  The Calar Alto Fiber-fed \'Echelle spectrograph (CAFE) is a high-resolution
spectrographs with high-precision radial velocity capabilities mounted in the
2.2m telescope of Calar Alto Observatory. It suffered from strong degradation
after 4 years of operations and it has now been upgraded. The upgrades of the
instrument (now named CAFE$_2$) aimed at improving the throughput and stability
thanks to the inclusion of a new grating, an active temperature control in the
isolated coud\'e room, and a new scrambling system among other minor changes.
In this paper, we present the results of the re-commissioning of the instrument
and a new pipeline (CAFExtractor) that provides the user with fully reduced
data including radial velocity measurements of FGK dwarf stars. We have
monitored the upgraded instrument for several months to characterize its main
properties and test the new pipeline. It uses part of the CERES code, improves
the wavelength calibration and radial velocity extraction (using the HARPS
masks adapted), applies nightly drift corrections. The finally reduced spectra
are presented in FITS files. The commissioning results show a clear improvement
in the instrument performance with respect to the degraded status before the
intervention. The room temperature is now stabilized down to 5 mK during one
night and below 50 mK over two months. CAFE$_2$ now provides 3 m/s precision on
the reference ThAr frames and the on-sky tests provide a radial velocity
precision of 8 m/s during one night (for S/N>50). The throughput of the
instrument is now back to nominal values with an efficiency of around 15% at
550 nm. The limiting magnitude of the instrument for a 1h exposure and S/N=20
is V=15. With all these properties, CAFE$_2$ enters into the small family of
high-resolution spectrographs mounted on 2-4 meter-class telescopes capable of
reaching radial velocity precisions below 10 m/s.
