Support symbolic links in input files

[jo-basevi]

This PR:

• adds a step to model setup to resolve the input directory paths to absolute paths and resolve symlinks.
• pass follow_symlink=True to copy commands when copying config files. However this is already a default value but I added in so it clear in the code that it's intentional.
• more tests for the above

In 0daf911, I had just one test that would run payu setup once and test that inputs, configuration files and executables that were set up as expected. In 6d97515, I split up the tests to try(?) make it simpler to read and have one test for one thing. My concern was that it would make running tests slower as were running a payu setup multiple times. It ended up only adding a couple seconds to the tests..

To check how current manifests are changed due to these changes, I ran payu setup for release-1deg_jra55_ryf branch in access-om2-configs(https://github.com/ACCESS-NRI/access-om2-configs/tree/release-1deg_jra55_ryf). One of the full path changes are in input.yaml manifest are:

 work/INPUT/JRA55_MOM1_conserve2nd.nc:
-  fullpath: /g/data/vk83/experiments/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/JRA55_MOM1_conserve2nd.nc
+  fullpath: /g/data/vk83/configurations/inputs/access-om2/remapping_weights/JRA55/global.1deg/2020.05.30/JRA55_MOM1_conserve2nd.nc
   hashes:
-    binhash: abe66e4b33cbb75d25c010ea5f96f053
+    binhash: 3ba86d1ae2c7641a29dce1179c55ad64
     md5: 00be8ec0f1126055b65dc68178ce4eb5

(as /g/data/vk83/experiments/ is a symlink for /g/data/vk83/configurations)

Closes #385
Closes #450

[coveralls]

coverage: 56.131% (+0.2%) from 55.951%
when pulling 6d97515 on ACCESS-NRI:450-support-symbolic-links
into 68d8482 on payu-org:master.

[aidanheerdegen]

LGTM. Thanks!