Fix check for inputs in subdirectories

[xylar]

When you add an input in a subdirectory and the target is also in the subdirectory of another step, polaris was previously incorrectly creating an absolute path to the input relative to the step's workdir, rather than the subdirectory where the symlink exists. This merge fixes that bug.

Checklist

• Testing comment in the PR documents testing used to verify the changes

closes #61

[xylar]

Testing

I create a new input file in the standard_physics/forward step in the sea-ice single-column test group under development:

        self.add_input_file(
            filename='restarts/restart.2000-02-01_00.00.00.nc',
            target='../../full_run/restarts/restart.2000-02-01_00.00.00.nc')

I then manually created this input file and could show that without this fix, the forward step failed:

OSError: input file(s) missing in step forward of seaice/single_column/standard_physics: ['/home/xylar/data/polaris_0.1/test_20230519/seaice_standard_physics2/seaice/single_column/standard_physics/full_run/restarts/restart.2000-02-01_00.00.00.nc']

but with this fix, the step fails later on due to internal issues with the test case unrelated to this PR.

The pr suite also ran successfully on my Ubuntu laptop with Gnu using this branch.

[darincomeau]

This fix worked for me - thanks!

(I swear I approved this earlier today)

[xylar]

Okay, and since @erinethomas said it worked for her on Friday, I'm going to merge.