Fix a bug that utility.isNote does not handle symlinks properly

lib/notational-velocity.coffee

@@ -73,8 +73,8 @@ module.exports =
   autodelete: (paneItem) ->
     return false unless paneItem?.getURI?()?
     uri = paneItem.getURI()
-    return unless Utility.isNote(uri)
-    return false unless paneItem?.isEmpty()
+    return false unless Utility.isNote(uri)
+    return false unless paneItem.isEmpty()
     fs.unlinkSync(uri)
     noteName = uri.substring(@rootDirectory.length + 1)
     atom.notifications.addInfo("Empty note #{noteName} is deleted.")

lib/utility.coffee

@@ -11,7 +11,16 @@ class Utility
   @getPrimaryNoteExtension: -> if atom.config.get('nvatom.extensions').length then atom.config.get('nvatom.extensions')[0] else '.md'
 
   @isNote: (filePath) ->
+    return false unless path.extname(filePath) in atom.config.get('nvatom.extensions')
+
     filePath = fs.normalize(filePath)
-    return filePath.startsWith(Utility.getNoteDirectory()) and path.extname(filePath) in atom.config.get('nvatom.extensions')
+    return true if filePath.startsWith(Utility.getNoteDirectory())
+    return true if filePath.startsWith(fs.realpathSync(Utility.getNoteDirectory()))
+    return false unless fs.existsSync(filePath)
+
+    filePath = fs.realpathSync(filePath)
+    return true if filePath.startsWith(Utility.getNoteDirectory())
+    return true if filePath.startsWith(fs.realpathSync(Utility.getNoteDirectory()))
+    return false
 
   @trim: (str) -> str?.replace /^\s+|\s+$/g, ''

spec/interlink-spec.coffee

@@ -3,6 +3,8 @@ path = require 'path'
 temp = require 'temp'
 Interlink = require '../lib/interlink'
 
+temp.track()
+
 describe 'Interlink', ->
   defaultDirectory = atom.config.get('nvatom.directory')
   noteDirectory = null

spec/notational-velocity-spec.coffee

@@ -1,6 +1,8 @@
 path = require 'path'
 temp = require 'temp'
 
+temp.track()
+
 describe "nvAtom", ->
   defaultDirectory = atom.config.get('nvatom.directory')
   activationPromise = null

spec/utility-spec.coffee

@@ -1,5 +1,10 @@
+fs = require 'fs-plus'
+path = require 'path'
+temp = require 'temp'
 Utility = require '../lib/utility'
 
+temp.track()
+
 describe "utility", ->
   defaultNoteDirectory = atom.config.get('nvatom.directory')
   defaultNoteExtensions = atom.config.get('nvatom.extensions')
@@ -23,3 +28,27 @@ describe "utility", ->
     expect(Utility.getPrimaryNoteExtension()).toBe('.markdown')
     atom.config.set('nvatom.extensions', [])
     expect(Utility.getPrimaryNoteExtension()).toBe('.md')
+
+  describe 'isNote handles symlinks correctly', ->
+    atom.config.set('nvatom.extensions', ['.md', '.markdown'])
+
+    tempDirectoryPath = path.join(temp.mkdirSync())
+    noteDirectoryPath = path.join(temp.mkdirSync())
+    noteDirectoryPathSymlink = path.join(tempDirectoryPath, 'note book')
+    notePath = path.join(noteDirectoryPath, 'note.md')
+    notePathSymlink = path.join(noteDirectoryPathSymlink, 'note symlink.md')
+
+    fs.writeFileSync(notePath, 'dummy')
+    fs.symlinkSync(noteDirectoryPath, noteDirectoryPathSymlink)
+    fs.symlinkSync(notePath, notePathSymlink)
+
+    expect(fs.existsSync(notePath)).toBe(true)
+    expect(fs.existsSync(fs.normalize(notePath))).toBe(true)
+
+    atom.config.set('nvatom.directory', noteDirectoryPath)
+    expect(Utility.isNote(notePath)).toBe(true)
+    expect(Utility.isNote(notePathSymlink)).toBe(true)
+
+    atom.config.set('nvatom.directory', noteDirectoryPathSymlink)
+    expect(Utility.isNote(notePath)).toBe(true)
+    expect(Utility.isNote(notePathSymlink)).toBe(true)