The economics of design do not allow for the time it takes to write a specification and assemble a project manual.
By my count there are four basic types of architectural fees. Variations on two of these basic types adds another four fee types.
A while back I posted an article about Additional Services. There are a lot of circumstances that arise where additional compensation for Additional Services is called for. In that first post I offered a simple way to get the issue on the table and approved. The second part of the issue is recognizing Additional Services.