How do I detect when the program has stopped and is awaiting input?

Usually programs should print out a prompt when they expect the user to respond - how else would the user know when and what kind of input is required?

Is there anyway to hide the input the user provides, such as passwords?

Yes, see Term::ReadKey. Edited from perlfaq8:

How do I ask the user for a password?

...
use Term::ReadKey;

print "Enter your password: ";
ReadMode('noecho');
$password = ReadLine(0);
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-- Dan