The principle of "least privilege" is a valuable practice. Far too many people just put "sudo" in front of everything when they're using *nix - particularly on the Raspberry Pi, which is often thought of as a sort of throw-away computer.
Fortunately, the Raspberry Pi folks were thinking ahead a bit and created the "gpio" group and rules in devd to set the ownership of the GPIO nodes in /sys so that you don't have to be root to use them - you just have to belong to the correct group.
There is one "gotcha" to this, however. To understand it, we need to look at how GPIO functions on the Raspberry Pi.
In /sys, there is a GPIO class - that is, a directory - at /sys/class/gpio (that's not actually where it is, but there's a symlink there, so for our purposes, we'll just say it's there). Inside that directory, there are two nodes "export" and "unexport". To take control of a GPIO pin, you open "export" and write the pin number there. When you do, a new directory will show up named "/sys/class/gpio/gpioX/" where X is the GPIO number. Inside that directory will appear a bunch of nodes that will allow you to take control of the pin.
The gotcha, however, is that the kernel driver doesn't know anything about the "gpio" group. It sets the ownership of all GPIO nodes to "root:root" and "rw-r--r--" (0644). devd comes along at some time after the nodes are created and resets the permissions so that the nodes are writable by the gpio group. Normally this isn't a big deal because most of the nodes in /sys are created when the driver is probed, usually at boot. But in this case, avrdude attempts to export the GPIO pins, and then immediately set their direction. If it does so too quickly, it will get EACCESS attempting to open /sys/class/gpio/gpioX/direction.
People have so far worked around this by simply running avrdude as root - either by prefacing it with "sudo" every time or by making the binary suid as root. These are bad ideas. If for no other reason, if you ask avrdude to read from the chip and write to a new file, that file will be owned by root, rather than by the user running avrdude.
One quick and dirty solution to the problem is to introduce a short delay between the export operation and the rest of the initialization. But more to the point, the delay must also yield the CPU so that devd gets a chance to run. To that effect, my patch just uses "sleep(1)". It's probably too long a delay, but it works consistently.
Another way to go is to remove the export and unexport operations from avrdude and instead leave the pins permanently exported, exporting them from some sort of script possibly run at boot. This is safe to do, since the linuxgpio driver in avrdude is careful to set all the pins as input before exiting, which will return them to high impedance state. I haven't implemented this change, but it would allow avrdude to run faster since there would not be a 1 second delay every time.
To proceed, download AVRDUDE 6.1 and apply this patch. Then build as usual. Having done so, you can now either make avrdude sgid and set its group to gpio, or - probably better - add yourself to the gpio group. No more sudo!