I've got a player who plans on investigating the effects of Warp on various items, mainly through generous application of Enigma's Gift and extra-sensory magic. Are there any guidelines for Warp on spell traces, auras, active spell effects, or even thoughts?

Not sure if that's ever been covered. So it's probably up to you on the if and how that is going to work.

For inspiration there are rules in RoP:Magic on Elemental spirits forming from warping base matter. The is also some discusion in Transforming Mythic Europe on the effects of warping including warping things like buildings.

Or you may want to go the other route and say "Nope no effect". Or at least require specialized spells.

Regarding investigating Warp effect, you can use the guideline for detecting spell or magical effect. You would have to House Rule the equivalent of Warp effect vs magnitude of spell to have a scale for the detection spell, assuming that small warp effect are harder to detect than high level one.

You will also need to decide if the Warp happen once (Mom duration), then you need to probably need to factor in an additional magnitude to detect effect which happened in the past depending on how far it was in the past. Or you decide that once Warp takes effect, it becomes part of the item's nature and time has no effect on it. Then either an InVi or InForm(Vi) 10 Reveal Warps of the Mundane item (based on InCo10 Revealed Flaws of the Mortal Flesh) could be enough.

All in all, a whole range of spells might have to be invented: first to detect the Realm of the Warp source (I know it has different name of each Realm, but overall, it is similar), then what was the source of the warp (spell/effect/magnitude) and finally, how does the warp manifest in the item (what strange properties did it impart on the item).
It could lead to some new Mysteries, where magi are trying to harness the power of the warp: can they impact certains effects in item that hermetic magic cannot, simply by fuelling in a control manner warp into item ? Considering its rather random nature, you can decide if it could lead to the discovery of a new form that was discuss in other topics: Fortunato or Luck - it is not completely out of question since other traditions can affect Luck.

Or if you want to give a more darker tone, the mysteries of the Warp are tided to the Great Void, where Cthulhu-esque creature dwells, unless it is a more Moorcock vision, with Chaotic entities.

To sense that I would use one InCo guideline with Vim requisite (casting Mentem requisite to more information).

One of the breakthroughs the player is interested in developing is a way to 'direct' the effects of Warp on mundanes; so the flaws and virtues they pick up from an advanced Warp score will be known and potentially selected ahead of time.

I don't know if that would make sense. I mean, it's like burning. You can study how stuff burns, and how to burn things in certain, controlled ways, but that doesn't allow you to control how you're burned by random sources.

My take is that this player could develop a breakthrough that allows him to give people virtues and flaws through controlled warping, but nothing can be done about what you get from regular warping, at least not through this discovery.

Except that essentially all of the Gifted practitioners of any of the mystic arts 'burn' the same way. Hermetic magi go into Twilight, Viktar lose their Gift for a time when they receive Warp, Gruagarchs turn into trolls, etc. Every one has done something to their Essential Nature that changes how they respond to Warp. The breakthrough here would be applying this same principle to mundanes.

Hmm. I didn't consider that, you're right in that you might be able to alter the nature of a being enough that warping does something completely different to them.

Still, there's always a random component to warping, and it's not like each magic tradition chose how they respond to warping. It would be logical to assume that "warp-attunement" is a side-effect of the opening of the Gift, since it happens as soon as this is done.

It could be an inherent flaw in the initiation rituals of each tradition, or maybe even an unavoidable consequence: Opening the Hermetic Arts also "opens" the Twilight, and altering this "reaction" to warping would also alter the "reaction" to Hermetic Arts. Same goes for other traditions. Following this premise, it could even follow that mundanes can't even react to warping in certain ways because they don't possess the Gift. Maybe the only way to alter somebody so they suffer Twilight is, precisely, to initiate them into the Hermetic Arts, for example.

Or, going way further, maybe this could lead to the inverse path: Opening the Gift to a particular, controlled reaction to warping would also attune it to an entirely new way to harness the Gift.

RoP:M has a section on warped things ( animals, trees, stones, ect). Most of it covers warped animals but it would be a good place to look.

I remember the term "warping to a pattern". Maybe in relation to covenfolks warping in the same way, I don't know, but it's out there.

Searching for such a place could give useful insight: Why do covenfolks of covenant A are warped randomy by its aura, while those of covenant B gain feeble-minded?

Oh, and IIRC, there's Dankmar in GoTF (name escapes me) who magically enslaves his covenfolk... I'm not sure, it's been a long time, but they may be left brain-addled as a result. If true, insight too!
=> In that vein, I'd use lots of different spells on test subjects, to see if it affects the outcome.

There's also the fact that different realms warp mundanes differently, which may be interesting to such a mage.