As a side-note, I figured my RAM was badly damaged, which explained many bugs and corrupted files I observed for a few months.
Since I changed it and removed the ~/.config/akonadi folder, I haven't seen anymore 100% CPU problem with akonadi.
I suspect akonadi has some difficulty to manage corrupted database. That what should be fixed, just in case.
As a side-note, I figured my RAM was badly damaged, which explained many bugs and corrupted files I observed for a few months.
Since I changed it and removed the ~/.config/akonadi folder, I haven't seen anymore 100% CPU problem with akonadi.
I suspect akonadi has some difficulty to manage corrupted database. That what should be fixed, just in case.