Ah, but Muto cannot be made "one-off": it must be sustained, limiting the duration to Year (or to Moon without a Ritual) -- barring weird mysteries and "special" magics.
Sorry, I was being unclear. I agree with everything you said. It is the case, however, that when trying to mine, there is no place for the pile of rubble to go. So all you've really done is turn an area of solid rock into an area of really, really well compacted, fits-perfectly-together, rubble.
I further agree with you that you could construct a Re(Pe)Te spell that mines out chambers, and that it isn't quite craft magic. Which goes back to what I was originally trying to say: the result of craft magic is a thing, not an empty space, which is why a completely destructive spell is not craft magic.
I think what I'd need to know before going down this path is how the folks in the Medieval era understood rocks to work. I doubt that in the era of alchemists that it was believed that one could compress one sort of rock into another sort of rock, which would imply that it actually doesn't work that way in AM by RAW. Obviously, different sagas have different preferences as to how AM physics differ from our own. 
All true, but it is also true that I could use muto to turn a statue into mud. That mud wouldn't hold its shape and when the spell wears off, the former statue stays as a puddle of now-solid rock again. For the mining, I'd use the muto effect to make the rock a) easier for the rego effect to move and shape it; and b) to make it so when it 'sets' again it is harder than it was originally, having been squished by the rego effect. Obviously, how much of this extra strength is allowed depends on the SG. You might not allow any extra strength and even I think that some soft dirts still wouldn't hold their shape without proper props and supports, and that would be for the SG to adjudicate.
For what it's worth, I also agree with ndkid that magi couldn't use ReTe to change chalk into marble or any sedimentary rock into its equivalent metamorphic rock - this was unknown even as an idea then, and caused a lot of controversy even in the 19th century I believe. Plus the amount of rego needed would be extortionate (very high pressures = very high magnitude), Ignem (for heat) would be a requisite too. I wouldn't allow my Muto idea above to make this sort of change permanently - it would be an example of how an ongoing muto effect needs an ongoing spell duration, like Ezzelino said.
If you dig a hole, you get a pile of rubble nicely piled next to the hole, not in the hole.
So, first you dig the entrance to your tunnel with a couple of spells -- and you get a pile of rubble next to the entrance, which you dispose of e.g. by carting it off. Then, you dig further, and with each spell you get a pile of rubble in the entrance that does not fill it since the entrance was carved with multiple spells. You dispose of that e.g. by carting it off, ... and so on.
In your opinion and in your saga, of course. Others would disagree, or have other considerations/concerns that might be applicable. 8)
There are several possible "valid" interpretations, depending on what part of the rules one leans towards.
To expand on this explanation - Muto is "unnatural", and Hermetic Magic cannot make an unnatural change permanently (withou vis). Rego changes something from one natural state to another - and that's what some are proposing - but it would be a rather open-ended saga that allows that particular interpretation.
The understanding of the exact relationship and process between sedimentary and metamorphic rocks is quite modern, yes. A mage's view, however, is that one substance can always be transformed into another, but that would indeed be Muto rather than Rego, as it would indeed be "unnatural" to, for instance, turn mere coal into diamonds. 
("Craft magic" might fuse sand into glass, but I can think of no other "craft" that would compact one rock into a (noticeably) denser form.)
Yes exactly, base craft magic gives you one man-day of work in an instant for each casting. No tools or knowledge required on the part of the caster. Just a finesse roll. Miners don't leave the rubble in the hole when they dig it, they sort it, pile up and haul it away. Mind you if it's just a touch spell I would say the rubble can't go very far.
For me adding a perdo requisite to such a spell means it's still craft magic. Just that you have the added bonus of need to clean up. Giving you magically skilled labor with the bonus of a little destruction. A Pe(Re)Te could give you perfectly carved holes, straight sides, even shapes, exact measurements, but you wouldn't get a mine dug as a miner would dig it. Such a spell to me equals destruction with some added control.
(There is a spell suggested in Covenants (p 96) that uses this approach - turns an animal into its "base components" - a pile of meat, the skeleton, the skin, etc - and destroys the contents of the stomach/gut.
That is listed as a PeAn spell w/ a Rego req, but it's important to remember that what determines the base Arts vs. the Requisite Arts are the Guidelines - the highest magnitude to achieve the effects is the base, the lower are the Req's, and "Kill an animal" is Base 30. If you started with a dead animal, it would possibly* be a Re(Pe)An instead and have the same end effect.)
(* Don't know, don't care - not relevant to this discussion.)
OTOH, it was known that all three types of rock plus seashells turn into quicklime when burned. And quicklime + water -> slaked lime + time to cure -> lime.
And magi have all sorts of experiments open to them for the cost of a few sponts - eg. Rock to Viscid Clay what happens if you fire the clay (or craft spell equivalent) before the spell expires when it does? what happens when you Muto 2 different materials into mixable liquids, mix them then let the spells wear off? What happens when you subject materials to temperatures and pressures that RL scientist won't be achieving for 800 years? Aristotle never asked the question let alone gave a hypothesis so should we assume the RL answer holds?
It is much easier to make up results for experimentation into magic which is a pure game construct than results for experimentation into a mostly naturalistic but nonetheless other gameworld. And it is the sort of thing that's very logical to make an interest of a PC magus - they are trained in experimental techniques, they respect pushing the boundaries of knowledge and they have a game mechanical use for philosophiae which includes natural philosophy. (Plus it's totally something I'd be doing if I had Hermetic Magic so I'm constantly tempted to have my characters do it.)
Never looked at it this way. Sounds perfectly fine to me. If magi were not already grossly over the top in power level this would have the potential to break the setting real fast. Still it might require someone to start the experimental trend 
Cheers,
Xavi
PSB_ together (quite appropiately talking about mixing substances and its consequences)
Sorry the idea was meant to include a bit more than just what i wrote(had it used in play), definetly a Re requisite, IIRC we didnt make it require an In requisite but i dont remember why.
Though i think we used a spell based on Muto instead, making all the parts of stone into liquids with different densities, ergo like modern refining of oil and other stuff, this allowing you to "harvest" all component parts of the stone you mine.
Ok, so we were crosstalking then. NP, i quite agree.
Because using magic, they can mine anyplace where whatever they want EXIST at all, magic can bring out the specific material relatively easy, there is no need for the material to be common enough as it would be for a mundane miner. A mundane mine needs to follow the best veins of ore to get enough material compared to the work needed(although rare exceptions exists, where someone is desperate enough for the material to heavily subsidise a poor mine). Magi intent on mining can make a few items for miners to use, relatively easily they can then do the mining silly much faster than a mundane miner could, meaning that they dont need to bother with following veins, they can still mine so much so fast that even if the gold, silver or whatever is just 1/1000 as much as would be needed for a regular mine, they will still make a similar profit without difficulty.
Ah, darned, i missed that... You´re absolutely correct though that mining was most certainly not unheard of or even uncommon.
First known mining operations are several thousand years before the regular game era.
Yeah, but as a requisite to a REGO spell, to achieve something permanent by temporarily using Muto together with Rego... Ie. the Muto part just acts as a temporary catalyst effect while the Rego effect is what makes the final effect permanent.
Why does rego need the help. Rego transforms it's target from one natural state into another natural state with out needing any intermediary stages. So craft magic takes raw material and transforms it into finished product instantly. It doesn't need to "do the work" except as a cosmetic effect.
Pile of wool (poof) blanket
Iron (poof) chainshirt
Lumber (poof) chair
The only advantage I could image is to change the raw material into a different substance, then use Rego Craft on that, and then allow it to return to the original - thus creating a highly unusual/unnatural end-product by using Rego Craft magic that could not normally be "crafted".
So, if you wanted to create a series of lacework glass balls within each other, you could turn a block of glass into soft stone, "carve" that using ReTe, and then allow it to change back to glass. (Probably some more powerful/impressive applications, but that jumped to mind.)
If you want to craft with magic, there's no point: just ReTe and be done with it. But here's a good example: You muto hardstone into clay, then let your crafter work it, then let it harden again. That'd prolly boost their productivity by a lot.
If you believe there is a "3-d glass carving" craft*, of course not, and then have fun with an Ease Factor in the 20's. Otherwise, that is the point, to get the material to where there is a craft for it.
Rego doesn't just "do stuff", nor does Rego Craft magic - it rearranges as a craftsman could.
Let's try a more extreme example. Let's say you wanted, for some reason, to "weave" 3 gems together into a braided finger ring - no craft to do that, so Rego is out. But Muto those 3 gems into clay for Diameter, and not only is it possible, but the Ease Factor to braid "clay" drops to single digits.
Even short of such extremes, Muto'ing one substance into another, one more friendly to a craft and the final product, could drop the EF to where it's not a bad bet.
As I said, other (more impressive?) applications will come to those interested in pursuing this line of thought.
(* "glass carving" was used for cameos and such, not 3-d balls within balls the way that ivory can be carved.)
Nice. I'm aware of examples like those, but nothing like what was achieved with "glass carving" at the height of the Roman era existed during the early middle ages afaik.
Regardless, the Ease Factor to carve glass at that level vs. to carve "soft stone" at that level would be significantly different.
This assumption of hauling as part of craft magic does bother me. My memory of Covenants is that the waste material is right beside the finished product; given that what we're really talking about here is everything being waste material, it's difficult for me to envision how it's going to become a small pile beside the finished product without simply moving the blockage of the cavern back slightly. I could see a second spell casting to teleport the pile of now-rubbled stone to the AC the magus has, but I think trying to get a non-trivial teleport out of a craft magic cast is a bit much. To me, following that train of logic implies that if a man can carry me on his back, say, 10 miles in a day, I should be able to teleport 10 miles with a Craft spell.
In summary: Craft magic can't move the object/waste; the ability to have them pile up nicely where the spell is cast is cosmetic; trying to have useful movement factored into the crafting spell would not be allowed in my saga, and would have to either be a second spell or a much harder "craft and teleport" spell, making it far less useful than a Pe(Re)Te or Re(Pe)Te spell.
For my saga, at least, I feel that way leads to madness. If someone wants to have fun playing with anachronistic technology in an AM setting, I'm sure that could be fun, but I think it doesn't blend well with more standard AM stories. YMMV, of course. I do not believe there is a RAW position on what "the truth" is on questions that the ancient philosophers did not touch.