All of those vpk files are grouped together as one collection and can only be opened via the "pak01_dir.vpk" file. Only open the "pak01_dir.vpk" file.

For now, use GCFScape to unpack the model files from the pak01_dir.vpk file. Note the "dir" in the file name; that file is like an index to all the pak01_* files. Crowbar currently can't unpack from vpk files that are split into multiple files using the "dir" naming scheme.

From chat with manatails on 16-Nov-2016:
04:56 - manatails: right now it does not doublequote the names of flexcontrollers
04:57 - manatails: so it causes problems when recompiling when there are spaces in the names

It seems the the procedural bones VRD file used by the $proceduralbones QC command does not allow the dot character '.' in bone names. This is even mentioned at the very bottom of the wiki page about the QC command: https://developer.valvesoftware.com/wiki/$proceduralbones

In the decompiled VRD file, I simply deleted the "valvebiped." part of 4 bone names and the compile completed without error.

Thus, I'll be changing Crowbar to write the bone name without any characters up to and including the dot when writing the VRD file.

Read the guide linked in the group's description.

Try decompiling with the most recent release of Crowbar. That issue should have been fixed.

Try reading the rest of the Download Crowbar page.

I did some testing with various inputs for "MDL file or folder" and discovered that if I put in a file name that does not exist, that error message appears. Maybe placing the spy model files into a subfolder would make it work.

I am not sure how file paths work or look on Mac. Would you describe where you originally had the spy.mdl file and what text you had in the "MDL file or folder" box?

Maybe looking at this guide and its comments section would help you get Crowbar working on Mac.

The spy file is identical to the spy file I extracted from TF2 on my PC. I'll have to think about what this means and how to fix it.