I really enjoyed having a peek into your garden.. ;D Those 'containers' are good..fair size planters for many different crops...and don't hurry with getting rid of the rocks..you could used them when you re-build something..part of the wall or raise beds or..I'm sure they will come handy.
As for the 'weeds'..it was quite hard to really see what they are as the pic wasn't that close up and your hand bit shaky..if you can take photo and post that, I'm sure we can tell what you are dealing with.
Af for pruning the little apple trees amongst the 'to-be-cleared-waste'...well..they looked quite new additions to me and I would not rush to prune those now. Yes, it is good time to prune if you want to reduce, restore or remove some dead or unwanted growth..but with young trees you will be better of with summer pruning, and by just reducing the lenght of the new whippy growth. If you prune in winter, you just incourage more whippy growth.
"winter prune for new growth and summer prune to get fruiting spurs".. ;)
Was those trees at the bottom of your garden fruit trees too?