docs: refresh user-facing docs to match v4.1.1 codebase

Align README.md, CONTRIBUTING.md, and docs/ with the same ground truth used
in the hierarchical AGENTS.md regeneration commit 1e7a7600a:

- README.md: '25+ built-in hooks' was undercounted by ~30 hooks; now reads
  '54+ lifecycle hooks (61 with Team Mode)' to match actual tier composition.
- CONTRIBUTING.md: src/hooks/ '52 hooks across 55 modules' -> '54 base (61 team) across 58 dirs';
  src/tools/ '26 tools across 16 directories' -> '20-39 tools (config-gated)';
  src/features/ '19 feature modules' -> '20 feature modules' (boulder-state, team-mode added).
- docs/reference/features.md: Core-agent order indices were off-by-one;
  Sisyphus 1/Hephaestus 2/Prometheus 3/Atlas 4 -> 0/1/2/3 (matches installAgentSortShim).
- docs/guide/overview.md: Sisyphus model recommendations now mention Kimi K2.6 alongside K2.5
  since K2.6 is the active default fallback in the primary Sisyphus chain
  (see src/shared/model-requirements.ts).

README.md

@@ -368,7 +368,7 @@ See [Configuration Documentation](docs/reference/configuration.md).
 - **Sisyphus Agent**: Main orchestrator with Prometheus (Planner) and Metis (Plan Consultant)
 - **Background Tasks**: Configure concurrency limits per provider/model
 - **Categories**: Domain-specific task delegation (`visual`, `business-logic`, custom)
-- **Hooks**: 25+ built-in hooks, all configurable via `disabled_hooks`
+- **Hooks**: 54+ lifecycle hooks (61 with Team Mode), all configurable via `disabled_hooks`
 - **MCPs**: Built-in websearch (Exa), context7 (docs), grep_app (GitHub search)
 - **LSP**: Full LSP support with refactoring tools
 - **Experimental**: Aggressive truncation, auto-resume, and more