Phenology phase is used in casa - it is an integer value that determines what part of the phenology cycle you are in for any given pft at any latitude. If I remember correctly, 0 is the dormant phase i.e winter, then it switches to 1 for when leaves appear, after 14 days it switches to 2 which is basically summer growth, 3 is another 14 day period when leaves start to fall. This is all determined by the data in the modis_phenology.txt file, at least for ESM1.5/1.6.
Phenology phase is calculated in the code but seems to be done relative to phenology phase at the previous call to CASA, which I presume is why it is carried in the restart file. I would have thought that the calculation could be set up as just dependent on the data in the modis file so it wouldn’t need to be carried, but perhaps that is less efficient??