How is caller id passed from the PSTN to the CallManager 7.x or CUBE when using a SIP trunk? Is there information somewhere on how to configure incoming transformations allowing click to call from call directories?
The number is in whatever format your provider chooses to send it in. SIP has no explicit requirement for E.164 formatting. You can debug it on CUBE to see what your provider is sending or just ask them.
Type of Number (TON) is an ISDN concept. Subscriber/National/International do not exist in SIP so all UC Manager can give you is Unknown.
UCM 7.1 did introduce a CSS option in addition to just the prefix for this exact scenario. You can create a CSS with multiple transformations in it if your provider does not send a consistent format.