found out what was wrong with diff

toolchain/bootstrap/format.sh

@@ -10,17 +10,15 @@ if [ "$1" == "diff" ]; then
 
     # Indent acc directives
     out_indent=""
-    fn=""
+    # for filename in src/simulation/m_bubbles.fpp; do
     for filename in src/*/*.f*; do
         out_indent+=$(python3 toolchain/indenter.py "$filename" "diff")
     done
-    echo out_indent
-    echo ${out_indent}
-    exit 0
-
+
     # Check prettify out
     out_prettify=$(fprettify ${@:-src} --exclude "src/*/autogen" $opts -s -d)
     if [ -z "${out_prettify}" ] && [ -z "${out_indent}" ]; then
+    # if [ -z "${out_indent}" ]; then
         echo "Already pretty!"
         exit 0
     else

toolchain/indenter.py

@@ -15,14 +15,16 @@ def main():
 
     adjust_indentation(infile, outfile)
     if num_args == 2:
-        print('replacing',infile,'with',outfile)
         os.replace(outfile,infile)
     if num_args == 3:
         same = filecmp.cmp(outfile,infile)
         if not same:
             print(infile)
+            cmd = 'diff ' + outfile + ' ' + infile
+            so = os.popen(cmd).read()
+            print(so)
             print('different!')
-        # os.remove(outfile)
+        os.remove(outfile)
 
 def adjust_indentation(input_file, output_file):
     startingchar='!$acc'