When an input is a full path to a file the logic for updating and/or removing file paths that have changed from the path in the input manifest is not correct.
When the all the local filepaths are unchanged but fullpaths are updated, but the original files still exist in the original location, then a change is not detected.
By the time check_manifests is called all the existing files have been happily linked in the model setup and removed from existing_filepaths when add_filepath is called here
When an input is a full path to a file the logic for updating and/or removing file paths that have changed from the path in the input manifest is not correct.
For the specific case of this MOM6 config
https://github.com/COSIMA/MOM6-CICE6/blob/main/config.yaml
When the all the local filepaths are unchanged but fullpaths are updated, but the original files still exist in the original location, then a change is not detected.
By the time
check_manifestsis called all the existing files have been happily linked in the model setup and removed fromexisting_filepathswhenadd_filepathis called herehttps://github.com/payu-org/payu/blob/105fdc0930a43ff0802c9091ebbc6d8c85d6fa40/payu/models/model.py#L231
Need to add some logic to check if the fullpath has changed in the manifest.