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OK. So, I assume you've figured out this can be fixed by using appropriate quoting. In this case:
DIR=`dirname "$1"`
INPUT=`basename "$1"` or, preferably:
DIR=$(dirname "$1")
INPUT=$(basenamae...

Positional parameters is the term you need to look for when searching. They should be documented in your shell's manual page. They are shell variables (aka parameters) of the form $1, $2 ... $N,...

If you store one file in appropriate associative arrays, and then update it from a second file, you can then disgorge the updated data as a normalized file. Deletes would be in how updates are...