diff --git a/test/blackbox-tests/test-cases/rocq-native/compose-installed-compat.t/run.t b/test/blackbox-tests/test-cases/rocq-native/compose-installed-compat.t/run.t
index f9f97592b1e..3673f47e11b 100644
--- a/test/blackbox-tests/test-cases/rocq-native/compose-installed-compat.t/run.t
+++ b/test/blackbox-tests/test-cases/rocq-native/compose-installed-compat.t/run.t
@@ -42,7 +42,7 @@ so this also tests that it won't be a problem.
 
 
 Next we go into our Dune project and build it.
-  $ dune build --root A
+  $ dune build --trace-file trace.json --root A
   Entering directory 'A'
   Inductive hello : Set :=
       I : hello | am : hello | an : hello | install : hello | loc : hello.
@@ -50,20 +50,52 @@ Next we go into our Dune project and build it.
 
 Now we check the flags that were passed to coqdep and coqc:
 
-  $ tail -4 A/_build/log | head -2 | ../scrub_coq_args.sh
-  rocq dep
-  -boot
-  -R coq/theories Corelib
-  -Q $TESTCASE_ROOT/lib/coq/user-contrib/B B
-  -R . A -dyndep opt -vos a.v >
-  _build/default/.A.theory.d
-  rocq compile -q
-  -w -deprecated-native-compiler-option -native-output-dir .
-  -native-compiler on
-  -nI lib/rocq-runtime/kernel
-  -nI .
-  -boot
-  -R coq/theories Corelib
-  -Q $TESTCASE_ROOT/lib/coq/user-contrib/B B
-  -R . A
-  a.v
+  $ jq '.[] | select(.cat == "process" and (.args.process_args.[0] | IN ("compile", "dep"))) | {name, args: (.args.process_args | map(sub(".*/coq-core"; "coq-core")))}' trace.json
+  {
+    "name": "rocq",
+    "args": [
+      "dep",
+      "-boot",
+      "-R",
+      "$TESTCASE_ROOT/lib/coq/theories",
+      "Corelib",
+      "-Q",
+      "$TESTCASE_ROOT/lib/coq/user-contrib/B",
+      "B",
+      "-R",
+      ".",
+      "A",
+      "-dyndep",
+      "opt",
+      "-vos",
+      "a.v"
+    ]
+  }
+  {
+    "name": "rocq",
+    "args": [
+      "compile",
+      "-q",
+      "-w",
+      "-deprecated-native-compiler-option",
+      "-native-output-dir",
+      ".",
+      "-native-compiler",
+      "on",
+      "-nI",
+      "/home/runner/work/dune/dune/_opam/lib/rocq-runtime/kernel",
+      "-nI",
+      ".",
+      "-boot",
+      "-R",
+      "$TESTCASE_ROOT/lib/coq/theories",
+      "Corelib",
+      "-Q",
+      "$TESTCASE_ROOT/lib/coq/user-contrib/B",
+      "B",
+      "-R",
+      ".",
+      "A",
+      "a.v"
+    ]
+  }
diff --git a/test/blackbox-tests/test-cases/rocq-native/coqtop/coqtop-flags.t/run.t b/test/blackbox-tests/test-cases/rocq-native/coqtop/coqtop-flags.t/run.t
index 9a0a42aa7aa..42ce25d9b6a 100644
--- a/test/blackbox-tests/test-cases/rocq-native/coqtop/coqtop-flags.t/run.t
+++ b/test/blackbox-tests/test-cases/rocq-native/coqtop/coqtop-flags.t/run.t
@@ -1,17 +1,29 @@
 Testing that the correct flags are being passed to dune rocq top
 
 The flags passed to coqc:
-  $ dune build && tail -1 _build/log | ../../scrub_coq_args.sh
-  rocq compile
-  -w -notation-overridden
-  -w -deprecated-native-compiler-option -native-output-dir .
-  -native-compiler on
-  -nI lib/rocq-runtime/kernel
-  -nI .
-  -boot
-  -R coq/theories Corelib
-  -R . minimal
-  Test.v
+  $ dune build --trace-file trace.json
+  $ jq '.[] | select(.cat == "process" and (.args.process_args.[0] == "compile")) | .args.process_args | .[] | sub(".*/coq/theories"; "coq/theories") | sub(".*/rocq-runtime/"; "rocq-runtime/")' trace.json
+  "compile"
+  "-w"
+  "-notation-overridden"
+  "-w"
+  "-deprecated-native-compiler-option"
+  "-native-output-dir"
+  "."
+  "-native-compiler"
+  "on"
+  "-nI"
+  "rocq-runtime/kernel"
+  "-nI"
+  "."
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "minimal"
+  "Test.v"
 
 The flags passed to coqtop:
   $ dune rocq top --toplevel=echo Test.v | ../../scrub_coq_args.sh
diff --git a/test/blackbox-tests/test-cases/rocq-native/flags.t b/test/blackbox-tests/test-cases/rocq-native/flags.t
index d8c02c0bcd7..79c4b043de5 100644
--- a/test/blackbox-tests/test-cases/rocq-native/flags.t
+++ b/test/blackbox-tests/test-cases/rocq-native/flags.t
@@ -9,6 +9,12 @@ Test cases to check Coq's flag setting is correct:
   > Definition t := 3.
   > EOF
 
+  $ runFlags() {
+  > dune clean
+  > dune build --trace-file trace.json foo.vo
+  > jq -c '.[] | select(.name == "rocq") | .args.process_args | .[] | sub(".*/coq/"; "coq/") | sub(".*/rocq-runtime/"; "rocq-runtime/")' trace.json
+  > }
+
 Test case: default flags
 
   $ cat > dune <<EOF
@@ -16,16 +22,40 @@ Test case: default flags
   >  (name foo))
   > EOF
 
-  $ dune build foo.vo && tail -n 1 _build/log | ./scrub_coq_args.sh
-  rocq compile -q
-  -w -deprecated-native-compiler-option -native-output-dir .
-  -native-compiler on
-  -nI lib/rocq-runtime/kernel
-  -nI .
-  -boot
-  -R coq/theories Corelib
-  -R . foo
-  foo.v
+  $ runFlags
+  "--config"
+  "dep"
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "-dyndep"
+  "opt"
+  "-vos"
+  "foo.v"
+  "compile"
+  "-q"
+  "-w"
+  "-deprecated-native-compiler-option"
+  "-native-output-dir"
+  "."
+  "-native-compiler"
+  "on"
+  "-nI"
+  "rocq-runtime/kernel"
+  "-nI"
+  "."
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "foo.v"
 
 TC: :standard
 
@@ -35,17 +65,40 @@ TC: :standard
   >  (flags :standard))
   > EOF
 
-  $ rm _build/default/foo.vo
-  $ dune build foo.vo && tail -n 1 _build/log | ./scrub_coq_args.sh
-  rocq compile -q
-  -w -deprecated-native-compiler-option -native-output-dir .
-  -native-compiler on
-  -nI lib/rocq-runtime/kernel
-  -nI .
-  -boot
-  -R coq/theories Corelib
-  -R . foo
-  foo.v
+  $ runFlags
+  "--config"
+  "dep"
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "-dyndep"
+  "opt"
+  "-vos"
+  "foo.v"
+  "compile"
+  "-q"
+  "-w"
+  "-deprecated-native-compiler-option"
+  "-native-output-dir"
+  "."
+  "-native-compiler"
+  "on"
+  "-nI"
+  "rocq-runtime/kernel"
+  "-nI"
+  "."
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "foo.v"
 
 TC: override :standard
 
@@ -55,16 +108,39 @@ TC: override :standard
   >  (flags ))
   > EOF
 
-  $ dune build foo.vo && tail -n 1 _build/log | ./scrub_coq_args.sh
-  rocq compile
-  -w -deprecated-native-compiler-option -native-output-dir .
-  -native-compiler on
-  -nI lib/rocq-runtime/kernel
-  -nI .
-  -boot
-  -R coq/theories Corelib
-  -R . foo
-  foo.v
+  $ runFlags
+  "--config"
+  "dep"
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "-dyndep"
+  "opt"
+  "-vos"
+  "foo.v"
+  "compile"
+  "-w"
+  "-deprecated-native-compiler-option"
+  "-native-output-dir"
+  "."
+  "-native-compiler"
+  "on"
+  "-nI"
+  "rocq-runtime/kernel"
+  "-nI"
+  "."
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "foo.v"
 
 TC: add to :standard
 
@@ -74,16 +150,41 @@ TC: add to :standard
   >  (flags :standard -type-in-type))
   > EOF
 
-  $ dune build foo.vo && tail -n 1 _build/log | ./scrub_coq_args.sh
-  rocq compile -q -type-in-type
-  -w -deprecated-native-compiler-option -native-output-dir .
-  -native-compiler on
-  -nI lib/rocq-runtime/kernel
-  -nI .
-  -boot
-  -R coq/theories Corelib
-  -R . foo
-  foo.v
+  $ runFlags
+  "--config"
+  "dep"
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "-dyndep"
+  "opt"
+  "-vos"
+  "foo.v"
+  "compile"
+  "-q"
+  "-type-in-type"
+  "-w"
+  "-deprecated-native-compiler-option"
+  "-native-output-dir"
+  "."
+  "-native-compiler"
+  "on"
+  "-nI"
+  "rocq-runtime/kernel"
+  "-nI"
+  "."
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "foo.v"
 
 TC: extend in workspace + override standard
 
@@ -98,16 +199,40 @@ TC: extend in workspace + override standard
   > (env (dev (rocq (flags -type-in-type))))
   > EOF
 
-  $ dune build foo.vo && tail -n 1 _build/log | ./scrub_coq_args.sh
-  rocq compile -type-in-type
-  -w -deprecated-native-compiler-option -native-output-dir .
-  -native-compiler on
-  -nI lib/rocq-runtime/kernel
-  -nI .
-  -boot
-  -R coq/theories Corelib
-  -R . foo
-  foo.v
+  $ runFlags
+  "--config"
+  "dep"
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "-dyndep"
+  "opt"
+  "-vos"
+  "foo.v"
+  "compile"
+  "-type-in-type"
+  "-w"
+  "-deprecated-native-compiler-option"
+  "-native-output-dir"
+  "."
+  "-native-compiler"
+  "on"
+  "-nI"
+  "rocq-runtime/kernel"
+  "-nI"
+  "."
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "foo.v"
 
 TC: extend in workspace + override standard
 
@@ -116,16 +241,41 @@ TC: extend in workspace + override standard
   > (env (dev (rocq (flags :standard -type-in-type))))
   > EOF
 
-  $ dune build foo.vo && tail -n 1 _build/log | ./scrub_coq_args.sh
-  rocq compile -q -type-in-type
-  -w -deprecated-native-compiler-option -native-output-dir .
-  -native-compiler on
-  -nI lib/rocq-runtime/kernel
-  -nI .
-  -boot
-  -R coq/theories Corelib
-  -R . foo
-  foo.v
+  $ runFlags
+  "--config"
+  "dep"
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "-dyndep"
+  "opt"
+  "-vos"
+  "foo.v"
+  "compile"
+  "-q"
+  "-type-in-type"
+  "-w"
+  "-deprecated-native-compiler-option"
+  "-native-output-dir"
+  "."
+  "-native-compiler"
+  "on"
+  "-nI"
+  "rocq-runtime/kernel"
+  "-nI"
+  "."
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "foo.v"
 
 TC: extend in dune (env) + override standard
 
@@ -135,17 +285,40 @@ TC: extend in dune (env) + override standard
   > (env (dev (rocq (flags -type-in-type))))
   > EOF
 
-  $ rm -rf _build/default/foo.vo
-  $ dune build foo.vo && tail -n 1 _build/log | ./scrub_coq_args.sh
-  rocq compile -type-in-type
-  -w -deprecated-native-compiler-option -native-output-dir .
-  -native-compiler on
-  -nI lib/rocq-runtime/kernel
-  -nI .
-  -boot
-  -R coq/theories Corelib
-  -R . foo
-  foo.v
+  $ runFlags
+  "--config"
+  "dep"
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "-dyndep"
+  "opt"
+  "-vos"
+  "foo.v"
+  "compile"
+  "-type-in-type"
+  "-w"
+  "-deprecated-native-compiler-option"
+  "-native-output-dir"
+  "."
+  "-native-compiler"
+  "on"
+  "-nI"
+  "rocq-runtime/kernel"
+  "-nI"
+  "."
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "foo.v"
 
 TC: extend in dune (env) + standard
 
@@ -155,17 +328,42 @@ TC: extend in dune (env) + standard
   > (env (dev (rocq (flags :standard -type-in-type))))
   > EOF
 
-  $ rm -rf _build/default/foo.vo
-  $ dune build foo.vo && tail -n 1 _build/log | ./scrub_coq_args.sh
-  rocq compile -q -type-in-type -type-in-type
-  -w -deprecated-native-compiler-option -native-output-dir .
-  -native-compiler on
-  -nI lib/rocq-runtime/kernel
-  -nI .
-  -boot
-  -R coq/theories Corelib
-  -R . foo
-  foo.v
+  $ runFlags
+  "--config"
+  "dep"
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "-dyndep"
+  "opt"
+  "-vos"
+  "foo.v"
+  "compile"
+  "-q"
+  "-type-in-type"
+  "-type-in-type"
+  "-w"
+  "-deprecated-native-compiler-option"
+  "-native-output-dir"
+  "."
+  "-native-compiler"
+  "on"
+  "-nI"
+  "rocq-runtime/kernel"
+  "-nI"
+  "."
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "foo.v"
 
 TC: extend in dune (env) + workspace + standard
 
@@ -180,14 +378,39 @@ TC: extend in dune (env) + workspace + standard
   > (env (dev (rocq (flags :standard -type-in-type))))
   > EOF
 
-  $ rm -rf _build/default/foo.vo
-  $ dune build foo.vo && tail -n 1 _build/log | ./scrub_coq_args.sh
-  rocq compile -q -type-in-type -bt
-  -w -deprecated-native-compiler-option -native-output-dir .
-  -native-compiler on
-  -nI lib/rocq-runtime/kernel
-  -nI .
-  -boot
-  -R coq/theories Corelib
-  -R . foo
-  foo.v
+  $ runFlags
+  "--config"
+  "dep"
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "-dyndep"
+  "opt"
+  "-vos"
+  "foo.v"
+  "compile"
+  "-q"
+  "-type-in-type"
+  "-bt"
+  "-w"
+  "-deprecated-native-compiler-option"
+  "-native-output-dir"
+  "."
+  "-native-compiler"
+  "on"
+  "-nI"
+  "rocq-runtime/kernel"
+  "-nI"
+  "."
+  "-boot"
+  "-R"
+  "coq/theories"
+  "Corelib"
+  "-R"
+  "."
+  "foo"
+  "foo.v"