docs: add missing container configuration flags to CLI reference

[Mossaka]

Summary

The CLI reference is missing several container configuration flags.

Missing flags

Flag	Type	Default	Description
--exclude-env <name>	string (repeatable)	-	Exclude a specific env var from --env-all passthrough
--env-file <path>	string	-	Read env vars from a file (KEY=VALUE format, one per line)
--memory-limit <limit>	string	6g	Memory limit for the agent container. Format: <number><unit> (b, k, m, g)
--agent-timeout <minutes>	number	no limit	Maximum time in minutes for the agent command to run
--audit-dir <path>	string	-	Directory for firewall audit artifacts (configs, policy manifest, iptables state)
--ruleset-file <path>	string (repeatable)	-	YAML rule file for domain allowlisting. Schema: version: 1, rules: [{domain, subdomains}]

Notes

• --exclude-env is important for security when using --env-all — allows users to exclude sensitive vars.
• --memory-limit defaults to 6g; users running large language model agents may need to increase this.
• --ruleset-file supports a structured YAML format as an alternative to --allow-domains and --allow-domains-file.