Thoroughly wash the limes, then slice them thinly or into wedges, including the peel.
Select a clean mason jar and place the lime slices inside.
In a saucepan, bring to a boil the water, vinegar, honey, brown sugar, salt, cinnamon stick, cloves, bay leaves, black peppercorns, mustard seeds, and chili flakes.
Once the pickling liquid comes to a boil, let it cool slightly so it's not too hot when poured over the limes. You want it warm, not scalding.
Pour the warm pickling liquid over the limes, making sure they are completely submerged.
Seal the jar and refrigerate for at least 24 hours. The longer they sit, the more flavorful they will become.
Before serving, let the jar sit at room temperature for 10 minutes to allow the flavors to fully develop.
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