Here's my quick analysis of the situation.
The agreement first defines some things:
"Amiga Mark" means any mark owned and/or registered or licensed by or to the Amiga Parties containing the word "Amiga" whether in stylized form (figurative mark) or otherwise.
"Documentation" means the publications listed on Exhibit 4 hereof.
"Software" means Amiga OS 3.1, which is the Operating System (including without limitation its Software Architecture as described in the Documentation) originally developed, owned and marketed by Commodore Business Machines (CBM) for their Amiga line of computers In 1994.
"Software Architecture" means the structure or structures of the system, which comprise software components, the externally visible properties of those components (i.e., those assumptions other elements can make of an element, such as its provided services, performance characteristics, fault handling, shared resource usage, and so on), and the relationships between them; the term also refers to documentation of a system's software architecture.
Here's the Exhibit 4:
EXHIBIT 4
LIST OF PUBLICATIONS COMPRISING THE DOCUMENTATION
1. The AmigaDOS Manual, 3rd edition,
ISBN 0-553-35403-5
2. Amiga ROM Kernel Reference Manual "Libraries", 3rd edition,
ISBN 0-201-56774-1
3. Amiga Hardware Reference Manual, 3rd edition,
ISBN 0-201-56776-8
4. Amiga ROM Kernel Reference Manual "Devices", 3rd edition,
ISBN 0-201-56775-x
5. Amiga ROM Kernel Reference Manual "Includes and Autodocs",
3rd edition, ISBN 0-201-56773-3
There is a clause:
In the event the Amiga Parties assign ownership of the Amiga Marks to a third party, including without limitation as result of a transfer by contract or by operation of law, such third party must agree in writing to be bound by the terms and conditions of this Agreement, and to assume the obligations of the Amiga Parties under this Agreement.
This means that if Commodore USA has obtained a valid license to use the name Amiga, they're now signees of the agreement.
**EDIT** Actually as a friend pointed out there is a difference between ownership and possession: "The law permits a trademark owner to license its marks as long as the owner controls the nature and quality of the goods or services bearing the marks." So this clause may not apply in this case after all. However, since the clause below includes wording "including through sub-licensing" I think the only relevance is defining the legal entity to sue in case of disagreement.
Further the agreement stipulates that:
the Amiga Parties shall during the term of this Agreement not commercialize anywhere in the world (including through sub-licensing), distribute (free of charge or otherwise) or make available to the public (free of charge or otherwise), in any way or form (including but not limited to Object Code and Source Code form), on any medium (now known or otherwise) and through any means (now known or otherwise) the Software (in part or as a whole) and any Operating System exhibiting a Software Architecture substantially similar to the Software Architecture of the Software as described in the Documentation, to the extent that such Software Architecture is protectable under the copyright laws of the United States (a "Substantially Similar Software Architecture").
At this point the case depends on the part "
to the extent that such Software Architecture is protectable under the copyright laws of the United States (a "Substantially Similar Software Architecture")".
There's no denying that AROS is substantially similar. However, considering copyright laws protect implementation and not ideas, this could be a hairy case.
**EDIT2** I am not a lawyer nor have I any kind of legal training. What I've done is read the agreement document and try to identify and understand the relevant parts for this situation. That is: I could be dead wrong here. Finally, as you might have noticed I didn't even try to determine which party would ultimately be right in their claims.