Changing lighting situations would be hard to deal with when shooting totally in manual mode. If you set the exposure for bright conditions, you need to reset it for cloudy situations, but only practice and experience will give you the right settings for those situations. In this particular case, you needed to let more light into the camera for a brighter picture and that could have been done a number of ways. You could have increased your ISO and made the sensor more sensitive to the light which would have given you a brighten image at the cost of increasing noise to the picture, not the best option considering your alternatives. Another option to increase the light in this situation would be to use a slower shutter speed to allow more time for the light to reach the sensor. Slower shutter speeds run the risk of introducing motion blur so that's not the best option either. Another way to let more light into the camera for brighter pictures is by opening the aperture, which would be my first choice for a brighter picture in this particular case. By opening your aperture from F8 to F7.1 or F6.3, you would be letting in more light and producing brighter pictures.
I have to admit that I don't really know how a manual lens works. I always assumed that a manual lens needed to be focused manually and have the aperture physically adjusted, but does a manual lens let the camera do any metering for you? Does the camera still indicate where the exposure should be before you take the pictures? Is there a sliding scale in the bottom of the viewfinder that moves from one side to the other when you look up at a bright sky and then down to a dark shadowed area? If the camera does meter the shot, try setting your exposure so the metering is more to the right of center which will give you brighter pictures in those situations. Another option if the camera does do the metering, is like Fraser suggested and that is to put the camera on aperture or shutter priority, set your metering mode to centerweighted and let the camera set the exposure with you making fine adjustments with the exposure compensation button. If the camera doesn't do any metering, well that would make things a little tougher on you and experience will probably be your best teacher. There is a formula used for calculating the right exposure without the aid of any light metering devices called the "Sunny 16 rule" which might be helpful to check out on google, but having your camera help with the light metering would be the easiest solution if that's even possible with a manual lens.
As for the picture you posted, don't be so disappointed with the results. Post processing can easily brighten this image. Most any photo processing software should allow brightening in one way or another. I use Picasa's free software most of the time because it's simple and user friendly but any photo editing software should allow for simple lightening or darkening. I used Picasa here to add some fill light to your picture just by moving a slider to the halfway point, probably a little too much lightening but I wanted to show what can be done with some minor adjustments in post production.