1. as far as i know there is no current IDE for extensions. simply use your favorite text editor. if you don't want to write an extension from scratch you can take a sample one and change the pertinent information.i simply use sublime text. there is a very bare almost useless autocomplete package for it, but i don't think it has been updated. it is pretty easy to browse the Scripting Reference PDF
2. you can find a tutorial for the manifest here https://github.com/Adobe-CEP - you will find the manifest right away in the "getting started" section
3. to test out your extension you can disable the signature check. on the mac you enter the command "defaults write com.adobe.CSXS.8 PlayerDebugMode 1" in terminal. for windows is something similar. you can find this instructions in the above link same with the signing process once your extension is ready
4. when you sign, the process includes creating a zxp package for distribution which you can upload to adobe. with the package, there will be an xml file with destinations for the different parts.
examples for all this stuff can be found on the github.
workflow for me is like this.
1 Manifest file - fill in the info required for my extension. name, version, window size, html file name, target app, etc.
2 CSInterface.js library - which enables talking to the app, you can link to this file through your html panel
3 extendscript file - this is where you write your script that directly interface with illustrator. refer to the Scripting Reference PDF for the possibilities here
4 html panel - it's basically an html page like any website. layout your interface, link your css styles and js files that you need. you can include libraries like jquery. the js for the panel doesn't manipulate illustrator directly. instead you will call on CSInterface.js to execute any function you define in the extendscript
anyway. everything is the githup. all the documentation is there - cookbook, examples, debugging, template manifest files, etc. organization is up to you as long as you link to the right files within the html and manifest.