diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5f1d377..4d948b7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,6 @@
+## 0.3.0
+- Fix the bug that the default note directory is within packages directory. If it happens, it **deletes** all of existing notes. If you read this before updating the package, please check your note directory before updating it.
+
 ## 0.2.0
 - Use DocQuery
 - Introduce autosave features
diff --git a/lib/notational-velocity.coffee b/lib/notational-velocity.coffee
index 0d7553a..132ecd5 100644
--- a/lib/notational-velocity.coffee
+++ b/lib/notational-velocity.coffee
@@ -8,12 +8,12 @@ module.exports =
       title: 'Note Directory'
       description: 'The directory to archive notes'
       type: 'string'
-      default: process.env.ATOM_HOME + '/packages/notational-velocity/notebook'
+      default: path.join(process.env.ATOM_HOME, 'notational-velocity-notes')
 
   notationalVelocityView: null
 
   activate: (state) ->
-    @rootDirectory = fs.realpathSync(atom.config.get('notational-velocity.directory'))
+    @rootDirectory = @ensureNoteDirectory()
 
     # Events subscribed to in atom's system can be easily cleaned up with a
     # CompositeDisposable
@@ -60,3 +60,25 @@ module.exports =
 
   autosaveAll: ->
     @autosave(paneItem) for paneItem in atom.workspace.getPaneItems()
+
+  ensureNoteDirectory: ->
+    noteDirectory = atom.config.get('notational-velocity.directory')
+    packagesDirectory = path.join(process.env.ATOM_HOME, 'packages')
+    defaultNoteDirectory = path.join(packagesDirectory, 'notational-velocity', 'notebook')
+
+    if noteDirectory.startsWith(packagesDirectory)
+      storageDirectory = path.join(packagesDirectory, 'storage')
+      throw new Error("""
+          The note directory (#{noteDirectory}) should NOT nest under #{packagesDirectory}.
+          It is likely that you updated the package to a newer version from v0.1.0.
+          It is likely that the note directory is overwritten.
+          Unfortunately, I couldn't find a way to recover overwritten notes.
+          You might recover partial notes from #{storageDirectory}.
+          I am extremely sorry.
+          - Seongjae Lee""")
+
+    if !fs.existsSync(noteDirectory)
+      fs.makeTreeSync(noteDirectory)
+      fs.copySync(defaultNoteDirectory, noteDirectory)
+
+    return fs.realpathSync(noteDirectory)
diff --git a/spec/notational-velocity-spec.coffee b/spec/notational-velocity-spec.coffee
index ff68de3..cfd9e22 100644
--- a/spec/notational-velocity-spec.coffee
+++ b/spec/notational-velocity-spec.coffee
@@ -1,7 +1,4 @@
-# Use the command `window:run-package-specs` (cmd-alt-ctrl-p) to run specs.
-#
-# To run a specific `it` or `describe` block add an `f` to the front (e.g. `fit`
-# or `fdescribe`). Remove the `f` to unfocus the block.
+path = require 'path'
 
 describe "NotationalVelocity", ->
   defaultDirectory = atom.config.get('notational-velocity.directory')
@@ -20,8 +17,7 @@ describe "NotationalVelocity", ->
     it "attaches and then detaches the view", ->
       expect(workspaceElement.querySelector('.notational-velocity')).not.toExist()
 
-      # This is an activation event, triggering it will cause the package to be
-      # activated.
+      # This is an activation event, triggering it will cause the package to be activated.
       atom.commands.dispatch workspaceElement, 'notational-velocity:toggle'
 
       waitsForPromise ->
@@ -30,3 +26,24 @@ describe "NotationalVelocity", ->
       runs ->
         expect(workspaceElement.querySelector('.notational-velocity')).toExist()
         atom.commands.dispatch workspaceElement, 'notational-velocity:toggle'
+
+    it "checks if we banned the default directory under packages directory", ->
+      atom.notifications.clear()
+
+      waitsForPromise ->
+        atom.packages.activatePackage('notifications')
+
+      runs ->
+        defaultNoteDirectory = path.join(process.env.ATOM_HOME, 'packages', 'notational-velocity', 'notebook')
+        atom.config.set('notational-velocity.directory', defaultNoteDirectory)
+
+        # This is an activation event, triggering it will cause the package to be activated.
+        atom.commands.dispatch workspaceElement, 'notational-velocity:toggle'
+
+        waitsForPromise ->
+          activationPromise
+
+        runs ->
+          notificationContainer = workspaceElement.querySelector('atom-notifications')
+          notification = notificationContainer.querySelector('atom-notification.fatal')
+          expect(notification).toExist()