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Encrypted data will be stored in file with .crypt suffix. To prevent loosing data by decrypting them with wrong encryption key, TkCryptDir will calculate MD5 fingerprint of the original (not encrypted) files before encrypting them, and store them in file with .crypt-md5 suffix. When decrypting those files, MD5 fingerprint of the decrypted file will be compared with the original MD5 fingerprint - if they didn't match, decryption of the file fails. This can make cracking even easier, and you can disable this feature by turning-off the ``Use MD5 Fingerprint?'' switch on the window.
The crypt command may not installed on some systems including most Linux systems. There is freely-distributable implementations of crypt and can be obtained from some sites - for example, you may find the package for redhat Linux at http://www.ibiblio.org/ as ``enigma-*.rpm'' (search enigma on the site). Of course, you can use more strong cryptography instead.