When comparing ecryptfs vs CipherShed, the Slant community recommends ecryptfs for most people. In the question“What are the best file encryption tools?” ecryptfs is ranked 10th while CipherShed is ranked 18th. The most important reason people chose ecryptfs is:
The entire user home directory or folder inside can be encrypted and unlocked during login.
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Pros
Pro Encrypt your home directory
The entire user home directory or folder inside can be encrypted and unlocked during login.
Pro Built on top of TrueCrypt
CipherShed is built on top of the famous and now abandoned TrueCrypt and it comes with a lot of things that TrueCrypt had.
Pro Completely free
CipherShed is completely free and open source.
Pro Cross-platform
Available on Windows, OS X and Linux
Cons
Con No single file encryption
Can't request a single file be encrypted.
Con Difficult to enhance key derivation
Since CipherShed decided to keep the TrueCrypt compatibility, and stick with that format they also have to stick with TrueCrypt's key derivation which was released in 2004 and understandably does not offer the same security that it did when first released.