feat: add home-based configuration and tool settings

[maralbahari]

Summary

• Add an Agentic API home directory, configurable through AGENTIC_API_HOME and defaulting to ~/.agentic-api.
• Move the default SQLite database from the current working directory to $AGENTIC_API_HOME/agentic_api.db.
• Add config.toml loading and first-run generation:
  • creates the home directory when needed;
  • writes configuration with 0640 permissions on Unix (group-readable so a container restart under a
    rotated arbitrary UID sharing the image's root group can still read it);
  • never overwrites an existing configuration;
  • stores non-secret settings and environment-variable references instead of API-key values.
• Add typed configuration for:
  • llm_api_base and database_url;
  • [web_search] provider URL and api_key_env;
  • [mcp] request-declared host allowlists;
  • HTTP and stdio [mcp_servers.<label>];
  • configured MCP allowed_tools and require_approval;
  • Messages API gateway tool aliases.
• Resolve runtime settings using CLI/process environment precedence over file configuration.
• Support operator-configured MCP servers that requests can select using only server_label.
• Treat configured MCP allowed_tools as a policy ceiling:
  • requests may narrow the configured tool set;
  • requests cannot expand it;
  • configured connection details cannot be overridden with server_url.
• Fail a request immediately with a clear error when an MCP declaration is invalid (for
  example, attempting to override a gateway-configured server's server_url), instead of
  silently absorbing it into per-server discovery-failure metadata, which could otherwise leave
  tool_choice pointed at zero available tools and surface as an opaque upstream error.
• Preserve request-declared MCP servers for self-contained requests and cassette recording.
• Remove the one-time MCP environment allowlist cache and pass the effective allowlist explicitly into request URL validation.
• Configure containers to use /var/lib/agentic-api as AGENTIC_API_HOME.
• Add scripts/smoke-mcp.sh, which verifies MCP discovery and completed say_hello and sum calls through a running gateway.
• Document the home directory, typed configuration, secret handling, configured MCP servers, precedence rules, and smoke-test workflow.

The default database location is a behavior change. Existing databases in the working directory are not moved automatically; deployments can continue using them by setting DATABASE_URL explicitly.

Test Plan

• cargo test -- --test-threads=2 passes across the workspace (357 passed / 3 ignored
  Postgres-only in agentic-server-core, plus all other crates).
• Fixed 4 agentic-server-core::tool::registry unit tests that combined a
  gateway-configured MCP server with a request declaration that also set server_url;
  updated their fixtures to declare the configured path by server_label alone, matching
  the policy-ceiling behavior this PR adds.
• Added a regression path so an invalid MCP declaration (for example, a request trying to
  override a configured server's server_url) fails the request immediately instead of
  being silently absorbed into discovery-failure metadata.
• cargo test -p agentic-server-core --test mcp_tool_test (8/8) after re-recording the
  gateway MCP cassettes; gateway output still matches the OpenAI reference cassettes.
• docker build succeeds end-to-end (release compile stage + Debian runtime stage).