This behavior still exists in Jaunty and Karmic and it is going to be handled 
in the user space at the policy level.  The user space tools are being extended 
to be able to handle, this in a couple of ways.
  1. There will be a global policy file where rules like the work around 
specified above can be added without having to update the profiles.
  2. The alias command is being extended to cover full regular expression 
rewriting which will allow the policy to contain the relationship between the 
encrypted dir and the users actual home.  The alias required for ecrypted homes 
will then be put in the global policy file described in part 1.

This solution can be applied to both Jaunty and Karmic.

-- 
apparmor paths are broken when using ecryptfs on jaunty
https://bugs.launchpad.net/bugs/359338
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which is subscribed to ecryptfs-utils in ubuntu.

Status in Ubuntu Release Notes: Fix Released
Status in “ecryptfs-utils” package in Ubuntu: Invalid
Status in “linux” package in Ubuntu: In Progress
Status in ecryptfs-utils in Ubuntu Karmic: Invalid
Status in linux in Ubuntu Karmic: In Progress

Bug description:
Binary package hint: ecryptfs-utils

klamav 0.46-2 with clamav 0.95.
Jaunty with encrypted home directory.

After installing klamav and first running it, it creates 
/home/user/.klamav/database, in which it downloads the signature databases. 
This directory gets created OK, but the database download fails with 'Can't 
create file' error, and the following entry in syslog:

Apr 11 01:11:39 utest-jj kernel: [  959.044919] type=1503 
audit(1239401499.961:33): operation="inode_create" requested_mask="a::" 
denied_mask="a::" fsuid=1000 
name="/home/gimre/.Private/ECRYPTFS_FNEK_ENCRYPTED.FWYWbBX-HCv7D-ShpT0P1qAlMITxm.e31aS9aW.rw0ebxHiizvzjKdHqek--/ECRYPTFS_FNEK_ENCRYPTED.FWYWbBX-HCv7D-ShpT0P1qAlMITxm.e31aS9FGYc1fWwp9RQW-wdr8CQZU--/ECRYPTFS_FNEK_ENCRYPTED.FYYWbBX-HCv7D-ShpT0P1qAlMITxm.e31aS9Pcj74.T8NOQNJ4OdUE2-.LWX5l6N.v2lDmBFyCvWlKqrrt-xoaiQuTGvsGqXcTCI"
 pid=5164 profile="/usr/bin/freshclam"
Apr 11 01:11:39 utest-jj kernel: [  959.044937] ecryptfs_do_create: Failure to 
create dentry in lower fs; rc = [-13]
Apr 11 01:11:39 utest-jj kernel: [  959.045149] ecryptfs_create: Failed to 
create file inlower filesystem

After stopping apparmor, the problem goes away, the database gets downloaded 
correctly.

Can be reproduced by correcting freshclam's apparmor profile, see the following 
bug:

https://bugs.launchpad.net/ubuntu/+source/clamav/+bug/359301

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