claude-settings.json now sets permissions.defaultMode=bypassPermissions
with a small deny list (WebFetch, WebSearch, Task, TodoWrite). The
per-flavor allow list and --tools / --allowedTools CLI flags are gone
— anything not denied auto-approves. mcp.rs loses ALLOWED_BUILTIN_TOOLS,
builtin_tools_arg, allow_list, allowed_mcp_tools. The extraMcpServers
allowedTools field is parsed for back-compat but no longer wired
anywhere; restrict via permissions.deny instead.
