A strange thing I noticed: The city where you have the "Master" level guild house doesn't get the basic level guild house bonus anymore.
Example: I had Master Thieves Guild in Venice, and Thieves Guild in Genoa => As a result, all my cities get the Master bonus, but in Genoa, my spies get BOTH the global Master bonus and the Basic city-specific bonus (So they are minimum +2 skill at the start).
Correction to this would be that Master guildhouses and HQs should give the global bonus AND in addition the basic guildhouse bonus to agents trained in that city. Otherwise the cities with basic guildhouses will build the more skilled agents, which doesn't make sense.
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