Recursively look for files with a specific extension

find $directory -type f -name "*.in"

is a bit shorter than that whole thing (and safer - deals with whitespace in filenames and directory names).

Your script is probably failing for entries that don't have a . in their name, making $extension empty.

find {directory} -type f -name '*.extension'

Example: To find all csv files in the current directory and its sub-directories, use:

find . -type f -name '*.csv'

The syntax I use is a bit different than what @Matt suggested:

find $directory -type f -name \*.in

(it's one less keystroke).

Without using find:

du -a $directory | awk '{print $2}' | grep '\.in$'

find "$PWD" -type f -name "*.in"