Hi ezed413,
actually this isn’t a bug, it’s a feature :D

As you can see in the small icon of the files within the HAL folder, these files are ‘Linked Resources’. This means that the files itself aren't located in the project folder. They are symbolic links to dedicated files, and these linked files you have to add manually.
Therefore please follow these steps:
1. Right click on the project -> New -> File

2. Advanced -> Link to file in the files system -> Browse
Then please navigate to the path of the missing .c file. This step is usually just necessary for .c files. Now, please add all missing files with this feature.

3. Right click on the project -> Properties
Even without making the paths relative, the project will have the missing references now, but please always make the paths relative.
4. Resource -> Linked Resources -> Tab: Linked Resources

5. Edit the paths of the newly added files so that they become to relative paths. In our built environment replace everything before ‘ThirdParty‘ with ‘${PARENT-4-PROJECT_LOC}‘. This actually means the same as “..\..\..\..”.

The reason for this principle is to make the project shareable in case that several developer use it at the same time. I highly recommend to following this principle every time when you add (linked) files that comes from a third party.
Best regards,
Tim