Removed instances of isUpgrade flag, separated standard and Phase1 code

- I removed most instances of the "isUpgrade" flag in DQM/SiPixel* (exceptions being in DQM/SiPixelCommon, where some instances were left behind so as not to make things incompatible with code outside DQM/)
- wherever "isUpgrade" was removed, I separated source files (and their associated header files and analyzer declarations in _cfi.py config files) into a standard-geometry version, which retains its original name, and a Phase1 version, in which the name has "Phase1" tacked onto the end (for instance, SiPixelMonitorRecHit/src/SiPixelRecHitModule.cc and SiPixelMonitorRecHit/src/SiPixelRecHitModulePhase1.cc)