Sprouts above foot are elm sprouts. Speaking of hurting the tree you have already buried part of its root crown with cobbles (and soil?).

it is said.. a tree is twice as big below ground.. as you see above ... in a pancake shape form ... so removing a LITTLE roots isnt a big deal .. short of using a bulldozer or some such ...

heck.. the roots you see could be from the same size tree a house or two down .. lol ...

removing the roots you see.. will cause the tree to replace those roots with new feeder roots.. and a few year down the line.. you may have more roots than when you started ... you might be better off.. just leaving them..and planting around them ... and only removing some.. when you see the growth indicating the plant you dont want ...

the root flare of a tree should be above ground ...like you see in these pix: https://duckduckgo.com/?t=ffcm&q=root+flare&iax=images&ia=images

the trunk of a tree is supposed to be dry above the soil line .. not underground ...

but i am not sure some rocks.. compared to soil.. will make much difference ... small rocks with complete drainage.. so the tree stays dry ... presuming you didnt put landscape fabric under such ..

id be curious to see the whole front of the house..and how the bed works.. looks like a pretty cool concept .. that is.. if you want to brag a bit .... the walkway is what caught my eye ...

ken

Ken, here are some other pics