It's fixed and the code from README should actually work

convert.sh

@@ -9,5 +9,5 @@ for filename in ../subs/*; do
 	ffmpeg -i $in $out
 	done
 
-rm ../subs.*vtt	
+rm ../subs/*vtt	
 echo "convert.sh finished its job"

download.sh

@@ -5,8 +5,8 @@ mkdir ../original
 
 #download subs
 cd ../subs
-youtube-dl --write-auto-sub --yes-playlist --skip-download -o '%(playlist_index)s' $1
+youtube-dl --write-auto-sub --yes-playlist --skip-download -o '%(playlist_index)s.%(ext)s' $1
 
 # download videos
 cd ../original
-youtube-dl -f 22 --yes-playlist -o '%(playlist_index)s' $1
+youtube-dl -f 22 --yes-playlist -o '%(playlist_index)s.%(ext)s' $1

gen-script.py

@@ -58,7 +58,7 @@ def write_list_rip(data, mode):
     file_rip.write('#!/bin/bash\n')
     for (i, d) in enumerate(data):
         if (d):
-            name = d['fname'][:2] # get a name without an extension
+            name = d['fname'].split('.')[0] # get a name without an extension
             outname ="../out/{}-{:0>2}.mp4".format(name, i)
 
             file_list.write("file '{}'\n".format(outname))