'git pull' complains that a locally resurrected directory would be overwritten by merge when no pulled changes are affecting that directory

In the FreeBSD ports repository I resurrected the directory (that was removed a long time ago) with the command:

 > $ git checkout {hash}~1 -- math/polymake

I made local changes to this directory and called 'git add math/polymake'.

Then 'git pull' complained:

 > $ git pull
 > error: Your local changes to the following files would be overwritten 
by merge:
 >   math/polymake/Makefile math/polymake/distinfo 
math/polymake/files/patch-Makefile 
math/polymake/files/patch-support_install.pl math/polymake/pkg-descr 
math/polymake/pkg-plist

No incoming changes affect math/polymake. Nobody has created this directory simultaneously with me. There is no intersection with incoming changes.

Why does 'git pull' complain then?

Yuri