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

[Yuri <yuri@xxxxxxxxx>]

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