Following updates of the libraries.

Following updates of the libraries.

Thanks to commit 5ff9e1d2, we are reverting in part commit f04aea8b.

Note that programs `test_max_speed_contour_ssh` and `test_weight`
depend on fortranGIS through the module derived_types. Compilation
worked without linking to fortranGIS because objects used by
`test_max_speed_contour_ssh` and `test_weight` in
derived types do not use fortranGIS.

Thanks to commit 5ff9e1d2, we are reverting in part commit 83123e30.

Because we are going to add preprocessor directives.

`test_nearby_extr` does not need NetCDF since commit 83123e30.

In case we are a sub-project.

Rename triplet to collection, `shp_tr` to shpc, shpt to shpc in
comments, identifiers and file names.

Instead of reading `extr_map.nc`, `ishape_last.txt` and shapefile
extremum. The problem was the consistency between `extr_map.nc` and
the two other files. `extr_map.nc` contains eddies with the two
orientations while extremum now contains a single orientation, with
eddies renumbered.

Use higher level procedures in main program
`test_set_max_speed`. Allows to output easily more information. Then,
for example in `test_mean_speed.py`, we will be able to read extremum
position from the shapefiles instead of asking the user to define it.

Use higher level procedures in main program
`test_set_max_speed`. Allows to read easily more information: cyclone,
`ssh_extremum`, `coord_extr` from the shapefiles. So we do not ask
this information to the user. The drawback is that we have to call
MPI (because of `read_field_indices`) even if we do not really use
it. We move the calls to `find_package` for EZMPI and `GPC_F` to the
top-level `CMakeLists.txt` since these libraries are now necessary in
both `Inst_eddies` and Overlap.

`read_eddy.f90`, `read_field_indices.f90` and `shp_tr_open.f90` will
become common to Overlap and `Inst_eddies` because they will be used
in `Inst_eddies/Tests/test_set_max_speed.f90`. So there are now enough
common files to justify a new directory.

Use higher level procedures in main program
`test_get_1_outerm`. Allows to output easily more information. Then in
program `test_set_max_speed` for example, we will be able to read information
about the extremum from the shapefiles instead of asking it to the
user.

Use higher level procedures in main program unit `test_set_all_outerm`.

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.

Following update of libraries: NetCDF-Fortran is private in NetCDF95
and MPI-Fortran is private in EZMPI.

Move Fortran source files used in tests of both parts, `Inst_eddies`
and Overlap, to directory Tests at root of repository.

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.