Can work documented within a manual be published in a journal? I work on an actively developed collaborative project. The project is a simulation package. The model has various manuals and guides. These guides are non-peer reviewed collaborative documents self published online. When features are added to the model it is important to keep the guides up to date. For example, when a new feature is added the user guide must be updated to enable users to use the new feature. 

I recently added a major update to the code. I documented the use of the new submodel and it's numerical verification in the collaborative user guides. 

To make this novel contribution permanently available to others (the guides are changing constantly) and to reach a wider audience, I submitted an article to an archived peer reviewed journal. The article included the theory, implementation and verification of the new submodel. i.e. some of the content from the guide is in the article. 

One of the reviewer's comments I received was:


  It bothers me that the present paper does not add any new findings or results to those already published in &lt;the guide>. Figures xyz of the current manuscript are same as the Figures abc of &lt;the guide>. Therefore, I do not recommend the publication of this paper in the &lt;journal> in its present form. The authors must delineate the similarities and differences between the works mentioned above.


I am the author of the relevant sections of the guide. The guide is not a permanently available archived peer reviewed journal. That is the reason I decided to publish in a journal. 

I would draw a parallel to a PhD thesis chapter (or an MSc thesis). These are publicly available, arguably more "peer reviewed" than manuals or guides and will be permanently archived. It is typical for thesis chapters to be converted in to journal articles - so why not a non peer reviewed, non permanent and unarchived manual?

Is this a valid and fair comment? Is content presented in manual or user guide be published in a journal?
I think the comment is fair, but can be rebutted. I would prepare an answer layered on two levels:


On the practical level, change figures xyz as much as you can. Maybe run some additional simulations, change the plots, legends, colours, etc.. This will show some willingness to the editor.
On the more crucial aspect of whether your work can be considered "novel enough" to be published in the journal: I would argue that 


the paper will provide a much more coherent context to the model (as only published articles can), and as such its dissemination will be facilitated;
the guide is subject to be changed in the future, while the published paper is a much more "stable" resource for future researchers;
depending on the model itself, you can argue that the paper will make it possible for researchers that don't use your code to implement the model in their own codes. If this is true, you might reword some parts of the manuscript to focus more on the model itself, which should be the paper's main selling point, than on its implementation in the code.