We want to be able to run `inst_eddies` from a directory other than
the directory containing the SHPC to be appended to. Preparing to
write `grid_nml.txt` and `used_config_nml.txt` in the current
directory. To be able to do this in parallel for several slices, we
need to be running in different directories.

For `Test_compare` version > 0.4.

We rewrite `inst_eddies_Aviso.py` so it is more convenient to use. The
script is only useful for several input files. Otherwise we can
directly use `inst_eddies.py`. So instead of optional arguments
template and last date, we use positional arguments. Then there is no
point in distinguishing dirname and basename. Also, it does not make
sense any longer to read the date from the content of the first
file. The script becomes more general: we do not assume that all input
NetCDF files are in the same -directory and that the time coordinate
is in days since 1950-1-1. The interface is also clearer.

Because `test_set_all_outerm` is now essentially the same as
`inst_eddies`. Replace `test_set_all_outerm` by `inst_eddies` in
tests.

Introduce two variables `Aviso_DT_dir` and `Eurec4A_NRT_dir` to
replace the single variable `large_input_dir`. This should remove the
need to create symbolic links to the files in these directories.

Dictionary instead of list, following update of `test_compare.py`.

Instead of symbolic links. We want to avoid creating symbolic links
above SHPC because we want to run several instances of `inst_eddies`
in parallel.

So the script can write to a slice other than 0.

Bug fix: do not provide standard input for `inst_eddies_Aviso.py`, it
does not read it.

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.

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.

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`.

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

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

Add tests for a case where the speed is not defined on a whole segment.

Following update of `test_compare.py`.

We can make a symbolic link or copy to `$large_input_dir`.

Following modifications of `CMakeLists.txt` files.

When there are more than 3 input files. We recover the convenience of
commit b34b85a8, with the underlying generality of commit d365e754.

Provide list of input files as arguments of `inst_eddies.py`,
following commit 8e0c03e1.

For programs `inst_eddies` and `test_get_1_outerm`, following commits
9a59d13 and 9dc139d.

Following commit b0e3ce55.

In commit d5e89eb9, the test was added with the useless key
"input". Now, after commit 29c37646, the useless key is the key "required".

Now that `inst_eddies` reads `main_nml` only on the first date, we do
not need to create a file `main_nml.txt` before running
`inst_eddies.py`. `inst_eddies.py` can just read `main_nml` from
standard input.

Replace positional argument template by optional argument. This
argument is now needed only in case we process several dates, since
the first date is now read from the NetCDF file.

Replace `/proju/lmd-oce/data/AVISO/DT_2018/2006/01` by
`$large_input_dir`.

This SHPC was made with an old version of `inst_eddies`: it contained
cyclones and anticyclones output together. We create a test `Region_6`
instead.

Make it 15 days long because we want to use it in place of
`Overlap/Tests/Input/Region_2_SHPC`.

Create separate collections of shapefiles for cyclones and anticyclones.

Preparing for two collections of shapefiles. We create the
procedure `write_nml` so we will be able to call it twice. But it
needs to access the namelist. So the namelist must be at the module level.

Take into account new structure of repository in JSon test files.

Also split the tests, Fortran source files, Python files and JSon
files. Keep at the top level the files used in both `Inst_eddies` and
Overlap.

Motivations for the split:

- The top directory contained many files.

- It may be useful to compile only one of the two sub-projects. For
example, only `Inst_eddies` on Ciclad, where MPI 3 is not available.