First off a nod to nicolaiplum (giggle outhouse) and blankinthefill (giggle hollow-core) for great advice. However I feel compelled to give you a bit more detail. Second, congrats on living the dream :-)

Comfort:
The first and foremost piece of the comfort puzzle will be the air (temperature, humidity, air-quality, etc.). Basically you will want to make sure that your 12x20 office doesn't become a 12x20 coffin or swamp or oven.

Given the small internal volume you may want to consider an air-exchanger (google it) to move outside air inside without dramatically heating or cooling the interior (saves money, and you don't suffocate or suffer from ozone created by electronics). It may be a good idea to throw a filter on this system as well, to lower airborne particulates.

If you live where humidity is a thing, you may want to look into a dehumidifier (opposite tech if it is Manitoba in the winter or Arizona anytime, but be careful! You will want to have it controlled by some sort of a humidity meter as to not mess up your gear while protecting your sinuses).

You will also need some method of heating and/or cooling depending on your climate (90% sure this is going to be electric given that it is an out-building), so maybe look into "mini-split" systems as they are typically the most efficient (if the budget allows). Otherwise it will be important figure if you are in a heating or cooling zone, and how far into that definition you are.

Then we come to insulation. Insulation in the floor and ceiling are the most important. If you are having this built for you, you will likely end up with a "sealed envelope". This means that the air exchanger is a good idea, so you don't have to leave a window open. Insulation wise you can satisfy the tinfoil hat guys with a foil-foam-foil type insulation for cheap in the walls (it will need to be installed with an air gap on both side FYI). In the ceiling, go for max R-Value. Don't forget to insulate the floor if your winters are below freezing for more than a month.

Speaking of flooring... Carpet is typically the most comfortable as it provides some insulation as well as cushion, but is harder to maintain in an out-building (especially with the mud you mentioned). However, you can get a 2 for 1 with a hardfloor option (Pergo, Marmoleum, Tile, whatever) if you install radiant heating (cold floors in the summer don't suck). That also means no rolling pad

Lighting should be “warm” (2700k-ish) regardless of bulb type, but LEDs last the longest obviously. Go for at least 3 separate light sources including a desk lamp to give the most comfort. Given you are in software, I recommend at least one source of indirect lighting, putting lighting on a dimmer.

Lastly, although views are nice, you need to ask what motivates you personally. If you are a view guy (I am), then make sure you place the window so that it looks onto something awesome 365 year. Don't worry about glare, as you can always go low tech and tape a piece of cardboard or paper on the part of the window responsible. Or go high tech and install dimming windows. Or in-between and use horizontal blinds (which can come in insulated varieties BTW, help with the
Security:
Security is all about getting a human enough time to intervene with a proverbial shotgun, whether physical or digital. Otherwise it is a "deterrent", like not leaving your Rolex on the dash of your car, or having a firewall.

Door-wise go for insulated steel on a steel frame. Locks were already covered by “blankinthefill”. Make sure the hinges aren’t accessible from the outside, and that you have at least one burly dead-bolt. This implies that door swings in not out FYI. This is enough to frustrate your average tweaker. However a truly determined individual will just take a chainsaw to the wall. Don’t worry about “doubling up studs”, and just sheet it in plywood before the decorative siding. Or for a budget option, just use T1-11. Unless there is some unknown reason to make it literally bomb proof?

If you just want a ventilation window you can put it at least 6 above grade to require a ladder for intrusion, and/or use security glass. Alarm systems are only work if you are a) home, and b) willing to do something about it. This is because LEO response times are typically too long to do much but catch the laziest, or file a report ASAP.

If you are really worried about breaking and entering, you can always install some decorative bars on said window.

Remember, you are not building Fort Knox. That being said, it is a good idea for the end of your trenching to be under the building, so there are no obvious wires externally.

If you fear industrial espionage, then there are some additional steps. However, given that tweakers and script kiddies only pray on the slow and unwary, this should be sufficient. Unless they personally observe you schlepping high-value items into your fortress of solitude.

Good luck!

Does dropping trou for an intelligence agency (foreign or domestic) count as a "breach"? Or is that just "business as usual"?

I would like to call your attention to the following quote from a WP article from November 24, 2009 speaking to their decision to shutdown all of their national offices: "...Brauchli, a former foreign correspondent for the Wall Street Journal, acknowledged that "unquestionably there are advantages to having someone on the ground at times." But, he said, "We are not a national news organization of record serving a general audience. Nor are we a wire service or cable channel." Maintaining that The Post's strength is to report issues through a "Washington prism," Brauchli cited recent examples of education and economic reporters filing major dispatches from other cities to illustrate national trends..." (Original article: http://www.washingtonpost.com/wp-dyn/content/article/2009/11/24/AR2009112403014.html ) I believe the telling bit is the "Washington Prism", or mouth piece of the very regimes which are being called out in the leaked information. In that light this comes as no surprise. Also the author is a "fellow" of AEI. To quote wikipedia "Some AEI scholars are considered to be some of the leading architects of the second Bush administration's public policy."

I would like to call your attention to the following quote from a WP article from November 24, 2009 speaking to their decision to shutdown all of their national offices: "...Brauchli, a former foreign correspondent for the Wall Street Journal, acknowledged that "unquestionably there are advantages to having someone on the ground at times." But, he said, "We are not a national news organization of record serving a general audience. Nor are we a wire service or cable channel." Maintaining that The Post's strength is to report issues through a "Washington prism," Brauchli cited recent examples of education and economic reporters filing major dispatches from other cities to illustrate national trends..." (Original article: http://www.washingtonpost.com/wp-dyn/content/article/2009/11/24/AR2009112403014.html ) I believe the telling bit is the "Washington Prism", or mouth piece of the very regimes which are being called out in the leaked information. In that light this comes as no surprise.

I would so mod you up if I had points right now! :)

Yeah, you didn't read the article.... So to spell it out. Bacteria lives on seaweed (and is able to eat it directly, and get energy from it). Japanese eats the seaweed, and thus the bacteria. The bacteria in the intestines swap notes with their cousins. Now part of the population in the intestine can do the digesting the seaweed trick. We have bacteria in and on our bodies. This bacteria outnumbers the cells we call "us". Most of this bacteria actually does a job, such as reducing inflammation around broken skin, or helping you digest your food. In the article, they were talking about gene transfer between bacteria living on the seaweed, and bacteria now found to be living in the intestines of some Japanese. Furthermore, current research suggests that humans "inherit" their population of intestinal flora from their mothers. So nowhere did anyone talk about phages, or any other virus. Accept you. I am saddened that a sufficient volume of accurate information, completely off topic, is "insightful".