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DRC marker persistence
Part of the 6.0 DRC architecture is marker persistence. This will allow you to work your way through a large set of DRC violations, flagging those that have already been checked as exceptions or some-such.
1) Store markers in board file or project file?
Board file is much easier (in fact currently zero-cost as it’s implemented in my tree), but it may cause heartache in “bloated diff” camp? (Note that you can always press Delete All Markers when you’re done with DRC, so you can choose to not have them in the board file.)
2) Should exceptions be of the form “ignore error type X between object Y and object Z”, or “this specific error condition is a false-positive”?
The first is more like a C++ #pragma. The second is arguably “safer”, but requires storing hashes of the entire data-state of objects Y and Z. Likely expensive to calculate on large boards (and somewhat expensive to implement).