Using the GNOME system monitor, I can't see anything that I wouldn't expect. There are a lot of processes starting with gvfsd, but given the G I'd assume that's part of GNOME.

Not even changing the permissions of the folders fixes the problem. I gave all users permission to create and delete files, but when I change file access to "read and write" it reverts right back even after I remove the properties window.

The offending folders are:
/proc/irq
/sys/bus/pci/drivers/agpart-intel
/sys/bus/pci/drivers/snd_hda/intel
/sys/module/intel-idle
/sys/module/snd_hda_intel
/sys/kernel/debug/tracing/events/hda_intel
There's also a large number of files that might or might not be related, as they weren't modified as recently as the folders.

Here's what ls -l reveals about /proc/irq. Your other commands all receive "permission denied".

total 0
dr-xr-xr-x 2 root root 0 May  9 16:50 0
dr-xr-xr-x 3 root root 0 May  9 16:50 1
dr-xr-xr-x 2 root root 0 May  9 16:50 10
dr-xr-xr-x 2 root root 0 May  9 16:50 11
dr-xr-xr-x 3 root root 0 May  9 16:50 12
dr-xr-xr-x 2 root root 0 May  9 16:50 13
dr-xr-xr-x 2 root root 0 May  9 16:50 14
dr-xr-xr-x 2 root root 0 May  9 16:50 15
d--x--x--x 3 root root 0 May  9 16:50 16
dr-xr-xr-x 6 root root 0 May  9 16:50 17
dr-xr-xr-x 6 root root 0 May  9 16:50 18
dr-xr-xr-x 3 root root 0 May  9 16:50 19
dr-xr-xr-x 2 root root 0 May  9 16:50 2
dr-xr-xr-x 2 root root 0 May  9 16:50 3
dr-xr-xr-x 2 root root 0 May  9 16:50 4
dr-xr-xr-x 3 root root 0 May  9 16:50 42
dr-xr-xr-x 2 root root 0 May  9 16:50 5
dr-xr-xr-x 2 root root 0 May  9 16:50 6
dr-xr-xr-x 2 root root 0 May  9 16:50 7
dr-xr-xr-x 3 root root 0 May  9 16:50 8
dr-xr-xr-x 3 root root 0 May  9 16:50 9
-rw------- 1 root root 0 May  9 16:50 default_smp_affinity

Are there any parts of the Trisquel system that are protected in this way? Could I delete the kernel if I wanted to? (I don't.) On Windows, there are certain files protected by TrustedInstaller, but you can get around that as an administrator. This really perplexes me.

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