I believe this is a problem that Dustin has ran into before.  It is due
to ext4 and zero-length files (http://thunk.org/tytso/blog/2009/03/12
/delayed-allocation-and-the-zero-length-file-problem/).

When a file is created in an eCryptfs mount, we go ahead and create the
file in the lower filesystem and write out the eCryptfs metadata
(encrypted file key, decrypted file size, etc.).  Anytime that a file
open is performed, we expect that metadata to be present or we consider
it a non-eCryptfs file and ignore it by returning -EIO.  You are seeing
the warning message from an open on a file that doesn't have the proper
eCryptfs metadata.

We may be able to let the zero-length files slide and generate and write
the header information on the first file write.  The problem with this
is that it may break the way that users expect ecryptfs_passthrough to
work.  You can touch a file in the lower filesystem (creating a zero
length file) and then any subsequent writes from the eCryptfs mount
point will be passed through instead of encrypting the data.

That may just be a little trick that I do for testing and not something
that any users actually do.  I need to think about that a little more.

-- 
Ecrypt errors in dmesg
https://bugs.launchpad.net/bugs/372014
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