flushchanges: corrupts gentoo/pentoo repos

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I recently learned that deleted files are ignored when saving changes with 
flushchanges (tnx ZC) because of aufs/squashfs.

This effectively corrupts the local gentoo/pentoo repositories.
Example:
1. Boot into virgin LiveCD
2. run 'layman -S', then 'flushchanges'
3. reboot the LiveCD
4. run 'emerge -p pentoo-installer'
==> Error: masked by: corruption
Full output see attached file "emerge-pentoo-installer.error.log"

Reason for the error:
Files being in the repo but not in the Manifest of the ebuild.
In this case "pentoo-installer-20131013.ebuild"

I have a hacky workaround, ....

Original issue reported on code.google.com by Wuod...@gmail.com on 27 Oct 2014 at 5:49

Attachments:

• emerge-pentoo-installer.error.log