Use out_cont%closed instead.

This avoids copying `cont_list(n_cont)` to `out_cont` if it has
insufficient area.

Add dummy arguments `cont_list` and `n_cont` to `get_1_outerm`.

Because we are going to add another intent out argument.

Remember that we do not write invalid eddies to shapefiles, so there
are no null shapes in `outermost_contour.shp`. So, in order to predict
the size of output, the interesting statistics is the number of points
divided by the number of non-null outermost contours.

Because the numbering changed when we decided not to write invalid eddies.

I do not remember why I chose to write to standard error. First it is
clearer to write only error messages to standard error. Second the
order of messages on standard error coming from the Fortran code and
from the shapelib C library does not seem deterministic, and this is
annoying to compare runs.

Because the numbering changed when we decided not to write invalid eddies.

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`.