diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c7b7034..bd66da0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,7 +11,8 @@ exclude: |
     .*\.o|
     flake.lock|
     dependencies.lock|
-    assets/case/
+    assets/case/|
+    docs/doxygen/
   )
 
 repos:
@@ -113,7 +114,8 @@ repos:
         name: doxygen code coverage
         language: system
         entry: tools/doxy-coverage.py
-        args: [docs/doxygen/xml, --threshold=40, --summary-only]
+        args:
+          [docs/doxygen/xml, --threshold=40, --summary-only, --generate-docs]
         types_or: [c, c++, header]
         verbose: false
         require_serial: true
diff --git a/bootloader b/bootloader
new file mode 160000
index 0000000..0bf633b
--- /dev/null
+++ b/bootloader
@@ -0,0 +1 @@
+Subproject commit 0bf633be000a2b62796e071a18b93c1018d3e369
diff --git a/tools/doxy-coverage.py b/tools/doxy-coverage.py
index 92cae26..ea42100 100755
--- a/tools/doxy-coverage.py
+++ b/tools/doxy-coverage.py
@@ -42,6 +42,7 @@ __copyright__ = "Copyright (C) 2014 Alvaro Lopez Ortega"
 
 from filecmp import cmp
 import os
+import subprocess
 import sys
 import argparse
 import xml.etree.ElementTree as ET
@@ -62,6 +63,20 @@ def FATAL(*objs):
     sys.exit(0 if ns.no_error else 1)
 
 
+def generate_docs():
+    print("Generating Doxygen documentation...")
+    proc = subprocess.run(
+        "doxygen Doxyfile",
+        shell=True,
+        stdout=subprocess.DEVNULL,
+        stderr=subprocess.DEVNULL,
+    )
+    if proc.returncode == 0:
+        print("Documentation generated")
+    else:
+        FATAL("Failed to generate documentation. Exiting.")
+
+
 def parse_file(fullpath):
     tree = ET.parse(fullpath)
 
@@ -200,12 +215,20 @@ def main():
         default=ACCEPTABLE_COVERAGE,
         type=int,
     )
+    parser.add_argument(
+        "--generate-docs",
+        action="store_true",
+        help="Generate Doxygen documentation before checking coverage",
+    )
 
     global ns
     ns = parser.parse_args()
     if not ns:
         FATAL("ERROR: Couldn't parse parameters")
 
+    if ns.generate_docs:
+        generate_docs()
+
     # Parse
     files = parse(ns.dir)