A naieve test of aufs directly shows that chown and chmod do cause a
copy up of the underlying files as expected.

In the read only layer before chmod/chown:

  drwxrwxr-x 2 apw apw 4096 Mar 18 09:16 D1
  drwxrwxr-x 2 apw apw 4096 Mar 18 09:16 D2
  drwxrwxr-x 2 apw apw 4096 Mar 18 09:16 D3

In the mount after:

  drwxrwxr-x 2 sbuild sbuild 4096 Mar 18 09:16 D1
  drwxrwxrwx 2 apw    apw    4096 Mar 18 09:16 D2
  drwxrwxrwx 2 apw    apw    4096 Mar 18 09:16 D3

The underlying permissions remain unchanged after these operations.
This all seems semantically correct.

I need a description of how we are using aufs in these this scenario (in
comment #2), for instance are we modifing the actual underlying files
while mounted which would be a no-no.

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https://bugs.launchpad.net/bugs/1293549

Title:
  Filesystem mount from lxc template causes filesystem permission
  breakages

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