Hello.

Ryan Seu wrote:
> Notice that upon restart, it seems like the preference gets overwritten and
> a mode=disabled (16) entry gets created.  So the question is, if according
> to the man page for tomoyo-init all that's done is load the
> /etc/tomoyo/profile (along with the other policy files) into the kernel
> memory, where does these extra entries get added?

These extra entries are kernel's default configuration.

> Does tomoyo disable enforcement mode by default?

Kernel's default configuration is mode=disabled.

Please read http://tomoyo.sourceforge.jp/2.5/chapter-9.html for details of
profile settings.

You are specifying only category-specific configuration and
functionality-specific configuration.
You did not specify default configuration which will be used unless overwritten
by category-specific or functionality-specific configuration.

> Or rather, is it because profile #3 implicitly includes the syscall types
> and not explicitly declares the parent it gets automatically added?

Right.

Regards.

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