to batch process the shapefiles save the following

#!/bin/bash
cd /Users/danbjoseph/Documents/PSU/psu_geog585/lesson3/PhiladelphiaBaseLayers/
for f in *.shp
  do ogr2ogr -skipfailures -clipsrc /Users/.../PhiladelphiaBaseLayers/clipFeature/city_limits.shp /Users/.../PhiladelphiaBaseLayers/clipped/$f /Users/.../PhiladelphiaBaseLayers/$f
  ogr2ogr -s_srs EPSG:4326 -t_srs EPSG:3857 /Users/.../PhiladelphiaBaseLayers/clippedAndProjected/$f /Users/.../PhiladelphiaBaseLayers/clipped/$f
  touch /Users/.../PhiladelphiaBaseLayers/clippedAndProjected/${f%.*}.qpj
  echo 'PROJCS["WGS 84 / Pseudo-Mercator",GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],AUTHORITY["EPSG","4326"]],PROJECTION["Mercator_1SP"],PARAMETER["central_meridian",0],PARAMETER["scale_factor",1],PARAMETER["false_easting",0],PARAMETER["false_northing",0],UNIT["metre",1,AUTHORITY["EPSG","9001"]],AXIS["X",EAST],AXIS["Y",NORTH],EXTENSION["PROJ4","+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=@null +wktext  +no_defs"],AUTHORITY["EPSG","3857"]]' >> /Users/.../PhiladelphiaBaseLayers/clippedAndProjected/${f%.*}.qpj
done

and then run it from terminal bash path/to/above/file/{{filename}}