Hi nemesi!
I can't help you much on the eyeOS side but I can guide you on OpenGoo's side.
A little background on OpenGoo's architecture:
OpenGoo implements the Model View Controller design pattern. In the application folder you have a controllers folder, a models folder and a views folder. The first contains PHP classes that execute actions called form the GUI (FilesController, AccessController, TaskController). The models folder contains PHP classes that are persisted in the database and that represent all the objects handled in OpenGoo (ProjectFile, User, ProjectTask). Finally, the views folder contains PHP files that generate the HTML (or anything other format) that the user will see (add_file.php, login.php, view_task.php). Besides the application folder you also have the environment folder that contains generic PHP functionality, the library folder that contains PHP libraries, the language folder that contains translations and the public folder that contains the CSSs, javascripts, images, etc.
An OpenGoo URL always includes a parameter indicating the controller, a parameter indicating the action to execute and other arguments specific to that action. For example, the URL index.php?c=files&a=edit_file&id=4 would call the add_file method of the FilesController class and there it would load the file with id 4. This action would load the view that will be displayed and pass it any objects it may need (in this case, the edit_file.php would be loaded and it would be passed the file with id 4). That HTML is returned to the server.
These URLs are actually invoked by ajax calls from the GUI, and need other parameters to work correctly that I omitted to simplify things for now. The response from the server is actually a JSON encoded string which contains information about errors, events and the HTML generated by the action. This JSON string is decoded by some javascript code and then processed to display error messages, fire events and load the content into the corresponding panel.
On the client side OpenGoo uses ExtJS as its main javascript library.
In order to import documents from eyeOS you will need to, for example, add a method to the FilesController called import_from_eyeos. This method should be similar to the add_file method, in the sense that it should create a ProjectFile object and save it into the database, so you might want to take a look at that method in order to have an idea of how to start. One important thing is that you should set some mime type for the eyedoc so that OpenGoo can know that the file is an eyedoc file (maybe just setting it to text/html will do).
For OpenGoo to handle eyedoc files correctly you might want to set an icon for that type and tell OpenGoo to open eyedoc files with FCKEditor (assuming that eyedoc files contain HTML). For the first thing there's a CSS file that associates an image to each mime type which is in public/assets/themes/default/stylesheets/file/types.css. There you should add an entry for the eyedoc file (if it's mime type isn't already there). To tell OpenGoo to open the eyedoc file with the FCKEditor you should change the getModifyUrl function in application/models/files/ProjectFile.class.php and return the appropriate URL for eyedoc files.
Ok, this should do for now. If you have any further questions or if anything isn't clear enough don't hesitate to ask.