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

Use `e_overestim.txt` instead of `node_id_param.json`. Since commit
43d2eff6, we wrote only `e_overestim` to the JSon file. Simpler to
write the value alone in a text file.

Since `NR_util` has been integrated into Jumble.

But reading from them is not here yet.

Since `shpc_open` is called by all processes, reading d0 and
`ishape_last` in `shpc_open` implies that we do not broadcast d0 and
`ishape_last`.

Store `ishape_last` and first date in components of derived type
shpc. We then remove arguments `d_init` and `ishape_last` of procedures
`read_snapshot` and `get_snapshot`.

It was confusing to mix opening an SHPC with broadcasting some part of
the resulting shpc variable.

Note that we then have to declare `d_init` before `ishape_last` in
procedure `get_snapshot`.

Before reading `ishape_last`, because we are going to use `d_init` as
lower bound of `ishape_last`.

We are reverting commit e48b7f7e. I think I did not really appreciate
then that the number of days since 1950-1-1 is another date index. It
is clearer to use just one date index, which is in the dbf files. So,
in effect, we replace everywhere the old 0-based date index k by `k -
d_init`. Note that we no longer need argument `d_init` for procedure
`dispatch_snapshot` and we no longer need to write `d_init` to file
`node_id_param.json`. Note also that the value of every node index
changes by the amount `d_init * e_overestim`.

Rename component `list_vis` of derived type snapshot to list. Since
there are no longer invisible (interpolated) eddies.

Rename component `number_vis_extr` of derived type snapshot to
`number_extr`. Since there is no longer another compoment including
interpolated eddies.

Because now there is a case when we want to open in appending mode: in
program `inst_eddies`.

Than ks to commit 5ff9e1d2, we are reverting in part commits e1aa5bcc and
fda1e6cd.

Remove `shpc_create` from use list in main program `test_overlap`. It
is no longer needed since commit 50d2f596.

Write file `node_id_param.json` from programs `test_overlap` and `eddy_graph`.

Write node indices instead of dates and eddy indices in
edgelist. Compute `e_overestim` from `ishape_last`. Remove header
lines of edgelist. See commit 3370733a. Replace argument d of procedure
overlap by arguments `e_overestim` and k.

Remove component `number_eddies` of derived type snapshot. It was the
same as `number_vis_extr` since there are no interpolated eddies any longer.

This is a big change, a big simplification. Creating interpolated
eddies was the way of Alexis Chaigneau. Rémi L. thinks it is no longer
useful.

So remove procedure `init_interpolated_eddy`; do not create SHPC for
interpolated eddies in programs `eddy_graph`, `test_overlap` and
`test_write_overlap`; remove argument `hshp_interp` of procedure
overlap; remove arguments `hshp_interp`, m, cyclone, `coord_extr_1`,
`ssh_extr_1`, `coord_extr_2` and `ssh_extr_2` of procedure
`write_overlap`.

Redefine `k_test_[12]` as date indices (0-based) instead of dates.

Follow-up to commit 3b68dd5.

To ease use of call with keywords.

Because variables in `grid_nml` should be all defined in the input file.

We now impose that all eddies in an SHPC have the same
orientation. Remove field `extr_cycl` from the derived type shpc and
add field cyclone to shpc. When reading an eddy, give it the
orientation of its SHPC. Add argument cyclone to procedure
`shpc_create`. Create a file `orientation.txt` in each SHPC. When
writing an eddy, check that its orientation matches that of the SHPC.

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

We are reverting commits 35fad1b7 and df2b397d because we want the
program `eddy_graph.sh` to read an SHPC containing a single
orientation.

Do not print arrays.

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.

Group `new_unit` and open in the same procedure, that we rename from
`set_unit_edge` to `open_edge_file`. This removes the need for a
special version of `new_unit` and it is closer to the use of the
`new_unit` keyword in Fortran 2008.

This makes the program `eddy_graph` heavier but it makes sense because
there can be no connection between the two graphs, and we need to make
the graphs as small as possible for large spatio-temporal domains.

`unit_edgelist` was just transmitted by procedure overlap from main
program unit to `write_overlap`. So now overlap does not see
`unit_edgelist`. Further motivation: we are going to split the edge
list file into two files.