diff --git a/Analysis/short_tests.json b/Analysis/short_tests.json
index 57444e2e8c86cc46b248db8c61c111542cf09d72..0736fca25cc3fb6445ee855e9cfb268864f80030 100644
--- a/Analysis/short_tests.json
+++ b/Analysis/short_tests.json
@@ -30,7 +30,7 @@
 	"command":
 	[
 	    "$src_dir/Analysis/plot_traj.py",
-	    "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet", "--save=png"
+	    "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet", "--save=png"
 	],
 	"required":
 	[
diff --git a/Overlap/Tests/Input/Region_2/SHP_triplet/extremum.dbf b/Overlap/Tests/Input/Region_2_SHP_triplet/extremum.dbf
similarity index 100%
rename from Overlap/Tests/Input/Region_2/SHP_triplet/extremum.dbf
rename to Overlap/Tests/Input/Region_2_SHP_triplet/extremum.dbf
diff --git a/Overlap/Tests/Input/Region_2/SHP_triplet/extremum.shp b/Overlap/Tests/Input/Region_2_SHP_triplet/extremum.shp
similarity index 100%
rename from Overlap/Tests/Input/Region_2/SHP_triplet/extremum.shp
rename to Overlap/Tests/Input/Region_2_SHP_triplet/extremum.shp
diff --git a/Overlap/Tests/Input/Region_2/SHP_triplet/extremum.shx b/Overlap/Tests/Input/Region_2_SHP_triplet/extremum.shx
similarity index 100%
rename from Overlap/Tests/Input/Region_2/SHP_triplet/extremum.shx
rename to Overlap/Tests/Input/Region_2_SHP_triplet/extremum.shx
diff --git a/Overlap/Tests/Input/Region_2/SHP_triplet/grid_nml.txt b/Overlap/Tests/Input/Region_2_SHP_triplet/grid_nml.txt
similarity index 100%
rename from Overlap/Tests/Input/Region_2/SHP_triplet/grid_nml.txt
rename to Overlap/Tests/Input/Region_2_SHP_triplet/grid_nml.txt
diff --git a/Overlap/Tests/Input/Region_2/SHP_triplet/ishape_last.txt b/Overlap/Tests/Input/Region_2_SHP_triplet/ishape_last.txt
similarity index 100%
rename from Overlap/Tests/Input/Region_2/SHP_triplet/ishape_last.txt
rename to Overlap/Tests/Input/Region_2_SHP_triplet/ishape_last.txt
diff --git a/Overlap/Tests/Input/Region_2/SHP_triplet/max_speed_contour.dbf b/Overlap/Tests/Input/Region_2_SHP_triplet/max_speed_contour.dbf
similarity index 100%
rename from Overlap/Tests/Input/Region_2/SHP_triplet/max_speed_contour.dbf
rename to Overlap/Tests/Input/Region_2_SHP_triplet/max_speed_contour.dbf
diff --git a/Overlap/Tests/Input/Region_2/SHP_triplet/max_speed_contour.shp b/Overlap/Tests/Input/Region_2_SHP_triplet/max_speed_contour.shp
similarity index 100%
rename from Overlap/Tests/Input/Region_2/SHP_triplet/max_speed_contour.shp
rename to Overlap/Tests/Input/Region_2_SHP_triplet/max_speed_contour.shp
diff --git a/Overlap/Tests/Input/Region_2/SHP_triplet/max_speed_contour.shx b/Overlap/Tests/Input/Region_2_SHP_triplet/max_speed_contour.shx
similarity index 100%
rename from Overlap/Tests/Input/Region_2/SHP_triplet/max_speed_contour.shx
rename to Overlap/Tests/Input/Region_2_SHP_triplet/max_speed_contour.shx
diff --git a/Overlap/Tests/Input/Region_2/SHP_triplet/outermost_contour.dbf b/Overlap/Tests/Input/Region_2_SHP_triplet/outermost_contour.dbf
similarity index 100%
rename from Overlap/Tests/Input/Region_2/SHP_triplet/outermost_contour.dbf
rename to Overlap/Tests/Input/Region_2_SHP_triplet/outermost_contour.dbf
diff --git a/Overlap/Tests/Input/Region_2/SHP_triplet/outermost_contour.shp b/Overlap/Tests/Input/Region_2_SHP_triplet/outermost_contour.shp
similarity index 100%
rename from Overlap/Tests/Input/Region_2/SHP_triplet/outermost_contour.shp
rename to Overlap/Tests/Input/Region_2_SHP_triplet/outermost_contour.shp
diff --git a/Overlap/Tests/Input/Region_2/SHP_triplet/outermost_contour.shx b/Overlap/Tests/Input/Region_2_SHP_triplet/outermost_contour.shx
similarity index 100%
rename from Overlap/Tests/Input/Region_2/SHP_triplet/outermost_contour.shx
rename to Overlap/Tests/Input/Region_2_SHP_triplet/outermost_contour.shx
diff --git a/Overlap/Tests/Input/Global/NSO_in.txt b/Overlap/Tests/Input/global_NSO_in.txt
similarity index 100%
rename from Overlap/Tests/Input/Global/NSO_in.txt
rename to Overlap/Tests/Input/global_NSO_in.txt
diff --git a/Overlap/Tests/Input/Global/successive_overlap_in.txt b/Overlap/Tests/Input/global_successive_overlap_in.txt
similarity index 100%
rename from Overlap/Tests/Input/Global/successive_overlap_in.txt
rename to Overlap/Tests/Input/global_successive_overlap_in.txt
diff --git a/Overlap/Tests/Input/Region_1/get_snapshot_nml.txt b/Overlap/Tests/Input/region_1_get_snapshot_nml.txt
similarity index 100%
rename from Overlap/Tests/Input/Region_1/get_snapshot_nml.txt
rename to Overlap/Tests/Input/region_1_get_snapshot_nml.txt
diff --git a/Overlap/Tests/Input/Region_1/get_snapshot_recv_nml.txt b/Overlap/Tests/Input/region_1_get_snapshot_recv_nml.txt
similarity index 100%
rename from Overlap/Tests/Input/Region_1/get_snapshot_recv_nml.txt
rename to Overlap/Tests/Input/region_1_get_snapshot_recv_nml.txt
diff --git a/Overlap/Tests/Input/Region_2/successive_overlap_in.txt b/Overlap/Tests/Input/region_2_successive_overlap_in.txt
similarity index 100%
rename from Overlap/Tests/Input/Region_2/successive_overlap_in.txt
rename to Overlap/Tests/Input/region_2_successive_overlap_in.txt
diff --git a/Overlap/Tests/Input/Region_5/NSO_in.txt b/Overlap/Tests/Input/region_5_NSO_in.txt
similarity index 100%
rename from Overlap/Tests/Input/Region_5/NSO_in.txt
rename to Overlap/Tests/Input/region_5_NSO_in.txt
diff --git a/Overlap/Tests/Input/Region_5/SOR5OD_in.txt b/Overlap/Tests/Input/region_5_SOR5OD_in.txt
similarity index 100%
rename from Overlap/Tests/Input/Region_5/SOR5OD_in.txt
rename to Overlap/Tests/Input/region_5_SOR5OD_in.txt
diff --git a/Overlap/Tests/Input/Region_5/SOR5_in.txt b/Overlap/Tests/Input/region_5_SOR5_in.txt
similarity index 100%
rename from Overlap/Tests/Input/Region_5/SOR5_in.txt
rename to Overlap/Tests/Input/region_5_SOR5_in.txt
diff --git a/Overlap/Tests/short_tests.json b/Overlap/Tests/short_tests.json
index 25450b68cd52bec23df939a338e297166b55dd98..7ad71a819db6cfca848fa3794043b97e3c9eb4e2 100644
--- a/Overlap/Tests/short_tests.json
+++ b/Overlap/Tests/short_tests.json
@@ -78,7 +78,7 @@
         ]
     },
     {
-        "stdin_filename": "$src_dir/Overlap/Tests/Input/Region_5/SOR5OD_in.txt",
+        "stdin_filename": "$src_dir/Overlap/Tests/Input/region_5_SOR5OD_in.txt",
         "description": "Same as Successive_overlap, but with larger domain: region 5 instead of region 4.",
         "title": "Successive_overlap_region_5_one_date",
         "stdout": "test_overlap_stdout.txt",
@@ -136,7 +136,7 @@
     },
     {
         "stdin_filename":
-	"$src_dir/Overlap/Tests/Input/Region_2/successive_overlap_in.txt",
+	"$src_dir/Overlap/Tests/Input/region_2_successive_overlap_in.txt",
         "description":
 	"Overlap of different snapshots. Same as Successive_overlap_different_snapshots, but with a larger region. The identifying numbers of the connected eddies are not the same for all edges.",
         "title": "Successive_overlap_region_2",
@@ -151,12 +151,12 @@
                 "-n",
                 "1",
                 "$build_dir/Overlap/test_overlap",
-                "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+                "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
             ]
         ]
     },
     {
-        "stdin_filename": "$src_dir/Overlap/Tests/Input/Region_5/SOR5_in.txt",
+        "stdin_filename": "$src_dir/Overlap/Tests/Input/region_5_SOR5_in.txt",
         "description": "Same as Successive_overlap_region_2, but with a larger region. We get some merging and splitting.",
         "title": "Successive_overlap_region_5",
         "stdout": "test_overlap_stdout.txt",
@@ -175,7 +175,8 @@
         ]
     },
     {
-        "stdin_filename": "$src_dir/Overlap/Tests/Input/Global/successive_overlap_in.txt",
+        "stdin_filename":
+	"$src_dir/Overlap/Tests/Input/global_successive_overlap_in.txt",
         "description": "Global grid, normal 0.25° resolution.",
         "title": "Successive_overlap_global",
         "stdout": "test_overlap_stdout.txt",
@@ -290,7 +291,7 @@
         ]
     },
     {
-        "stdin_filename": "$src_dir/Overlap/Tests/Input/Region_5/NSO_in.txt",
+        "stdin_filename": "$src_dir/Overlap/Tests/Input/region_5_NSO_in.txt",
         "description": "Same as Successive_overlap_region_5, except for max_delta.",
         "title": "NSO_region_5",
         "stdout": "test_overlap_stdout.txt",
@@ -309,7 +310,7 @@
         ]
     },
     {
-        "stdin_filename": "$src_dir/Overlap/Tests/Input/Global/NSO_in.txt",
+        "stdin_filename": "$src_dir/Overlap/Tests/Input/global_NSO_in.txt",
         "description": "Same as Successive_overlap_global, except for max_delta.",
         "title": "NSO_global",
         "stdout": "test_overlap_stdout.txt",
@@ -366,7 +367,7 @@
         ]
     },
     {
-        "stdin_filename": "$src_dir/Overlap/Tests/Input/Region_1/get_snapshot_nml.txt",
+        "stdin_filename": "$src_dir/Overlap/Tests/Input/region_1_get_snapshot_nml.txt",
         "title": "Get_dispatch_snap",
         "stdout": "test_get_dispatch_snap_stdout.txt",
         "commands": [
@@ -384,7 +385,7 @@
         ]
     },
     {
-        "stdin_filename": "$src_dir/Overlap/Tests/Input/Region_1/get_snapshot_recv_nml.txt",
+        "stdin_filename": "$src_dir/Overlap/Tests/Input/region_1_get_snapshot_recv_nml.txt",
         "description": "Receive case for one of the processes in procedure get_snapshot.",
         "title": "Get_dispatch_snap_recv",
         "stdout": "test_get_dispatch_snap_stdout.txt",
@@ -450,7 +451,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "1",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -463,7 +464,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "2",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -476,7 +477,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "1",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -489,7 +490,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "1",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -502,7 +503,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "1",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -515,7 +516,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "1",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -528,7 +529,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "1",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -541,7 +542,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "1",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -554,7 +555,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "2",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -567,7 +568,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "3",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -580,7 +581,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "1",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -593,7 +594,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "1",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -606,7 +607,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "1",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -619,7 +620,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "1",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -632,7 +633,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "2",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {
@@ -645,7 +646,7 @@
             "mpiexec=$mpiexec",
             "$build_dir/Overlap/eddy_graph.sh",
             "3",
-            "$src_dir/Overlap/Tests/Input/Region_2/SHP_triplet"
+            "$src_dir/Overlap/Tests/Input/Region_2_SHP_triplet"
         ]
     },
     {