I'm using ArcGIS Desktop 10.3. My workspace parameters are set correctly, to the geodatabase with all the other feature class files. When I run the Clip tool, it adds an extra ".shp" to the output filename, and then gives me the error that the output name contains invalid characters (the period).
I've tried deleting the .shp in the name before running. I've tried running the tool in Arcpy, with the same result.
The data I'm clipping is from a state agency, gis shapefile made publicly available.
Any ideas what to try next?