Fix chmod command in safe_copy

[billsacks]

Test suite: manual testing only (see below); did NOT run
scripts_regression_tests, since it seems this line must not be covered
by automated testing (otherwise tests would have failed)
Test baseline: n/a
Test namelist changes: none
Test status: bit for bit

Manual testing:

I created a temporary refdir:

[/glade/p/cesmdata/cseg/inputdata/cesm2_init/bill.test]
$ ls 0501-01-01/
b.e21.B1850.f09_g17.CMIP6-piControl.001.clm2.r.0501-01-01-00000.nc  rpointer.lnd

Then did the following:

./create_newcase --case $scratch/test_refcase_baseline_0123a --res f09_g17 --compset X --run-unsupported
./xmlchange RUN_TYPE=hybrid,RUN_REFCASE=bill.test,RUN_REFDIR=cesm2_init,RUN_REFDATE=0501-01-01
./xmlchange GET_REFCASE=TRUE
./case.setup
./case.build
^C
# Changed rpointer.lnd file in the refdir
./case.build
# Verified that the run directory has the new rpointer.lnd

I first verified that the second case.build command failed from the
baseline code (i.e., that I could properly reproduce the problem). With
the new code, the safe_copy no longer fails and the new rpointer.lnd
file is copied as desired.

Fixes #3363

User interface changes?: N

Update gh-pages html (Y/N)?: N

Code review:

[jedwards4b]

Thanks!

[billsacks]

@fischer-ncar if possible it would be good to get this fix into CESM2.1.2.

@jgfouca FYI. I didn't bother assigning you as a reviewer since the fix seems trivial enough, but feel free to look at this if you want.

[jgfouca]

Thanks for finding and fixing this. I apologize for introducing this bug... not sure how it got through testing.

[fischer-ncar]

I'll get this into cesm2.1.2.