Fix a bug in retrofit-worktree.sh

[kwankyu]

as shown in https://github.com/sagemath/sage/actions/runs/10919536449/job/30307397930?pr=38659, where the error message

[sagemath_doc_html-none] [spkg-install] [installat] /sage/src/doc/en/installation/linux.rst: WARNING: document isn't included in any toctree

is due to the file src/doc/en/installation/linux.rst that is not cleaned up in the "new" branch being tested.

The problem is that the script does not clean the worktree well enough when checking out the "new" branch.

Test: https://github.com/sagemath/sage/actions/runs/10934323900/job/30354225389?pr=38659, an excerpt from which is

#30 6.340 + cd worktree-pre
#30 6.340 + git add -A
#30 6.989 + git commit --quiet --allow-empty -m old -a
#30 7.071 + git tag -f old
#30 7.073 + git checkout -f new
#30 7.106 Previous HEAD position was 98054dd old
#30 7.106 HEAD is now at b05f634 new
#30 7.107 + git clean -fd
#30 7.159 Removing src/doc/en/installation/linux.rst
#30 7.159 + git status
#30 7.243 HEAD detached at new
#30 7.243 nothing to commit, working tree clean

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