On my Gentoo changing the ownership was not sufficient. After changing the 
ownership I had to

git reset --hard HEAD

which revealed that

Updating f894105d0d..b36eca1990
error: The following untracked working tree files would be overwritten by 
merge:

To correct this:

git clean -f build/pkgs/barvinok/
git clean -f build/pkgs/isl/
git clean -f build/pkgs/lcalc/patches/
git clean -f build/pkgs/polylib/

and now 'git pull' is up to date. This is all very strange.

On Sunday, November 25, 2018 at 9:41:58 PM UTC-6, Samuel Lelievre wrote:
>
> > As far as I can recall 'git pull' was always done as a normal user. 
> > Note the timestamp on the folders, which predates 8.5.beta4. 
> > And this issue did not manifest itself then. But going forward, 
> > how to correct things? 
>
> Change to your SAGE_ROOT directory and run this as a normal user 
>
>     $ sudo chown -v -R $(id -u):$(id -g) . 
>
> to set the owner and group of SAGE_ROOT (and recursively all 
> the included files and directories) to your user and your group. 
>

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