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**Description** This PR fixes two types of bugs discovered when cycling `gsi.x` and `enkf.x` with intel/2022 in the global workflow 1. modify variables written to netcdf diagnostic files by `gsi.x` to be consistent with codes which read netcdf diagnostic files 2. modify `lrun_subdirs=.true.` option of `gsi.x` to properly handle the case in which sub-directories already exist in the run directory Fixes #623 **Type of change** - [x] Bug fix (non-breaking change which fixes an issue) **How Has This Been Tested?** Ctests have been on Hera, Orion, and WCOSS2 (Cactus) with acceptable behavior. A global parallel covering the period 2021073106 through 2021080118 has been run on Hera, Orion, and WCOSS2 (Cactus). All global workflow jobs ran as expected. **Checklist** - [x] My code follows the style guidelines of this project - [x] I have performed a self-review of my own code - [x] New and existing tests pass with my changes
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