Looks like your bike was equipped with puncture resistant Kenda tires. If you do encounter an unusual number of punctures you might consider puncture resistant tubes filled with liquid sealant. But wait and see unless you can't afford any late days. I don't mind the extra weight so I like the liquid sealant filled tubes.

For a mini-pump, I'd suggest one with at least a short extension hose and threaded head. Much easier to handle than most pumps with direct connections and friction clamp lock heads. I like the Topeak Race Rocket HP, even though it isn't ideally suited to my 700x40 tires. It needs more strokes than a larger volume or longer tube, but each stroke is easy and I can get it up to 40-50 psi relatively easily, enough to get to my destination and later top off with my floor pump to the usual 60-75 psi. If you can safely leave the pump on the bike, a longer tube or larger pump will be better. But I usually take my pump with me for errands, and the little Topeak fits into my pocket or the camera waist pack that doubles as my handlebar bag.

Besides front and rear LEDs, I also carry flexible reflective arm/leg bands, yellow and orange/red. They cost only a buck a pair at the nearby dollar store, but you can buy 'em online. During the day I wrap the bands around my bike frame tubes and seat tube, and another around the rear rack. If I expect to ride after dark or very early morning I snap 'em around my ankles and maybe the left arm. They're very handy, quick and easy to use. Just pop the spring loaded strip and it conforms to most ankles and forearms, unless you're built like Fred Flintstone.

Snacks for a quick energy boost, especially if you occasionally experience low blood sugar in the morning without a proper breakfast (I do). I like bananas and chocolate. Breakfast of champions, along with coffee.

I usually tote a minimal first aid kit in a quart size ziplock baggie, containing a couple of small clotting pads, bandaids, disinfectant/analgesic ointment, gauze pads, paper or cloth bandage tape, a couple of ibuprofen and benadryl for emergency allergic reactions (useful if you're vulnerable to insect stings, but don't need an EpiPen), my asthma inhaler (which I need almost every ride). Sometimes I'll take a more complete kit on longer rides.

Commuting clothing... depends on your area, whether you can shower and change at work, whether you can store clothes at work or must carry them with you:

• I used to carry a lightweight yellow rain parka, one that could roll up into a sandwich sized baggie. Not great for regular use, but good in a pinch if caught in the rain.
• Years ago when I cycle commuted I'd change at work into uniform or hospital scrubs, and rode wearing merino wool jerseys and cycling shorts. Often I had time to shower at work too. Nowadays I'd probably consider a lightweight wicking layer undershirt, in case I didn't have time to change clothes. I was skeptical about those fancypants expensive wicking baselayers, but after a few rides with a Pearl Izumi undershirt, I can see why some riders like them despite the cost. Very comfy, not nearly as clammy as cotton t-shirts. After a long Saturday ride, wearing a Shimano Storm Jacket in 45 degree temp, my open weave cotton sweater was soaked, but the Pearl Izumi undershirt was nearly dry.

If rain or puddles from watering are a problem you might want fenders. But I've been surprised by how much my rear rack traps, and the fat aluminum down tube on the bike frame blocks some water kicked up by the front tire. However I've ridden in rain only a couple of times the past few months.