Nothing really wrong with your script so I'll nitpick

    next if /^(\s)*$/;  # skip blank lines
    my($Temp)=$_; #Store each line from $FileName to $Temp
    chomp ($Temp); #strip eol character
    push @fileExtArr, $Temp;
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The parens around \s are unnecessary. $Temp is unnecessary, just continue to use $_

# go to this key for value
...
# check this key for these values
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Bad comments. I like comments, but they have to give more information than what you can as easily read from the code itself. If words like 'this' and 'these' show up frequently, the comments likely are wasted time.