Put the sliced tomatoes in the stoneware crock, sprinkling each layer with salt. Let stand overnight and drain off the juice. Chop the tomatoes roughly. Add to the heavy-bottomed saucepan along with the onions, mustard, pepper, ginger, allspice, red pepper flakes, and brown sugar. Pour the vinegar over all, bring to a simmer and cook very gently for 1½ hours.
Sterilize the jars, their lids, and rings by boiling for 10 minutes. Dry the jars by draining them. Do not use a cloth to dry. While the jars are hot, pack the relish in them and cover with lids and rings. Process 10 minutes in boiling water in an open kettle canner. Store about 4 weeks in a cool, dark place before using.