diff --git a/Makefile.am b/Makefile.am
index 576124d7..5be2caa8 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -115,6 +115,7 @@ swupd_SOURCES = \
 	src/swupd_lib/hashdump.c \
 	src/swupd_lib/helpers.c \
 	src/swupd_lib/heuristics.c \
+	src/swupd_lib/heuristics.h \
 	src/swupd_lib/lock.c \
 	src/swupd_lib/manifest.c \
 	src/swupd_lib/manifest.h \
diff --git a/src/cmds/bundle_add.c b/src/cmds/bundle_add.c
index 6515d486..f726fff1 100644
--- a/src/cmds/bundle_add.c
+++ b/src/cmds/bundle_add.c
@@ -33,6 +33,7 @@
 #include "swupd_lib/alias.h"
 #include "swupd.h"
 #include "swupd_lib/target_root.h"
+#include "swupd_lib/heuristics.h"
 
 #define MODE_RW_O (S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH)
 #define VERIFY_NOPICKY 0
@@ -217,15 +218,8 @@ static int compute_bundle_dependecies(struct manifest *mom, struct list *bundles
 
 static enum swupd_code apply_heuristics_for_new_files(struct list *files)
 {
-	struct list *iter;
-	struct file *file;
-
 	timelist_timer_start(globals.global_times, "Applying heuristics");
-	for (iter = files; iter; iter = iter->next) {
-		file = iter->data;
-		(void)ignore(file);
-		apply_heuristics(file);
-	}
+	heuristics_apply(files);
 	timelist_timer_stop(globals.global_times);
 
 	return SWUPD_OK;
diff --git a/src/cmds/update.c b/src/cmds/update.c
index a0b4d4a8..654ae813 100644
--- a/src/cmds/update.c
+++ b/src/cmds/update.c
@@ -34,6 +34,7 @@
 #include "swupd.h"
 #include "swupd_lib/signature.h"
 #include "swupd_lib/target_root.h"
+#include "swupd_lib/heuristics.h"
 
 #define FLAG_DOWNLOAD_ONLY 2000
 #define FLAG_UPDATE_SEARCH_FILE_INDEX 2001
@@ -243,11 +244,6 @@ static struct list *create_update_list(struct manifest *server)
 		 * files, so they will not have a peer. */
 		if (!file->peer ||
 		    (file->peer && file->last_change > file->peer->last_change)) {
-			/* check and if needed mark as do_not_update */
-			(void)ignore(file);
-			/* check if we need to run scripts/update the bootloader/etc */
-			apply_heuristics(file);
-
 			output = list_prepend_data(output, file);
 			continue;
 		}
@@ -415,6 +411,9 @@ enum swupd_code execute_update_extra(extra_proc_fn_t post_update_fn, extra_proc_
 	print_statistics(current_version, server_version);
 	timelist_timer_stop(globals.global_times); // closing: Create update list
 
+	timelist_timer_start(globals.global_times, "Applying heuristics");
+	heuristics_apply(updates);
+	timelist_timer_stop(globals.global_times); // closing: Applying heuristics
 	/* downloading and applying updates */
 	/* need update list in filename order to insure directories are
 	 * created before their contents */
diff --git a/src/cmds/verify.c b/src/cmds/verify.c
index 0ab0994e..1f3cb4bb 100644
--- a/src/cmds/verify.c
+++ b/src/cmds/verify.c
@@ -35,6 +35,7 @@
 #include "swupd.h"
 #include "swupd_lib/signature.h"
 #include "swupd_lib/target_root.h"
+#include "swupd_lib/heuristics.h"
 
 #define FLAG_EXTRA_FILES_ONLY 2000
 #define FLAG_FILE 2001
@@ -369,8 +370,7 @@ static void add_missing_files(struct manifest *official_manifest, struct list *f
 		iter = iter->next;
 		complete++;
 
-		if ((file->is_deleted) ||
-		    (file->do_not_update)) {
+		if (file->is_deleted || file->do_not_update) {
 			goto progress;
 		}
 
@@ -439,7 +439,7 @@ static void check_and_fix_one(struct file *file, struct manifest *official_manif
 	char *fullname;
 
 	// Note: boot files not marked as deleted are candidates for verify/fix
-	if (file->is_deleted || ignore(file) || file->do_not_update) {
+	if (file->is_deleted || file->do_not_update) {
 		return;
 	}
 
@@ -563,17 +563,14 @@ static void remove_orphaned_files(struct list *files_to_verify, bool repair)
 		iter = iter->next;
 		complete++;
 
-		/* Do not remove files that have not been deleted, are config files, or
-		 * are marked as ghosted */
-		if (!file->is_deleted || file->is_config || file->is_ghosted) {
-			goto progress;
-		}
-
-		/* Note: boot files marked as deleted should not be deleted by
-		 * verify/fix; this task is delegated to an external program
-		 * (currently /usr/bin/clr-boot-manager).
+		/*
+		 * Don't remove files set as do_not_update, like:
+		 *  - Config files
+		 *  - ghosted files
+		 *  - boot files, that should be managed by the external tool
+		 *    clr-boot-manager
 		 */
-		if (ignore(file)) {
+		if (!file->is_deleted || file->do_not_update) {
 			goto progress;
 		}
 
@@ -899,6 +896,15 @@ static struct list *keep_matching_path(struct list *all_files)
 	return list_head(matching_files);
 }
 
+static enum swupd_code apply_heuristics_for_files(struct list *files)
+{
+	timelist_timer_start(globals.global_times, "Applying heuristics");
+	heuristics_apply(files);
+	timelist_timer_stop(globals.global_times);
+
+	return SWUPD_OK;
+}
+
 /* This function does a simple verification of files listed in the
  * subscribed bundle manifests.  If the optional "fix" or "install" parameter
  * is specified, the disk will be modified at each point during the
@@ -1176,6 +1182,7 @@ enum swupd_code execute_verify_extra(extra_proc_fn_t post_verify_fn)
 			goto extra_files;
 		}
 	}
+	apply_heuristics_for_files(files_to_verify);
 
 	if (cmdline_option_extra_files_only) {
 		/* user wants to deal only with the extra files, so skip everything else */
diff --git a/src/swupd.h b/src/swupd.h
index 20b17917..02609e84 100644
--- a/src/swupd.h
+++ b/src/swupd.h
@@ -169,9 +169,6 @@ extern bool get_distribution_string(char *path_prefix, char *dist);
 extern int get_current_format(void);
 extern int get_server_format(int server_version);
 
-extern bool ignore(struct file *file);
-extern void apply_heuristics(struct file *file);
-
 extern struct manifest *load_mom(int version, int *err);
 extern struct manifest *load_manifest(int version, struct file *file, struct manifest *mom, bool header_only, int *err);
 extern void link_manifests(struct manifest *m1, struct manifest *m2);
diff --git a/src/swupd_lib/heuristics.c b/src/swupd_lib/heuristics.c
index 03b9e640..005a643e 100644
--- a/src/swupd_lib/heuristics.c
+++ b/src/swupd_lib/heuristics.c
@@ -27,6 +27,7 @@
 #include <unistd.h>
 
 #include "swupd.h"
+#include "heuristics.h"
 
 /* trailing slash is to indicate dir itself is expected to exist, but
  * contents are ignored */
@@ -124,21 +125,13 @@ static void boot_manager_heuristics(struct file *file)
 	}
 }
 
-void apply_heuristics(struct file *file)
-{
-	runtime_state_heuristics(file);
-	boot_file_heuristics(file);
-	config_file_heuristics(file);
-	boot_manager_heuristics(file);
-}
-
 /* Determines whether or not FILE should be ignored for this swupd action. Note
  * that boot files are ignored only if they are marked as deleted; this does
  * not happen in current manifests produced by swupd-server, but this check is
  * enabled in case swupd-server ever allows for deleted boot files in manifests
  * in the future.
  */
-bool ignore(struct file *file)
+static void check_ignore_file(struct file *file)
 {
 	if ((OS_IS_STATELESS && file->is_config) ||
 	    (OS_IS_STATELESS && is_config(file->filename)) || // ideally we trust the manifest but short term reapply check here
@@ -148,8 +141,25 @@ bool ignore(struct file *file)
 	    (file->is_orphan) ||
 	    (file->is_ghosted)) {
 		file->do_not_update = 1;
-		return true;
 	}
-
-	return false;
+}
+
+static void apply_heuristics_for_file(struct file *file)
+{
+	runtime_state_heuristics(file);
+	boot_file_heuristics(file);
+	config_file_heuristics(file);
+	boot_manager_heuristics(file);
+	check_ignore_file(file);
+}
+
+void heuristics_apply(struct list *files)
+{
+	struct list *iter;
+	struct file *file;
+
+	for (iter = files; iter; iter = iter->next) {
+		file = iter->data;
+		apply_heuristics_for_file(file);
+	}
 }
diff --git a/src/swupd_lib/heuristics.h b/src/swupd_lib/heuristics.h
new file mode 100644
index 00000000..70931e2b
--- /dev/null
+++ b/src/swupd_lib/heuristics.h
@@ -0,0 +1,35 @@
+#ifndef __HEURISTICS__
+#define __HEURISTICS__
+
+/**
+ * @file
+ * @brief Heuristics system to define which scripts to run and which files to
+ * ignore on installation time.
+ */
+
+#include <stdbool.h>
+#include <stdint.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/**
+ * @brief Use heuristics to define which files should be updated and which
+ * scripts should be executed.
+ *
+ * Use the path and properties of the file to define it's type and by that
+ * define if the file should be set with a do_not_update flag or is_boot flag.
+ * Also use that information to check if the bootloader or systemd update
+ * scripts should be executed.
+ *
+ * @param files The list of struct file objects where swupd heuristics will be
+ * applied.
+ */
+void heuristics_apply(struct list *files);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif