diff --git a/.codechecker.json b/.codechecker.json
deleted file mode 100644
index 6e07a33350999cd211e8b5b573d484517d2ab890..0000000000000000000000000000000000000000
--- a/.codechecker.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
-  "analyze": [
-    "--analyzers=clang-tidy",
-    "--file=*/dune-common/*.cc"
-  ],
-  "parse": [
-    "--file=*/dune-common/*"
-  ]
-}
diff --git a/.codechecker/config.json b/.codechecker/config.json
new file mode 100644
index 0000000000000000000000000000000000000000..95a596d2783f17903385a23dc08062d483777930
--- /dev/null
+++ b/.codechecker/config.json
@@ -0,0 +1,12 @@
+{
+  "analyze": [
+    "--disable", "default",
+    "--analyzers=clang-tidy",
+    "--file=*/dune-common/*.cc",
+    "--skip", ".codechecker/skipfile",
+    "-e", "misc-include-cleaner"
+  ],
+  "parse": [
+    "--file=*/dune-common/*"
+  ]
+}
diff --git a/.codechecker.json.license b/.codechecker/config.json.license
similarity index 100%
rename from .codechecker.json.license
rename to .codechecker/config.json.license
diff --git a/.codechecker/skipfile b/.codechecker/skipfile
new file mode 100644
index 0000000000000000000000000000000000000000..2b72d18881b88c8f6636a61b33ecfb237debeaa6
--- /dev/null
+++ b/.codechecker/skipfile
@@ -0,0 +1,2 @@
+-*/densematrixassignmenttest.cc
+-*/genericiterator_compile_fail.cc
diff --git a/.codechecker/skipfile.license b/.codechecker/skipfile.license
new file mode 100644
index 0000000000000000000000000000000000000000..ab53c287aa3ac0813eb9af172f0a542bae67f6ba
--- /dev/null
+++ b/.codechecker/skipfile.license
@@ -0,0 +1,2 @@
+SPDX-FileCopyrightInfo: Copyright © DUNE Project contributors, see file LICENSE.md in module root
+SPDX-License-Identifier: LicenseRef-GPL-2.0-only-with-DUNE-exception
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index dc2692395be2a68e59058e15a88325d98a626368..4b5ddaa5afdafd7c1c30554f3046db68583ebdbf 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -48,8 +48,8 @@ debian:11 clang-11-20-nobindings:
   extends: .common
   after_script:
     - source /duneci/venv/bin/activate
-    - CodeChecker analyze build-cmake/compile_commands.json --config .codechecker.json -o ./reports || echo "CodeChecker analyzer failed with exit status $?"
-    - CodeChecker parse --config .codechecker.json --trim-path-prefix $PWD -e codeclimate ./reports > ./reports/gl-code-quality-report.json || echo "CodeChecker parser failed with exit status $?"
+    - CodeChecker analyze build-cmake/compile_commands.json --config .codechecker/config.json -o ./reports || echo "CodeChecker analyzer failed with exit status $?"
+    - CodeChecker parse --config .codechecker/config.json --trim-path-prefix $PWD -e codeclimate ./reports > ./reports/gl-code-quality-report.json || echo "CodeChecker parser failed with exit status $?"
   image: registry.dune-project.org/docker/ci/debian:11
   variables:
     DUNECI_TOOLCHAIN: clang-11-20