Fixes bugs in regrid-xy, restore original directory structure

.cspell/ok-unknown-words.txt

@@ -551,5 +551,11 @@ zfactor
 zonavg
 zsurf
 zxvf
+donwell
+hartfield
+longbourn
+pemberley
+openedfile
+lonxlat
 njobs
-RDHPCS
+RDHPCS

fre/app/freapp.py

@@ -65,6 +65,10 @@ def remap(input_dir, output_dir, begin_date, current_chunk,
                         ts_workaround, ens_mem)
 
 @app_cli.command()
+@click.option("--yamlfile",
+              type = str,
+              help = "Path to yaml configuration file",
+              required = True)
 @click.option("-i", "--input_dir",
               type = str,
               help = "`inputDir` / `input_dir` (env var) specifies input directory to regrid, " + \
@@ -75,14 +79,9 @@ def remap(input_dir, output_dir, begin_date, current_chunk,
               help = "`outputDir` / `output_dir` (env var) specifies target location for output" + \
                      " regridded files",
               required = True)
-@click.option("-b", "--begin",
-              type = str,
-              help = "`begin` / `begin` (env var) ISO8601 datetime format specification for" + \
-                     " starting date of data, part of input target file name",
-              required = True)
-@click.option("-tmp", "--tmp_dir",
+@click.option("-w", "--work_dir",
               type = str,
-              help = "`TMPDIR` / `tmp_dir` (env var) temp directory for location of file " + \
+              help = "`TMPDIR` / `workdir_dir` (env var) work directory for location of file " + \
                      "read/writes",
               required = True)
 @click.option("-rd", "--remap_dir",
@@ -96,19 +95,16 @@ def remap(input_dir, output_dir, begin_date, current_chunk,
                      "within input directory to target for regridding. the value for `source` " + \
                      "must be present in at least one component's configuration fields",
               required = True)
-@click.option("-g", "--grid_spec",
+@click.option("-id", "--input_date",
               type = str,
-              help = "`gridSpec` / `grid_spec` (env var) file containing mosaic for regridding",
-              required = True)
-@click.option("--rose_config",
-              type = str,
-              help = "Path to Rose app configuration (to be removed soon)",
-              required = True)
-def regrid( input_dir, output_dir, begin, tmp_dir,
-            remap_dir, source, grid_spec, rose_config ):
+              help = "`input_date` / `input_date` (env var) ISO8601 datetime format specification for" + \
+                     " starting date of data, part of input target file name")
+def regrid(yamlfile, input_dir, output_dir, work_dir,
+           remap_dir, source, input_date):
     ''' regrid target netcdf file '''
-    regrid_xy( input_dir, output_dir, begin, tmp_dir,
-               remap_dir, source, grid_spec, rose_config )
+    regrid_xy(yamlfile, input_dir, output_dir, work_dir,
+              remap_dir, source, input_date)
+
 
 @app_cli.command()
 @click.option("-i", "--infile",