skip three files when staging refcase files to avoid a rmtree error

[minxu74]

Skip linking the three files ('timing', 'spio_stats', and 'memory.*') when
staging files from refcase directory to the branch run directory.

Test suite: NA
Test baseline: NA
Test namelist changes: None
Test status: [bit for bit]

Fixes #4697, E3SM-Project/E3SM#6704

User interface changes?: No

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

[jasonb5]

@minxu74 Please run pre-commit to fix any issues. Install pre-commit, run pre-commit run -a and commit the fixes. Thanks!

[minxu74]

@jasonb5 I have run the pre-commit and fixed the format of the modifications to meet the black requirement. The PR has passed all checks.