  We present the results of extensive multi-waveband monitoring of the blazar
3C~279 between 1996 and 2007 at X-ray energies (2-10 keV), optical R band, and
14.5 GHz, as well as imaging with the Very Long Baseline Array (VLBA) at 43
GHz. In all bands the power spectral density corresponds to "red noise" that
can be fit by a single power law over the sampled time scales. Variations in
flux at all three wavebands are significantly correlated. The time delay
between high and low frequency bands changes substantially on time scales of
years. A major multi-frequency flare in 2001 coincided with a swing of the jet
toward a more southerly direction, and in general the X-ray flux is modulated
by changes in the position angle of the jet near the core. The flux density in
the core at 43 GHz--increases in which indicate the appearance of new
superluminal knots--is significantly correlated with the X-ray flux.
  We decompose the X-ray and optical light curves into individual flares,
finding that X-ray leads optical variations (XO) in 6 flares, the reverse
occurs in 3 flares (OX), and there is essentially zero lag in 4 flares. Upon
comparing theoretical expectations with the data, we conclude that (1) XO
flares can be explained by gradual acceleration of radiating electrons to the
highest energies; (2) OX flares can result from either light-travel delays of
the seed photons (synchrotron self-Compton scattering) or gradients in maximum
electron energy behind shock fronts; and (3) events with similar X-ray and
optical radiative energy output originate well upstream of the 43 GHz core,
while those in which the optical radiative output dominates occur at or
downstream of the core.
