Restoration will reduce the length of clumsy, stupefied, and enfeebled (and drained at higher ranks). Dispel magic will remove magical effects, and neutralise poison/remove disease/curse, and restore senses as their names imply. That covers most conditions.

Resting will reduce some conditions as well, like drained. You could play it that a rest also reduces things like clumsy/stupefied/enfeebled.

It could also be that this specific haunt is just missing a duration or other text indicating how to remove the condition.

Ultimately it’s up to the GM to adjudicate this if they feel like something is amiss or unfairly punishing.

According to the rules on conditions, they last until the duration ends, until they are removed, or the terms dictated in the condition to end it are fulfilled.

https://2e.aonprd.com/Rules.aspx?ID=774

The one exception I’m aware of is persistent damage, which generally ends after 1 minute if you are unable to succeed your DC15 flat check.

If the NPC is expected to see combat, you can use the Archives of Nethys NPC database as a starting point or you can use the Monster creation rules to start from scratch.

For certain things, like recalling knowledge where a critical failure leads to false information, secret checks I feel are necessary. I usually try to make it so that the false knowledge isn’t detrimental and they can usually figure it out after the first time. Things like stealth, perception, and social skills are important for players not to know the result. Partly, it prevents meta gaming, but mostly it keeps things moving smoothly. Using a VTT makes it trivial and I usually let the players roll the check, with me rolling on rare occasions for when the players should be looking for something, but don’t explicitly say they are.

I think they meant for it to cover more than just feats. For instance, maybe you have an item you activate that increases your damage die size or you’re under the effects of a spell. It would be too verbose for them to enumerate everything. They could have instead stated “effect” or “anything” if they intended it to cover traits. There is also this from the definition of trait (emphasis mine):

A trait is a keyword that conveys additional information about a rules element, such as a school of magic or rarity. Often, a trait indicates how other rules interact with an ability, creature, item, or another rules element that has that trait.

Trait specifically calls out ability as something separate from a trait.

I think this largely depends on whether you consider traits abilities or not. My interpretation would be that abilities are things like class features/feats, but traits are not, and would therefore not impact the ruffian’s sneak attack specifically.

The Augury spell has a DC 6 flat check to see if the spell produces a reading other than nothing.