Create several docs which are side by side and independent from each other?

I start using DocumentJS which for some reason I did not use before.

Ist it possible, to create more than one doc?

What I want:

1. I want to create a developers-doc similar to the doc of JMVC / canjs etc. itself, where co-developers can have a look to understand the code.
2. I want to create a user-manual, in which the usage of the apṕ is explained. The advantage is, that I can render a link to the specific page of the usermanual in every widget of the app automatically.
3. Same as 2. but for the admins of the app. So when I solve 2. I have this topic as well.

I do not want to deliver the developers-doc in a production-build. So I want the different docs in different folders.

I am able to manipulate scripts/docjs:

1. load('steal/rhino/rhino.js');
2. steal("documentjs", function(DocumentJS){
3.     DocumentJS('myapp/index.html', {
4.         out: 'myapp/docs',
5.         markdown : ['myapp', 'steal', 'jquerypp', 'can', 'funcunit'],
6.         parent : 'myapp',
7.                 templates : 'myapp/lib/doctemplates'
8.     });
9.         DocumentJS('myapp/index.html', {
10.         out: 'myapp/docs2',
11.         markdown : ['myapp', 'steal', 'jquerypp', 'can', 'funcunit'],
12.         parent : 'myapp',
13.                 templates : 'myapp/lib/doctemplates'
14.     });
15. });

It produces the different folders as I want it to. But how could I tell the script, which files to use for the docs.

The developer-docs are made by information given in the .js files itself. For the userguide I could touch an md.file.

eg:

model.js contains the dev-doc-information

modelUG.md contains the Userguide-infomation.

modelAG.md contains the Adminguide-information.

It is no problem, to strukture it using the directives, but I want it to be separated in the folders.

What I coul do is to put the md-files in a different folder structure. But when I do so, it is less comfortable to maintain the Guides.

Any Idea?