From 6ce70860d8776f6d9278f3a50438802619c85e59 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <gerasimos.chourdakis@ipvs.uni-stuttgart.de>
Date: Thu, 2 Jul 2026 11:18:48 +0200
Subject: [PATCH 1/6] Make partitioned-burgers-1d/clean-tutorial.sh a link

---
 partitioned-burgers-1d/clean-tutorial.sh          | 15 +--------------
 partitioned-burgers-1d/dirichlet-scipy/clean.sh   |  1 +
 partitioned-burgers-1d/neumann-scipy/clean.sh     |  1 +
 partitioned-burgers-1d/neumann-surrogate/clean.sh |  3 ++-
 partitioned-burgers-1d/solver-scipy/clean.sh      |  1 +
 tools/clean-tutorial-base.sh                      |  2 +-
 6 files changed, 7 insertions(+), 16 deletions(-)
 mode change 100755 => 120000 partitioned-burgers-1d/clean-tutorial.sh

diff --git a/partitioned-burgers-1d/clean-tutorial.sh b/partitioned-burgers-1d/clean-tutorial.sh
deleted file mode 100755
index 0eb18b112..000000000
--- a/partitioned-burgers-1d/clean-tutorial.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env sh
-set -e -u
-
-# shellcheck disable=SC1091
-. ../tools/cleaning-tools.sh
-
-clean_tutorial .
-clean_precice_logs .
-rm -fv ./*.log
-rm -fv ./*.vtu
-
-# Clean up root directory
-rm -f initial_condition.npz
-rm -rf output/
diff --git a/partitioned-burgers-1d/clean-tutorial.sh b/partitioned-burgers-1d/clean-tutorial.sh
new file mode 120000
index 000000000..4713f5092
--- /dev/null
+++ b/partitioned-burgers-1d/clean-tutorial.sh
@@ -0,0 +1 @@
+../tools/clean-tutorial-base.sh
\ No newline at end of file
diff --git a/partitioned-burgers-1d/dirichlet-scipy/clean.sh b/partitioned-burgers-1d/dirichlet-scipy/clean.sh
index 8461c99bc..71140f86e 100755
--- a/partitioned-burgers-1d/dirichlet-scipy/clean.sh
+++ b/partitioned-burgers-1d/dirichlet-scipy/clean.sh
@@ -7,3 +7,4 @@ set -e -u
 clean_precice_logs .
 clean_case_logs .
 rm -f dirichlet.npz
+rm -f ../initial_condition.npz
diff --git a/partitioned-burgers-1d/neumann-scipy/clean.sh b/partitioned-burgers-1d/neumann-scipy/clean.sh
index 53ac460c9..bc01024e8 100755
--- a/partitioned-burgers-1d/neumann-scipy/clean.sh
+++ b/partitioned-burgers-1d/neumann-scipy/clean.sh
@@ -7,3 +7,4 @@ set -e -u
 clean_precice_logs .
 clean_case_logs .
 rm -f neumann.npz
+rm -f ../initial_condition.npz
diff --git a/partitioned-burgers-1d/neumann-surrogate/clean.sh b/partitioned-burgers-1d/neumann-surrogate/clean.sh
index 461eb004e..bbb8da75d 100755
--- a/partitioned-burgers-1d/neumann-surrogate/clean.sh
+++ b/partitioned-burgers-1d/neumann-surrogate/clean.sh
@@ -6,4 +6,5 @@ set -e -u
 
 clean_precice_logs .
 clean_case_logs .
-rm -f surrogate.npz
\ No newline at end of file
+rm -f surrogate.npz
+rm -f ../initial_condition.npz
\ No newline at end of file
diff --git a/partitioned-burgers-1d/solver-scipy/clean.sh b/partitioned-burgers-1d/solver-scipy/clean.sh
index 2727f243a..320a8c631 100644
--- a/partitioned-burgers-1d/solver-scipy/clean.sh
+++ b/partitioned-burgers-1d/solver-scipy/clean.sh
@@ -6,3 +6,4 @@ set -e -u
 
 clean_case_logs .
 rm -f full_domain.npz
+rm -f ../initial_condition.npz
diff --git a/tools/clean-tutorial-base.sh b/tools/clean-tutorial-base.sh
index 5d8a0ba74..1f050ad1c 100755
--- a/tools/clean-tutorial-base.sh
+++ b/tools/clean-tutorial-base.sh
@@ -12,4 +12,4 @@ clean_tutorial .
 clean_precice_logs .
 rm -fv ./*.log
 rm -fv ./*.vtu
-
+rm -rf output/

From 784d0774c9472266cd2416de9c7b73896eacf613 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <gerasimos.chourdakis@ipvs.uni-stuttgart.de>
Date: Thu, 2 Jul 2026 11:20:22 +0200
Subject: [PATCH 2/6] Make partitioned-heat-conduction-3d/clean-tutorial.sh a
 link

---
 partitioned-heat-conduction-3d/clean-tutorial.sh | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)
 mode change 100755 => 120000 partitioned-heat-conduction-3d/clean-tutorial.sh

diff --git a/partitioned-heat-conduction-3d/clean-tutorial.sh b/partitioned-heat-conduction-3d/clean-tutorial.sh
deleted file mode 100755
index 56e40d689..000000000
--- a/partitioned-heat-conduction-3d/clean-tutorial.sh
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env sh
-set -e -u
-
-# shellcheck disable=SC1091
-. ../tools/cleaning-tools.sh
-
-clean_tutorial .
-clean_precice_logs .
-rm -fv ./*.log
-
diff --git a/partitioned-heat-conduction-3d/clean-tutorial.sh b/partitioned-heat-conduction-3d/clean-tutorial.sh
new file mode 120000
index 000000000..4713f5092
--- /dev/null
+++ b/partitioned-heat-conduction-3d/clean-tutorial.sh
@@ -0,0 +1 @@
+../tools/clean-tutorial-base.sh
\ No newline at end of file

From 47e4964af1abdb80608fec8df8d4c10f0a7a42c2 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <gerasimos.chourdakis@ipvs.uni-stuttgart.de>
Date: Thu, 2 Jul 2026 11:21:45 +0200
Subject: [PATCH 3/6] Make partitioned-heat-conduction-direct/clean-tutorial.sh
 a link

---
 .../clean-tutorial.sh                               | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)
 mode change 100755 => 120000 partitioned-heat-conduction-direct/clean-tutorial.sh

diff --git a/partitioned-heat-conduction-direct/clean-tutorial.sh b/partitioned-heat-conduction-direct/clean-tutorial.sh
deleted file mode 100755
index 1230bc6bc..000000000
--- a/partitioned-heat-conduction-direct/clean-tutorial.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env sh
-set -e -u
-
-# Determine the tutorial directory (where the symlink is located)
-TUTORIAL_DIR="$(cd "$(dirname "$0")" && pwd)"
-cd "$TUTORIAL_DIR"
-
-# shellcheck disable=SC1091
-. ../tools/cleaning-tools.sh
-
-clean_tutorial .
-
diff --git a/partitioned-heat-conduction-direct/clean-tutorial.sh b/partitioned-heat-conduction-direct/clean-tutorial.sh
new file mode 120000
index 000000000..4713f5092
--- /dev/null
+++ b/partitioned-heat-conduction-direct/clean-tutorial.sh
@@ -0,0 +1 @@
+../tools/clean-tutorial-base.sh
\ No newline at end of file

From dd42c5c165b772dd0ed1003316cddb0329d6f6e9 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <gerasimos.chourdakis@ipvs.uni-stuttgart.de>
Date: Thu, 2 Jul 2026 11:22:50 +0200
Subject: [PATCH 4/6] Make partitioned-pipe-multiscale/clean-tutorial.sh a link

---
 partitioned-pipe-multiscale/clean-tutorial.sh | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)
 mode change 100755 => 120000 partitioned-pipe-multiscale/clean-tutorial.sh

diff --git a/partitioned-pipe-multiscale/clean-tutorial.sh b/partitioned-pipe-multiscale/clean-tutorial.sh
deleted file mode 100755
index 5dbb6c639..000000000
--- a/partitioned-pipe-multiscale/clean-tutorial.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env sh
-set -e -u
-
-# shellcheck disable=SC1091
-. ../tools/cleaning-tools.sh
-
-clean_tutorial .
-clean_precice_logs .
-rm -fv ./*.log
-rm -fv ./*.vtu
-
diff --git a/partitioned-pipe-multiscale/clean-tutorial.sh b/partitioned-pipe-multiscale/clean-tutorial.sh
new file mode 120000
index 000000000..4713f5092
--- /dev/null
+++ b/partitioned-pipe-multiscale/clean-tutorial.sh
@@ -0,0 +1 @@
+../tools/clean-tutorial-base.sh
\ No newline at end of file

From d0c2accf09f57b7819e80c919d131d1354bdd003 Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <gerasimos.chourdakis@ipvs.uni-stuttgart.de>
Date: Thu, 2 Jul 2026 11:23:36 +0200
Subject: [PATCH 5/6] Make partitioned-pipe-multiscale/clean-tutorial.sh a link

---
 water-hammer/clean-tutorial.sh | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)
 mode change 100755 => 120000 water-hammer/clean-tutorial.sh

diff --git a/water-hammer/clean-tutorial.sh b/water-hammer/clean-tutorial.sh
deleted file mode 100755
index 5dbb6c639..000000000
--- a/water-hammer/clean-tutorial.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/env sh
-set -e -u
-
-# shellcheck disable=SC1091
-. ../tools/cleaning-tools.sh
-
-clean_tutorial .
-clean_precice_logs .
-rm -fv ./*.log
-rm -fv ./*.vtu
-
diff --git a/water-hammer/clean-tutorial.sh b/water-hammer/clean-tutorial.sh
new file mode 120000
index 000000000..4713f5092
--- /dev/null
+++ b/water-hammer/clean-tutorial.sh
@@ -0,0 +1 @@
+../tools/clean-tutorial-base.sh
\ No newline at end of file

From b34cbc3693a0ada4572f277d685845732488faff Mon Sep 17 00:00:00 2001
From: Gerasimos Chourdakis <gerasimos.chourdakis@ipvs.uni-stuttgart.de>
Date: Thu, 2 Jul 2026 11:25:57 +0200
Subject: [PATCH 6/6] Switch some remaining scripts to /usr/bin/env bash

---
 partitioned-pipe-multiscale/set-case.sh      | 2 +-
 perpendicular-flap-stress/solid-gismo/run.sh | 2 +-
 water-hammer/set-case.sh                     | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/partitioned-pipe-multiscale/set-case.sh b/partitioned-pipe-multiscale/set-case.sh
index ea4bad095..f38857eb3 100755
--- a/partitioned-pipe-multiscale/set-case.sh
+++ b/partitioned-pipe-multiscale/set-case.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -e -u
 
 if [ "$1" = "1d3d" ]; then
diff --git a/perpendicular-flap-stress/solid-gismo/run.sh b/perpendicular-flap-stress/solid-gismo/run.sh
index 624de5f23..ac9a29c2b 100755
--- a/perpendicular-flap-stress/solid-gismo/run.sh
+++ b/perpendicular-flap-stress/solid-gismo/run.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -e -u
 
 . ../../tools/log.sh
diff --git a/water-hammer/set-case.sh b/water-hammer/set-case.sh
index ea4bad095..f38857eb3 100755
--- a/water-hammer/set-case.sh
+++ b/water-hammer/set-case.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -e -u
 
 if [ "$1" = "1d3d" ]; then