extract_science.py rebuild fix

[bblay-mo]

• Fixes a FileExistsError in extract_science.py when rebuilding.
• Updates the copy to only target newer files.

Note: There is a subsequent error in the dependerator when rebuilding (not related to the changes in this pr). The workaound is: rm applications/lfric_atm/working/build_lfric_atm/dependencies.db

Todo:

• Stem test failing from timeout. Investigating

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[bblay-mo]

Since we're invoking a CLI tool, we could consider using rsync, which can remove files too.

[bblay-mo]

This line is almost certainly redundant, so we could remove it instead of fixing it.