Extract From: "THE GUILD OF AMERICAN LUTHIERS data sheet #45"
Tuning the 1st and 6th strings: The E, open 1st string, must be in pure unison with the harmonic of the E, 6th string at the fifth fret. When these two strings have been properly tuned with each other, continue as follows. Tuning the 4th string: Play a harmonic on the (in tune) 6th string at twelve, and as this harmonic sounds, adjust the 4th string until the tone E on the second fret is in pure unison. Now you have the E, open 1st string, 1st on the 4th string at two, and E, open 6th string tuned pure (permissible because they are octaves).
Tuning the 2nd string: Play a harmonic on the (in tune) 4th string at twelve. As this sounds, adjust the 2nd string until D at the third fret is in pure unison. As you have used two fretted tones for references and as the frets are positioned for tempered intervals, you now have the open 1st, 2nd 4th and 6th strings in tempered tuning.
Tuning the 3rd string: As it is easier to adjust a string while listening to a continuous reference tone, you may first try the following: Play a harmonic on the (in tune) 4th string at twelve and as this sounds, adjust the 3rd string until D at the 7th fret is in pure unison.
Double check: Now make this check to see if you have been accurate or if the instrument plays tune when fretted at seven. Play a harmonic on the (now tuned) G string at twelve, and as this tone sounds, play G on the 1st string at three. The two tones should be in pure unison. If they are not, either you are at fault or the instrument doesn't fret tune at seven. Go back to the beginning and carefully check each step up to this point. If the tones are still faulty, then readjust the 3rd string until the harmonic at twelve is in unison with the 1st at three. Do not tamper with the 1st and 4th strings because it is the 3rd string you are trying to bring in tune. When you have the 1st, 6th, 4th, 2nd and 3rd strings in tune, in that order, continue with the remaining 5th string.
Tuning the 5th string: Play the tone A on the (in tune) 3rd string, at the second fret. Listen to this pitch carefully and now adjust the 5th string until the harmonic at twelve is in pure unison. When the foregoing steps are followed correctly, the strings will be tuned perfectly to equal temperament. No further tuning adjustments are permissible.
The complete document can be found here.