Here is just another solution using biter scripting language.
To do the same thing for many files - it is a common technique called the file loop. See this tutorial - http://www.biterscripting.com/Learn... - Section 4.1. FILE DIRECTORY LOOP.
The script for your requirement can be as follows.
var str list, file, name ; lf -n "*.wav" > $list
while ($list <> "")
lex "1" $list > $file ; stex -p "]^.^" $file > $name
encoder.exe $file ($name+".bit")