Maybe I'm looking at this wrong, but it appears to be a conflict between the repository and pyrevitfile installation set.
Pyrevitfile shows
basepublic = ['bin',
'extensions/pyRevitCore.extension',
'extensions/pyRevitRun.run',
'extensions/pyRevitTags.extension',
'extensions/pyRevitTools.extension',
'extensions/pyRevitTutor.extension',
'extensions/extensions.json',
'pyrevitlib',
'site-packages',
'pyRevitfile']

repo/extensions shows this:

Command running:
pyrevit clone BasePublic BasePublic --dest="c:\pyRevit\clones"
Result:
Error: Can not find a valid clone inside extracted package.
| Error copying "C:\Users<username>\AppData\Local\Temp\master\pyRevit-master\extensions/pyRevitRun.run" to "C:\pyRevit\clones\BasePublic\extensions/pyRevitRun.run"
| Could not find a part of the path 'C:\Users<username>\AppData\Local\Temp\master\pyRevit-master\extensions\pyRevitRun.run'.