This is missing at least one line. The footprint file format starts with a tag called footprint that includes the timestamp and footprint name.
Anyhow if you have overlapping pads they need to have the same pin number assigned. So both through hole pads and the smd pad need the same number.
The reason for this is this: How does KiCad know which symbol pin represents which pad of the footprint?
If two overlapping pads have differing pin numbers then they get different nets. Especially empty pad numbers always get a special net assigned that is unique to that pad. (This ensures that pads with empty pad numbers are never connected to anything)
Your tht pads have silk enabled which is a bit strange. Is this on purpose? I would also guess that you do not need paste on the smd pad.
Here my take of the FP. Note that i did not check the footprint outline and courtyard. (This privilege is reserved for contributions to the official lib 
)
cal_linux_fp.kicad_mod (1.3 KB)