Remove some input files

Revert parts of commits 845752bc and ef7abf1b. It is true that having
the input files in the repository allowed us to run tests for the
first time more easily. But the drawbacks were:

- The large number of input files obscured the repository tree.

- Some files are input files for a test and are actually produced by
another test. These files did not evolve automatically with the
executables that produced them.

- It was a burden to log how these input files were produced.

To alleviate the problem of running the tests for the first time, we
take the input files from tests in the current series of tests, when
possible, instead of from the old series. (Before commits 845752bc and
ef7abf1b, the input files came from `$test_old_dir`.) We do not always
do this because we want to be able to run the various series of tests
independently. For example, we want to be able to run the Overlap
series before the `Inst_eddies` series. So, for the files that are
produced in one series of tests and used as input files in another
series of tests, we go back to pre-commit ef7abf1b and use
`$test_old_dir`.

Inst_eddies/Tests/Input/Get_1_outerm/test.json

-{
-   "args": "/home/guez/build/Detection_eddies/test_get_1_outerm",
-   "input": "&main_nml /\n",
-   "required": [
-      [
-         "/home/guez/ownCloud/Vierne_documents/Informatique_fonctionnement/Programs/Detection_eddies/Tests/Input/h_region_1.nc",
-         "h.nc"
-      ],
-      [
-         "/home/guez/ownCloud/Vierne_documents/Informatique_fonctionnement/Programs/Detection_eddies/Tests/Input/outside_points_get_1_outerm.csv",
-         "outside_points.csv"
-      ]
-   ],
-   "title": "Get_1_outerm"
-}

Inst_eddies/Tests/Input/Get_1_outerm/test_get_1_outerm_stdout.txt

-&MAIN_NML
- IND_TARG_EXTR=         19,         11,
- INNERMOST_LEVEL= 0.293300003    ,
- CYCLONE=T,
- /
- Enter namelist main_nml.
-&MAIN_NML
- IND_TARG_EXTR=         19,         11,
- INNERMOST_LEVEL= 0.293300003    ,
- CYCLONE=T,
- /
- Reading from "h.nc"...
- Reading from outside_points.csv...
- Radius of disk of equal area:    82.5294418     km
- Created shapefile "test_get_1_outerm".

Inst_eddies/Tests/Input/Get_1_outerm_noise_2_8/test.json

-{
-   "args": "/home/guez/build/Detection_eddies/test_get_1_outerm",
-   "description": "Assume insufficient amplitude for extrema 2 and 8. Even if extremum 8 does not have a particularly small amplitude, we just want to see the target extremum, 6, grow its outermost contour compared to the case without minimum amplitude.",
-   "input": "&main_nml /\n",
-   "required": [
-      [
-         "/home/guez/ownCloud/Vierne_documents/Informatique_fonctionnement/Programs/Detection_eddies/Tests/Input/h_region_1.nc",
-         "h.nc"
-      ],
-      "/home/guez/ownCloud/Vierne_documents/Informatique_fonctionnement/Programs/Detection_eddies/Tests/Input/outside_points.csv"
-   ],
-   "title": "Get_1_outerm_noise_2_8"
-}

Inst_eddies/Tests/Input/Get_1_outerm_noise_2_8/test_get_1_outerm_stdout.txt

-&MAIN_NML
- IND_TARG_EXTR=         19,         11,
- INNERMOST_LEVEL= 0.293300003    ,
- CYCLONE=T,
- /
- Enter namelist main_nml.
-&MAIN_NML
- IND_TARG_EXTR=         19,         11,
- INNERMOST_LEVEL= 0.293300003    ,
- CYCLONE=T,
- /
- Reading from "h.nc"...
- Reading from outside_points.csv...
- Radius of disk of equal area:    108.869049     km
- Created shapefile "test_get_1_outerm".

Inst_eddies/Tests/Input/Region_1/Local_extrema/test_local_extrema.csv

- "longitude index" "latitude index"
- "" "" "" "degrees east" "degrees north" "m" "m"
- ilon ilat cyclone longitude latitude ssh innermost_level
-          14           2 T   8.37500000      -36.1250000      0.297899991      0.299299985    
-          18           3 T   9.37500000      -35.8750000      0.314000010      0.314099997    
-           5           5 T   6.12500000      -35.3750000      0.362300009      0.363400012    
-          13           8 F   8.12500000      -34.6250000      0.653100014      0.645900011    
-          24           8 F   10.8750000      -34.6250000      0.685899973      0.675100029    
-          19          11 T   9.62500000      -33.8750000      0.275900006      0.293300003    
-           4          14 F   5.87500000      -33.1250000      0.772899985      0.772199988    
-          13          14 T   8.12500000      -33.1250000      0.433400005      0.437999994    

Inst_eddies/Tests/Input/Region_1/Local_extrema/test_local_extrema_stdout.txt

- periodic = ? 
- periodic =  F
- Reading from /home/guez/ownCloud/Vierne_documents/Informatique_fonctionnement/Programs/Detection_eddies/Tests/Input/h_region_1.nc...
- Created file "test_local_extrema.csv".
- Created file "extr_map.nc".

Inst_eddies/Tests/short_tests.json

@@ -172,18 +172,9 @@
         "title": "Mean_speed",
         "required": [
             "$src_dir/Inst_eddies/Tests/Input/Region_1/uv.nc",
-            [
-                "$src_dir/Inst_eddies/Tests/Input/Get_1_outerm/test_get_1_outerm.shp",
-                "contour.shp"
-            ],
-            [
-                "$src_dir/Inst_eddies/Tests/Input/Get_1_outerm/test_get_1_outerm.dbf",
-                "contour.dbf"
-            ],
-            [
-                "$src_dir/Inst_eddies/Tests/Input/Get_1_outerm/test_get_1_outerm.shx",
-                "contour.shx"
-            ]
+            ["$PWD/Get_1_outerm/test_get_1_outerm.shp", "contour.shp"],
+            ["$PWD/Get_1_outerm/test_get_1_outerm.dbf", "contour.dbf"],
+            ["$PWD/Get_1_outerm/test_get_1_outerm.shx", "contour.shx"]
         ],
         "command": "$build_dir/Inst_eddies/test_mean_speed"
     },
@@ -222,7 +213,7 @@
                 "$src_dir/Inst_eddies/Tests/Input/empty_outside_points.csv",
                 "outside_points.csv"
             ],
-            "$src_dir/Inst_eddies/Tests/Input/Get_1_outerm/test_get_1_outerm.*"
+            "$PWD/Get_1_outerm/test_get_1_outerm.*"
         ],
         "title": "Set_max_speed",
         "command": "$build_dir/Inst_eddies/test_set_max_speed"
@@ -233,7 +224,7 @@
             "$src_dir/Inst_eddies/Tests/Input/Region_1/h.nc",
             "$src_dir/Inst_eddies/Tests/Input/Region_1/uv.nc",
             "$src_dir/Inst_eddies/Tests/Input/Region_1/outside_points.csv",
-            "$src_dir/Inst_eddies/Tests/Input/Get_1_outerm_noise_2_8/test_get_1_outerm.*"
+            "$PWD/Get_1_outerm_noise_2_8/test_get_1_outerm.*"
         ],
         "title": "Set_max_speed_noise",
         "command": "$build_dir/Inst_eddies/test_set_max_speed"
@@ -320,7 +311,7 @@
         "required": [
             "$src_dir/Tests/Region_1_SHP_triplet_noise/extremum.*",
             "$src_dir/Tests/Region_1_SHP_triplet_noise/ishape_last.txt",
-            "$src_dir/Inst_eddies/Tests/Input/Region_1/Local_extrema/extr_map.nc"
+            "$PWD/Local_extrema/extr_map.nc"
         ],
         "title": "Nearby_extr",
         "command": "$build_dir/Inst_eddies/test_nearby_extr"

Overlap/Tests/Input/Global/Extraction_eddies_periodic/SHP_triplet/grid_nml.txt

-&grid_nml CORNER_deg  = 0.000000       , -81.00000      ,
- STEP_deg    = 20.00000       , 18.00000       ,
- NLON    = 18,
- NLAT    = 10,
-/

Overlap/Tests/Input/Global/Extraction_eddies_periodic/SHP_triplet/ishape_last.txt

-4