I will try to address some of the issues you have here:
1. About crashing project. Please send us an email to support[at]icenium.com with your project name and mail under which the problematic project is created.
2. About uncompleted command (console log alert and others). The code analysis is designed to alert you if you have errors in your code. You may turn this functionality off from options/advance/code analysis.
3. I was not able to reproduce "new line blank chars" issue - can you please provide more info about it?