Maybe not everyone maintains their bike as "thoroughly" as some of the previous posters would do.
Its fine, enjoy your bike.
I run 7 bike and I don't want to stay on top of all their needs 24/7. I gave up repairing flats years ago. I just fit new tubes.
2 year old chain best in the bin. Chains don't stretch, they wear out.
Change the chain as a start its obviously worn by your description. Inspect the teeth on the cogs front and rear. If they are nice and square in shape then great. If they are pointed like teeth then you need to think about replacements.
You don't need new front and rear cogs when you change a chain. Just replace what's worn. Probably just the chain. Try just changing the chain and giving it sometime to bed in.
Yes, bolts rust sometimes, its not your fault. Bromptons do rust in lots of areas regardless of good maintenance. Get new bolts if they don't clean up.
Maybe think about using a wax product to keep frame cleaner for longer?