Because `$tests_old_dir/Extraction_eddies_region_5/SHPC` is opened
with `SHPC_class` in test `Plot_eddy_contours_window`, which will
create `n_slices.txt`, so there will always be this file only in
`$tests_old_dir/Extraction_eddies_region_5/SHPC`.

We import in the test infrastructure the experiment `Inst_eddies_4`
because we want to no longer keep invalid contours, so we will need to
update the experiment.

As `grid_lon_lat` may be false, we define `e%extr%coord_proj`.

I do not see why this was not done in commit 24b5b079.

This shortens the file `test_get_1_outerm.f90`.

We will need this new shapefile in program `eddy_graph` only for a non
longitude-latitude grid. We add a new dummy argument `grid_lon_lat` to
procedure `shpc_create` to decide whether we create the shapefile
`extr_proj`.

Add component `innermost_level` to derived type eddy. So
`innermost_level` does not transit as an argument through main program
unit `inst_eddies` any longer.

Extract definition of extrema from procedure `set_all_outerm` into new
procedure `set_all_extr`. So we are reverting part of commit
f5f4298d. The drawback, for now, is that `innermost_level` has to
transit in the main program unit from `set_all_extr` to
`set_all_outerm`.

Rename file `test_write_eddy.f90` to `test_write_null.f90`. The name
was badly chosen because the program is not a unit test of procedure
`write_eddy`. In fact, it does not even call `write_eddy`.

Use relative path to Overlap from `Inst_eddies/Tests`. For symmetry
with what we do in `Overlap/Tests`. So now the directories Overlap and
`Inst_eddies` can be added from the top-level `CMakeLists.txt` in
either order.

Following update of NetCDF95.

Update `CMakeLists.txt` files to take into account commit 3289c070.

We are trying to define clearly the directories and what Fortran files
they should contain:

- `Inst_eddies`: May only contain program units which make up the
program `inst_eddies`. If a program unit does not go into
`inst_eddies`, it should not be here. Not all program units going into
`inst_eddies` must be here: some could be in directory Common.

- `Inst_eddies/Tests`: Main programs of unit tests for procedures in
directory `Inst_eddies`. Plus procedures used only in these unit tests.

- `Overlap`: May only contain program units which make up the program
`eddy_graph`. If a program unit does not go into `eddy_graph`, it
should not be here. Not all program units going into `eddy_graph` must
be here: some could be in directory Common.

- `Overlap/Tests`: Main programs of unit tests for procedures in
directory `Overlap`. Plus procedures used only in these unit tests.

- Common: Procedures that are used in both programs `inst_eddies` and
`eddy_graph`.

- Common/Tests: Main programs of unit tests for procedures in
directory `Common`. Plus procedures used only in these unit
tests. Plus procedures used in unit tests of both `Inst_eddies` and
`Overlap` directories but not used in either program `inst_eddies` nor
`eddy_graph`.

Remove dummy arguments nlon, nlat, corner, step of procedure
`read_snapshot`, use module variables instead. Note that we keep copy
as a dummy argument instead of using the variable of module
`config_graph_m`, because we want the procedure `read_snapshot` to be
usable outside of the `eddy_graph` program.

Add `config_graph.f90`and `read_grid.F90` to lists of source files.

Move files from `Anticyclones/Slice_0` to `Slice_0/Anticyclones`.

Changing my mind. In an SHPC, store shapefiles in
"Slice_{slice}/{orientation}" instead of
"{orientation}/Slice_{slice}". Two reasons: easier to store accessory
files from running `inst_eddies`, such as `perf_report` and output
from Torque submission script; clearer that a slice should contain the
same dates for both orientations.

Read `used_nml.txt` at the SHPC level, only one file for both
orientations. Remove dummy argument exist of procedure config. Demote
`config_nml` to local scope. Remove procedure `write_nml`.

Remove procedure `write_aux`. Write to `ishape_last.txt` in procedure
`write_snapshot` and write `grid_nml` in procedure `input_ssh`. In
`input_ssh`, if `grid_nml.txt` already exists, check consistency with
input NetCDF files. Downgrade dummy arguments `corner_deg` and
`step_deg` of `input_ssh` to local variables. Read and write
`grid_nml` at SHPC level, only one file for both orientations and all
slices.

Assume that a slice is in a directory
"{shpc_dir}/{orientation}/Slice_{slice}" where shpc_dir can be any
name, orientation is "Anticyclones" or "Cyclones" and slice is an
integer. Do not read or create any longer a file "orientation.txt" in
the slice directory. Add procedure `get_slice_dir`. Add dummy
arguments cyclone and slice to procedure `shpc_open`. Add dummy
argument slice to procedure `shpc_create`.

Not needed since commit 53e5c983.

Not needed since commit 6dc504df.

Rename `main_nml` to `config_nml` in module `config_m`.

Extract code from program `inst_eddies` into new procedure `write_snapshot`.

Extract code from program `inst_eddies` into new procedure `input_ssh`.

Split derived type `shpc_slice_handler` into `shpc_slice_handler` and
`shpc_slice_meta out`. Do not mix what is necessary to open, create
and close, analogous to a logical unit, with what comes from reading
the files.

Create component `unit` for `ishape_last.txt` in derived type
`shpc_slice_handler`. Open, create and close `ishape_last.txt` at the
same time we open, create and close the shapefiles. So we use
`read_opcol` instead of `read_column` when we need to read
`ishape_last.txt`.

We are more clearly separating opening files and reading from them.