diff --git a/.travis.yml b/.travis.yml
index 13ec3b0..5fc178b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -17,6 +17,6 @@ script:
   - export CC=gcc-9
   - gcc --version
   - python --version
-  - python autogen.py -e -b -cv -r
+  - python autogen.py -e -b -cv -r -nf
 after_success:
   - bash <(curl -s https://codecov.io/bash)
diff --git a/autogen.py b/autogen.py
index b5b2644..1073528 100644
--- a/autogen.py
+++ b/autogen.py
@@ -43,6 +43,8 @@ SRC_DIR = f"{OUTPUT_DIR}/{DIR_MAP['SOURCE']}"
 OBJ_DIR = BUILD_DIR
 # The name of the main test executable
 TEST_EXE = f'{OUTPUT_DIR}/main.exe'
+# Where .gcov files should go
+GCOV_DIR = f'{BUILD_DIR}/gcov'
 
 # Compiler
 
@@ -50,8 +52,12 @@ TEST_EXE = f'{OUTPUT_DIR}/main.exe'
 CC = 'gcc'
 # Compilation Flags
 CFLAGS = ['-Wall', '-Werror']
+# Link flags
+LFLAGS = []
 # Coverage Flags
 CVFLAGS = ['--coverage', '-O0']
+# gcov flags
+GCOV_FLAGS = []
 # Include to the main Library
 # const
 INCLUDE = ['-I', './src']
@@ -82,10 +88,13 @@ CONFIG = f'''Directory Settings
     INCLUDE_DIR = {INCLUDE_DIR}
     SRC_DIR = {SRC_DIR}
     OBJ_DIR = {OBJ_DIR}
+    GCOV_DIR = {GCOV_DIR}
 Compiler Settings
     CC = {CC}
     CFLAGS = {CFLAGS}
+    LFLAGS = {LFLAGS}
     CVFLAGS = {CVFLAGS}
+    GCOV_FLAGS = {GCOV_FLAGS}
     INCLUDE = {INCLUDE}
     TINCLUDE = {TINCLUDE}
 Macro Expansion
@@ -165,6 +174,7 @@ def assert_structure():
 
     assert_dir(BUILD_DIR)
     assert_dir(OBJ_DIR)
+    assert_dir(GCOV_DIR)
 
     for lib in ALL_LIBS:
         assert_dir(f'{OBJ_DIR}/{lib.lower()}')
@@ -174,11 +184,13 @@ def clean_build(cleanfull: bool):
     '''
         Removes all files generated by compilation and code coverage along with folders.
     '''
-    execute_command(['rm', '-r', '*.gcov'])
+    execute_command(['rm', '-r', f'{GCOV_DIR}/*.gcov'])
     execute_command(['rm', TEST_EXE])
+    execute_command(['rm', '-r', BUILD_DIR])
 
-    for directory in [BUILD_DIR, SRC_DIR, INCLUDE_DIR]:
-        execute_command(['rm', '-r', directory])
+    if cleanfull:
+        execute_command(['rm', '-r', SRC_DIR])
+        execute_command(['rm', '-r', INCLUDE_DIR])
 
 
 def expand_code():
@@ -268,6 +280,7 @@ def build_tests(with_coverage: bool):
         Build all object files and the main executable for tests
     '''
     cflags = CFLAGS.copy()
+    lflags = CFLAGS.copy()
 
     if with_coverage:
         cflags += CVFLAGS
@@ -295,6 +308,7 @@ def build_tests(with_coverage: bool):
     # Link everything producing OUTPUT_DIR/main.exe
     cmd = [CC]
     cmd += cflags
+    cmd += LFLAGS
     cmd += ['-o', TEST_EXE]
     cmd += [f'{OBJ_DIR}/main.o']
     cmd += [f'{OBJ_DIR}/{data["LIB"].lower()}/{data["SNAME"]}.o' for data in COLLECTIONS]
@@ -308,9 +322,10 @@ def run_tests(coverage: bool):
     execute_command([full_path(TEST_EXE)])
 
     if coverage:
-        objects = [f'{OBJ_DIR}/main.o']
-        objects += [f'{OBJ_DIR}/{data["LIB"].lower()}/{data["SNAME"]}.o' for data in COLLECTIONS]
-        execute_command(['gcov'] + objects)
+        objects = [f'{OBJ_DIR}/main.gcda']
+        objects += [f'{OBJ_DIR}/{data["LIB"].lower()}/{data["SNAME"]}.gcda' for data in COLLECTIONS]
+        execute_command(['gcov'] + GCOV_FLAGS + objects)
+        execute_command(['mv', '*.gcov', GCOV_DIR])
 
 
 if __name__ == '__main__':
@@ -395,6 +410,10 @@ if __name__ == '__main__':
         if not args.noformat:
             assert_executable('clang-format')
             format_expand()
+        else:
+            # In case the next task is to build the code from source
+            # This warning is a very annoying one from gcc
+            CFLAGS += ['-Wno-misleading-indentation']
 
     if args.fmt_source or args.fmt_tests:
         assert_executable('find')