Introduce a unified passthrough for adapter configuration options across
all three LLM providers (Claude, Codex, Amp). The Session module now
forwards `permission_mode`, `max_turns`, `system_prompt`, and `sdk_opts`
to every adapter, and passes `project_dir` as `cwd` to the Claude adapter
so the CLI runs in the correct working directory.

Key changes:
- Add normalized option forwarding in Session for Claude, Codex, and Amp
  adapter construction.
- Pass `cwd` to ClaudeAdapter from `project_dir`.
- Bump `agent_session_manager` dependency from ~> 0.5.1 to ~> 0.6.0.
- Standardize `permission_mode` values to `:dangerously_skip_permissions`
  across example configs, replacing `:bypass_permissions`.
- Rewrite README.md with CLI reference, multi-repo section, and
  architecture diagram reflecting current module responsibilities.
- Expand configuration.md with full config precedence, file format
  specifications, logging details, and validation documentation.
- Update getting-started.md with detailed CLI commands, output modes,
  and session lifecycle explanation.
- Revise multi-repo.md with repo group nesting, commit behavior, and
  CLI override documentation.
- Revise providers.md with normalized options table, event normalization
  mapping, and session lifecycle details.
- Update CHANGELOG.md to reflect all additions.