Layer missing Native SRS in geoserver

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I'm currently trying to get a couple of layers uploaded to a geoserver and I'm having trouble getting the projection recognized. The result of the curl command is that the two layers are both missing the Native SRS, which should be EPSG: 3857.

I'm able to fix by manually going to the layer, choosing a Declared SRS, and computing the Lat/Lon Bounding Box from the native bounds. This allows me access to the layer via WMS ,which is what I want.

But this is not a good solution. I have a lot of layers that I need to upload, so I don't want to manually fix the missing Native SRS problem for each layer. So how can I fix the shapefiles so that geoserver can find the Native SRS on its own?

I got the correct .prj file from here: http://hub.qgis.org/issues/7368So both the .prj and the .qpj files are set to this for the two shapefiles:

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"]]

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