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It is normally specified by the designer. A lot of pcb material two ounces of copper per square foot. I had many circuit boards where we ordered six ounces plated on top the basic board. These were for high power circuits.
The stackup definition is intended for your documentation purpose and normally not passed on to the PCB manufacturer. Eagle in particular doesn't support CAM formats like ODB++ that can optionally contain stackup information.
Most standard PCB boards are made with 35 µm (1 oz) copper. If you are ordering simple boards without explicite copper weight and stackup information, you expect to get it made with a standard process.
Gerber files do not contain any data on stackup, you have to provide that info to the manufacturer via some other means. Usually I include a readme.txt along with the gerbers which has miscellaneous info such as stackup, copper weight, finish, etc.
Stackup description is included in ODB++ v7, but most likely no recent tool is supporting it yet. And of course, a separate human readable doucmentation should be provided in any case.
Yes it is supported but most ODB++ output gateways and inputs to front end systems ignore it, it has been there for several years and I would have loved it to function as it would save manually having to provide the information.
When I get 5 minutes I will try and find out if anyone is using this info, I know at the moment my CAD system does not output it despite numerous requests in the past.
You have to define your layer stack up in your CAD system if you are doing any signal integrity work or impedance calculations, this includes the laminates and pre-pregs.
In the situation I was working in we had specification drawings for everything we had made off campus. They always included the type of base material, usually mil-specification types. Things like the bare board thickness and thickness of plated on copper and tolerances were always specified.
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