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How to use two dimensional arrays in legacy code?

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I have a C function with a structure, inside the struct is a two dimensional array
typedef struct {
double my_array[3][3];
} my_struct;
The legacy code tool complains that it cannot accept the array with two dimensions, so I had to put the struct like
typedef struct {
double my_array[9];
} my_struct;
I was wondering if there is a way to use two dimensional arrays.

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