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The classic self-referenced frequency comb acts as an unrivaled ruler for precision optical metrology in both time and frequency. Two decades after its invention, the frequency comb is now used in numerous active sensing applications. Many of these applications, however, are limited by the tradeoffs inherent in the rigidity of the comb output and operate far from quantum-limited sensitivity. Here we demonstrate an agile programmable frequency comb where the pulse time and phase are digitally controlled with +/- 2 attosecond accuracy. This agility enables quantum-limited sensitivity in sensing applications since the programmable comb can be configured to coherently track weak returning pulse trains at the shot-noise limit. To highlight its capabilities, we use this programmable comb in a ranging system, reducing the detection threshold by ~5,000-fold to enable nearly quantum-limited ranging at mean pulse photon number of 1/77 while retaining the full accuracy and precision of a rigid frequency comb. Beyond ranging and imaging, applications in time/frequency metrology, comb-based spectroscopy, pump-probe experiments, and compressive sensing should benefit from coherent control of the comb-pulse time and phase.