When referring to the reference manual looking for explanation of Derby properties, one finds the section. "Derby properties", whose first sentence reads:
"The Derby properties are used for configuring the system and database, as well as for diagnostics such as logging statements, and monitoring and tracing locks."
There is no mention of server specific properties (these are explained in the "Setting Network Server properties" in the server manual).
Still, these are "Derby properties" and would be perceived as such by many users, so I think this section in the reference manual should
point the user to the server manual also: This section does, after all, not explain all Derby properties. The tools properties are probably not necessary to mention/crosslink from here.