitor'
 import NylasProtocolHandler from './nylas-protocol-handler';
+import PackageMigrationManager from './package-migration-manager';
 import ConfigPersistenceManager from './config-persistence-manager';
 
 import {BrowserWindow, Menu, app, ipcMain, dialog} from 'electron';
@@ -44,7 +45,8 @@ export default class Application extends EventEmitter {
     this.configPersistenceManager = new ConfigPersistenceManager({configDirPath, resourcePath});
     config.load();
 
-    this.temporaryInitializeDisabledPackages();
+    this.packageMigrationManager = new PackageMigrationManager({config, configDirPath, version})
+    this.packageMigrationManager.migrate()
 
     let initializeInBackground = options.background;
     if (initializeInBackground === undefined) {
@@ -78,51 +80,6 @@ export default class Application extends EventEmitter {
     return this.quitting;
   }
 
-  temporaryInitializeDisabledPackages() {
-    if (this.config.get('core.disabledPackagesInitialized')) {
-      return;
-    }
-
-    const exampleNewNames = {
-      'N1-Message-View-on-Github': 'message-view-on-github',
-      'N1-Personal-Level-Indicators': 'personal-level-indicators',
-      'N1-Phishing-Detection': 'phishing-detection',
-      'N1-Github-Contact-Card-Section': 'github-contact-card',
-      'N1-Keybase': 'keybase',
-      'N1-Markdown': 'composer-markdown',
-    }
-    const exampleOldNames = Object.keys(exampleNewNames);
-    let examplesEnabled = [];
-
-    // Temporary: Find the examples that have been manually installed
-    if (fs.existsSync(path.join(this.configDirPath, 'packages'))) {
-      const packages = fs.readdirSync(path.join(this.configDirPath, 'packages'));
-      examplesEnabled = packages.filter((packageName) =>
-         exampleOldNames.includes(packageName) && (packageName[0] !== '.')
-      );
-
-      // Move old installed examples to a deprecated folder
-      const deprecatedPath = path.join(this.configDirPath, 'packages-deprecated')
-      if (!fs.existsSync(deprecatedPath)) {
-        fs.mkdirSync(deprecatedPath);
-      }
-      examplesEnabled.forEach((dir) => {
-        const prevPath = path.join(this.configDirPath, 'packages', dir)
-        const nextPath = path.join(deprecatedPath, dir)
-        fs.renameSync(prevPath, nextPath);
-      });
-    }
-
-    // Disable examples not specifically enabled
-    for (const oldName of Object.keys(exampleNewNames)) {
-      if (examplesEnabled.includes(oldName)) {
-        continue;
-      }
-      this.config.pushAtKeyPath('core.disabledPackages', exampleNewNames[oldName]);
-    }
-    this.config.set('core.disabledPackagesInitialized', true);
-  }
-
   temporaryMigrateConfig() {
     const oldConfigFilePath = fs.resolve(this.configDirPath, 'config.cson');
     const newConfigFilePath = path.join(this.configDirPath, 'config.json');
diff --git a/src/browser/package-migration-manager.es6 b/src/browser/package-migration-manager.es6
new file mode 100644
index 000000000..0063b3abc
--- /dev/null
+++ b/src/browser/package-migration-manager.es6
@@ -0,0 +1,82 @@
+import fs from 'fs'
+import path from 'path'
+import semver from 'semver'
+
+
+const PACKAGE_MIGRATIONS = [
+  {
+    "version": "0.4.50",
+    "package-migrations": [{
+      "new-name": "composer-markdown",
+      "old-name": "N1-Markdown-Composer",
+      "enabled-by-default": false,
+    }],
+  },
+]
+
+class PackageMigrationManager {
+
+  constructor({config, version, configDirPath} = {}) {
+    this.config = config
+    this.configDirPath = configDirPath
+    this.version = version
+    this.savedMigrationVersion = this.config.get('core.packageMigrationVersion')
+  }
+
+  getMigrationsToRun() {
+    let migrations;
+    if (this.savedMigrationVersion) {
+      migrations = PACKAGE_MIGRATIONS
+      .filter((migration) => semver.gt(migration.version, this.savedMigrationVersion))
+      .map(migration => migration['package-migrations'])
+    } else {
+      migrations = PACKAGE_MIGRATIONS.map(migration => migration['package-migrations'])
+    }
+    return [].concat.apply([], migrations)
+  }
+
+  migrate() {
+    if (this.savedMigrationVersion === this.version) { return }
+    const migrations = this.getMigrationsToRun()
+    const oldPackNames = migrations.map((mig) => mig['old-name'])
+    const disabledPackNames = this.config.get('core.disabledPackages') || []
+    let oldEnabledPackNames = []
+
+    if (fs.existsSync(path.join(this.configDirPath, 'packages'))) {
+      // Find any external packages that have been manually installed
+      const toMigrate = fs.readdirSync(path.join(this.configDirPath, 'packages'))
+      .filter((packName) => oldPackNames.includes(packName))
+      .filter((packName) => packName[0] !== '.')
+
+      // Move old installed packages to a deprecated folder
+      const deprecatedPath = path.join(this.configDirPath, 'packages-deprecated')
+      if (!fs.existsSync(deprecatedPath)) {
+        fs.mkdirSync(deprecatedPath);
+      }
+      toMigrate.forEach((packName) => {
+        const prevPath = path.join(this.configDirPath, 'packages', packName)
+        const nextPath = path.join(deprecatedPath, packName)
+        fs.renameSync(prevPath, nextPath);
+      });
+
+      oldEnabledPackNames = toMigrate.filter((packName) => (
+        !(disabledPackNames).includes(packName)
+      ))
+    }
+
+    // Enable any packages that were migrated from an old install and were
+    // enabled, or that should be enabled by default
+    migrations.forEach((migration) => {
+      // If the old install was enabled, keep it that way
+      if (oldEnabledPackNames.includes(migration['old-name'])) { return }
+      // If we want to enable the package by default,
+      if (migration['enabled-by-default']) { return }
+      const newName = migration['new-name']
+      this.config.pushAtKeyPath('core.disabledPackages', newName);
+    })
+
+    this.config.set('core.packageMigrationVersion', this.version)
+  }
+}
+
+export default PackageMigrationManager