As per the cliché, after getting hit by a truck, our protagonist finds herself in a 'swords and sorcery' fantasy world. Also as per the cliché, she is granted an overpowered ability to make her new life easier. In this case she gains the ability to summon/create anything she can imagine as long as she has a reasonable (layman's) grasp on how the thing works.
Unfortunately, the world is on the verge of being overrun by the vile, undead minions of a group of necromancers. Having witnessed for herself exactly what kind of atrocities the necromancers are committing against the living (with suffering and death being powerful fuel for their foul magic) she vows to remove the taint of their existence from the world. Fortunately she has played plenty of shooters and RTS games to have some idea of the weapons she can use against them. However, those are designed to work against living, human targets.

Available tech

The world is a fairly generic medieval fantasy world. The enemy skeletons are limited in armor and weapons to medieval level. I'm thinking of equiping the skeletons with sword and/or longbow and wearing up to full plate armor.

The protagonist has access to modern day knowledge of weapons and tactics. This includes weapons and tools that could semi-realistically be built with modern technology even if in practice the expense/complexity would be unfeasible. For example, remotely/AI controlled tanks and machine guns, and maybe even a version of the 'rods of god'. (If I find a way to justify summoning something not just in orbital position but having orbital velocity as well.)

The enemy

Skeletons are animated dead. They are not so much dead bodies given life again as they are a conveniently arranged collection of bones whose parts are enchanted with magic to make them move again. Even if a skeleton is damaged, any separated parts will continue to move and act on their own. For example, a disembodied arm will use its hand to crawl along the floor and grab at opponents' legs. As long as any part is still able to move it will continue to try to harm the living in any way possible. A 'complete' skeleton will fight with any weapons it can find while any 'spare parts' will bite, scratch, grab and kick as able.

This unfortunately means that it is not enough to simply remove the head or destroy the brain. Also unfortunately, the undead remain animated even if the necromancer that raised them is killed. The sheer malice of the magic giving them life ensures they only stop when fully destroyed or rendered immobile.

The question

What sort of modern weapons could the protagonist use against skeletons, if the goal is to destroy them as completely as possible? How would you destroy large groups in the open? What about enemies occupying a town when you want to keep the buildings and any innocents in one piece? What about clearing them out of a building without demolishing it?

Note that the skeleton enemies will be actively fighting back and they will number in the dozens to hundreds. Being in melee range of them is generally a bad idea, so unless the melee weapon is particularly effective a ranged approach is probably prefered, though ammunition is a potential concern. Note that the engagement is one against many, not army vs army.

Below are my own initial ideas.

Melee weapons
Bludgeoning weapons seem the most effective option, though I wonder how much physical strength would be nescessary to break enough bones to take out an undead. The use of a powered exoskeleton (i.e. power armor) could mitigate some of the danger, but engaging in melee still seems like a bad idea.

Small arms
Pistols and rifles of sufficient power will break bones - if they hit and don't simply pass through the gaps in the skeleton or glance off a bone. After the torso or spine is destroyed, hitting individual limbs would be a lot harder too. Either a form of saturation fire or expert reflexes and accuracy would be needed.

Explosives
If my understanding of explosives is correct, it's the pressure of the shockwave that kill the target through internal trauma. That means that at the very least, performance against skeletons is (much?) worse than against living humans.

Kinetic bombardment
Useful against massed concentrations of undead. Basically, drop a mass of rocks on the enemy from as high as possible. Either artillery or aircraft drop something like the Lazy Dog bomb on the enemy. Though, like bullets, a lot of them would need to be dropped to ensure complete destruction of the target.

Acids
Throwing an acid or similar onto a skeleton might be easier than filling its entire space with bullets. Chlorine trifluoride comes to mind, which reacts violenty with pretty much with anything, though this would probably not be safe for the user.

Use immobilizing foam to neutralize the skeletons and then the villagers can go in with hammers or similar and finish them off. This will be therapeutic for the villagers in that they feel they are getting to fight back and will ensure total destruction of the skeletons.

To be sure once the skeletons are smashed up with hammers they should be swept up and burnt, ground in mills, or otherwise permanently neutralized.

How would you destroy large groups in the open?

The Soviet RDS-220 hydrogen bomb, known by Western nations as Tsar Bomba, was the most powerful nuclear weapon ever created (...), it also remains the most powerful explosive ever detonated.

This works best if blown up from a few kilometers above ground. Maybe summon it already up.

What about enemies occupying a town when you want to keep the buildings and any innocents in one piece?

You can't save everyone, you'll always have casualties.

Other than that: use a net launcher to snare them:

... Then drones to drag them into open fields, then:

What about clearing them out of a building without demolishing it?

Once again:

1-)

2-) Drag them to the open fields

3-)

4-) ???

5-) Profit!!!!

We here, in the Department of Skeletal Removement use pitchforks (and showels) and wood chippers.

You simply load preferred amount of skeletons on your pitchfork like in the instructional picture below

And then load them into wood chippers.

For the extra sureness of bone removementss you can sprinkle them with phosphorus or fluoride

Always follow the safety rules and wear face mask. We don't want to inhale the bone flour. It itch in the throat for days.

For large scale destruction using bombs would be effective but it wouldn't completely destroy any skeletons they hit so i would suggest attempting to capture them and then either powder-rising them with a car compactor, something of that ilk or chucking them into an incinerator therefor completely destroying them which is what you want to do. for smaller spaces like a town... create a small ramming device that can be held that transmits a force into a target it is in contact with pulverising it. other than that, high velocity spinning blades that pulverise anything they touch, or just break it it don't mater, the objective is to destroy not injure until dead like a human.