diff --git a/doxygen/mbedtls.doxyfile b/doxygen/mbedtls.doxyfile
index f2f660366..8ba8fd3ac 100644
--- a/doxygen/mbedtls.doxyfile
+++ b/doxygen/mbedtls.doxyfile
@@ -664,7 +664,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = ..
+INPUT                  = ../include input
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -696,7 +696,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = ../configs ../yotta/module
+EXCLUDE                =
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
diff --git a/tests/scripts/all.sh b/tests/scripts/all.sh
index fed631f24..a07060e82 100755
--- a/tests/scripts/all.sh
+++ b/tests/scripts/all.sh
@@ -416,25 +416,25 @@ OPENSSL="$OPENSSL" OPENSSL_LEGACY="$OPENSSL_LEGACY" GNUTLS_CLI="$GNUTLS_CLI" \
     ARMC6_CC="$ARMC6_CC" RUN_ARMCC="$RUN_ARMCC" scripts/output_env.sh
 
 msg "test: recursion.pl" # < 1s
-tests/scripts/recursion.pl library/*.c
+record_status tests/scripts/recursion.pl library/*.c
 
 msg "test: freshness of generated source files" # < 1s
-tests/scripts/check-generated-files.sh
+record_status tests/scripts/check-generated-files.sh
 
 msg "test: doxygen markup outside doxygen blocks" # < 1s
-tests/scripts/check-doxy-blocks.pl
+record_status tests/scripts/check-doxy-blocks.pl
 
 msg "test: check-files.py" # < 1s
 cleanup
-tests/scripts/check-files.py
+record_status tests/scripts/check-files.py
 
 msg "test/build: declared and exported names" # < 3s
 cleanup
-tests/scripts/check-names.sh
+record_status tests/scripts/check-names.sh
 
 msg "test: doxygen warnings" # ~ 3s
 cleanup
-tests/scripts/doxygen.sh
+record_status tests/scripts/doxygen.sh
 
 
 
@@ -511,10 +511,10 @@ msg "test: RSA_NO_CRT - main suites (inc. selftests) (ASan build)" # ~ 50s
 make test
 
 msg "test: RSA_NO_CRT - RSA-related part of ssl-opt.sh (ASan build)" # ~ 5s
-tests/ssl-opt.sh -f RSA
+if_build_succeeded tests/ssl-opt.sh -f RSA
 
 msg "test: RSA_NO_CRT - RSA-related part of compat.sh (ASan build)" # ~ 3 min
-tests/compat.sh -t RSA
+if_build_succeeded tests/compat.sh -t RSA
 
 msg "build: cmake, full config, clang" # ~ 50s
 cleanup
diff --git a/tests/scripts/check-files.py b/tests/scripts/check-files.py
index f560d0378..0fb2117a3 100755
--- a/tests/scripts/check-files.py
+++ b/tests/scripts/check-files.py
@@ -155,6 +155,12 @@ class IntegrityChecker(object):
             ".c", ".h", ".sh", ".pl", ".py", ".md", ".function", ".data",
             "Makefile", "CMakeLists.txt", "ChangeLog"
         )
+        self.excluded_directories = ['.git', 'mbed-os']
+        self.excluded_paths = list(map(os.path.normpath, [
+            'cov-int',
+            'examples',
+            'yotta/module'
+        ]))
         self.issues_to_check = [
             PermissionIssueTracker(),
             EndOfFileNewlineIssueTracker(),
@@ -179,12 +185,19 @@ class IntegrityChecker(object):
             console = logging.StreamHandler()
             self.logger.addHandler(console)
 
+    def prune_branch(self, root, d):
+        if d in self.excluded_directories:
+            return True
+        if os.path.normpath(os.path.join(root, d)) in self.excluded_paths:
+            return True
+        return False
+
     def check_files(self):
-        for root, dirs, files in sorted(os.walk(".")):
+        for root, dirs, files in os.walk("."):
+            dirs[:] = sorted(d for d in dirs if not self.prune_branch(root, d))
             for filename in sorted(files):
                 filepath = os.path.join(root, filename)
-                if (os.path.join("yotta", "module") in filepath or
-                        not filepath.endswith(self.files_to_check)):
+                if not filepath.endswith(self.files_to_check):
                     continue
                 for issue_to_check in self.issues_to_check:
                     if issue_to_check.should_check_file(filepath):