Spec a target tolerance. Contractually this is difficult to hold to, but provides a method to explain the importance of the allowable tolerance.
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Advice
Example of a mainly successful project: Brock Commons — involved a high degree of collaboration: Integrated Design Process — design offered 3-4 options for every connection, which every stakeholder vetted — invested in building a mock-up, where many problems were solved in advance of construction — the design worked with standard panel sizes
Advice
Tolerances are different for each different trade. Mitigate potential problems with communication in the procurement phase.