In a heavy 4- to 5-quart pot, warm oil over medium-low heat. Add shallots and cook, stirring often, until soft, about 4 minutes. Add mustard seeds, red pepper flakes, salt and pepper; cook, stirring, for 1 minute.
Stir in remaining ingredients except raisins. Raise heat to medium-high; bring to a boil. Lower heat and simmer, stirring occasionally, until most liquid has evaporated, 45 to 50 minutes. Remove from heat. Stir in raisins; let cool. Divide among 6 clean and dry 1 1/4-cup-capacity jars with lids. Keep refrigerated.