Add version number to project settings.
HTML5 Template: Use runWithScene when loading first scene 

Using runWithScene produces assertion error:

`Assertion failed: Use runWithScene: instead to start the director`
Show and publish json files
Remove old publish dir if version mis-match and we want to re-publish
Merge remote-tracking branch 'upstream/develop' into force_republish
Move store the project setting to appDelegate and fix a typo.
Mark need republish when clean cache is clicked.
Merge pull request #360 from ayuer/force_republish

Fix issue #329, Force republish
Fixed issues with republishing files when updating version
Merge branch 'patch-1' of https://github.com/SevInf/CocosBuilder into develop
Merge pull request #359 from SevInf/json

Show and publish json files
Merge branch 'develop' of github.com:cocos2d/CocosBuilder into develop
Improves autocomplete
Fixes issue with build not being correctly cleaned with newer versions of Xcode
Fixes potential issue with redirection of stdout
Merge pull request #12 from cocos2d/develop

merge 17/5