A CLI tool fails to update its own config file with "EPERM: operation not permitted, rename 'config.json.tmp.XXX' -> 'config.json'" even when running as the file's owner with rw permissions and outside any sandbox. Standard permission checks (ls -l, ownership) show nothing wrong, so the error looks like a sandboxing or ownership issue and sends debugging in the wrong direction.

MCP server configured in ~/.claude/settings.json under mcpServers is silently ignored. The MCP tools never appear in the session toolset. No error is shown — the server simply does not load. Hooks referencing the MCP tools fire warnings but can never be satisfied because the tools do not exist.