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Without this the file was missing on first run, load_builtin_permissions()
returned {}, and the agent fell through to _DEFAULTS={Bash:'ask'} even
though the Settings UI showed green 'always_allow' checkmarks (because the
UI defaulted missing entries to always_allow for DISPLAY but the agent
defaults to ask for SAFETY). The mismatch meant users got prompted on
every ls/cd/pwd despite having flipped Bash to always_allow in the UI.
Lifespan now seeds the file with Bash=ask and everything else=always_allow,
matching agent_manager._DEFAULTS. Idempotent: only writes if a tool is
missing; never clobbers a policy the user already set.