mcp keys: tool-management tools aligned with BYOK (test_mcp_tool runs on user key, mcp_status marks key slots)

Pass explicit ToolContext to tools instead of hidden ContextVars ...

Add ToolContext dataclass (session_id, event_sink, stop_event, model,
user_id, user_role, user_info) and thread it through the execution chain:
Agent._execute_tools_with_sink → ToolExecutor → tool.execute().

All ~25 tools updated to accept ctx parameter. Tools that previously
read ContextVar now prefer ctx when provided, falling back to
ContextVar for backward compatibility.

Tests updated to pass ToolContext explicitly — no more test fixtures
that set current_session_id / current_user_id ContextVars.

ContextVar setters remain as fallback for non-tool consumers
(ai_helper, context_builder, planning) and will be removed in a
follow-up refactor.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Refactor: move tool helper modules into _internal subpackage ...

Moves non-tool infrastructure out of navi/tools/ root so that only
actual tool classes live there:

  base.py           → _internal/base.py
  loader.py         → _internal/loader.py
  middleware.py     → _internal/middleware.py
  logging_middleware.py → _internal/logging_middleware.py
  _time_parser.py   → _internal/time_parser.py

All imports updated across core/, api/, mcp/, tools/, and tests/.
No proxy files remain in navi/tools/ root.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

feat: add create_mcp_server and test_mcp_tool builtins ...

create_mcp_server:
- Scaffolds mcp-servers/<name>/ directory with venv, pyproject.toml,
  app/__init__.py, and annotated mcp_server.py template
- Runs pip install -e . in isolated thread to avoid event-loop issues
- Validates template with python -m py_compile

test_mcp_tool:
- Execute a single MCP tool call for isolated testing
- Detailed diagnostics: not connected, empty response, timeout, crash
- Fallback to module-level _mcp_manager if startup wiring skipped

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>