Fix #25 so that it ensures the note directory does not nest within the package directory

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)