I don't often recommend glyphosate but onion weed would be one of the exceptions. It's generally either a case of digging them out including their bulbs or poisoning them. Giving that it's notoriously hard to dig them out without leaving bulbs behind that easily break off, I'd recommend a poison. You'll certainly never be able to remove onion weed by hand in a garden bed that has stones, as when you pull the weed it will leave bulbs behind.
To keep the use of poison to a minimum I would recommend using Yates 250mL Zero Triple Strike Garden Weedkiller Concentrate and applying it with a Yates Zero Weeding Herbicide Applicator Brush. This type of applicator is great, especially around other plants. It allows you to brush the product onto the onion weed without touching the surrounding plants. - MitchellMc
Onion weed isn't a big problem in most lawns. If it's popping up it's just a sign that your lawn needs some love. If you try pulling it up you'll probably just make the problem worse as you'll spread the bulbs. Best way is to just ensure your lawn is healthy and growing fast. It will soon outgrow and dominate the onion weed. You could try things like boiling water or glyphosate but they will obviously also kill your grass. Regular feeding is important. - greygardener
Onion Weed is a nightmare. We had it in our garden when we were in our old house. I tried everything from glyphosate painted on and diesel painted on and it would go yellow BUT still keep growing! It was dreadful. The only way to remove it properly is to dig out by hand. You MUST make sure you also remove the bulbs as they break, drop onto the ground and start growing again. Remove them and put them in a plastic bag, then put in the bin. Do not throw them in your compost. - mich1972
The only way to control onion weed is to try and kill it in situ. Glyphosate will do the job but it will be more than a one time thing. It'll be a pain but you need to stop the food supply in the next season. So - kill the foliage, it will shoot again and then kill it again. Using a weed wand or a paint brush will allow you to plant around it. Never ever use diesel - it will stay in the soil forever. - robchin
I'm not a plant expert by any means but I have the same problem and I am currently trying weed mat and I cut out holes for my main plants to grow through. If it works for strawberry farmers it should work for my ornamental plants. But in your case I would take out the pebbles then cut holes for your main plants then lay the weed mat down and then cover up with the pebbles again. Hopefully the onion grass will not be smart enough to travel to the open parts of the weed mat. - redracer01