Say that -entirely hypothetically and for the sake of a practical example- we are talking about a new "single file container/archive that can be reconstructed even after total loss of file system structures" .... This code is licensed under the AGPL and written in Python.
Basically what I would want is: if some dev/company want to make use the file format in a closed source commercial project/product, we should reach some kind of agreement with a different licensing.
Or said in another way:
Can anyone take this idea and reimplement it for instance in Ruby and would this implementation be subject to the AGPL?
The quick answer is that anyone can likely reimplement this file format under any license they like, assuming no code is borrowed from the original implementation.
Your code and the specification for this file format are AGPL-licensed alright... but nothing more.
My opinion is that the idea of a novel file format is not in the realm of copyright protection but instead this is in the realm of patent protection.
Therefore only thing that might grant you some monopoly on this idea is a patent. Copyright only grants you a monopoly on the expression in a "fixed medium", e.g. on the source code and/or binaries.
Some supporting references:
Generally speaking, copyright protects the expression of an idea but it does not protect the underlying idea itself. Applying that rationale to computer programs, copyright in computer programs typically does not extend to the functionality, operational interfaces or the programming language of the program, although it can protect the source code, object code and preparatory design materials of the program. Accordingly, developing and using a program that has the same or similar functionality and operational interfaces of another computer program would not of itself usually amount to copyright infringement, but copying the underlying source (or object) code would.
For the European arena, there is recent authority in SAS Institute Inc v World Programming Limited that the format of a program's data files are not protected by copyright when reverse engineered without the source code.
Can a graphics file be copyrighted?
A graphics file itself cannot normally be copyrighted under United States copyright laws (although the rulings of some judges may disagree). The specification of a format and the "contents" of a graphics file, however, are subject to copyright. In other words, your secret barbecue sauce, or its recipe, can win a blue ribbon at the county fair but not the jar you put the sauce in, or the paper you wrote the recipe on.