add developer docs

docs-site/mkdocs.yml

@@ -52,9 +52,22 @@ nav:
   - Getting started:
       - installation.md
       - reproducibility.md
+  - System design:
+      - system-design/layers.md
+      - system-design/state-and-data-flow.md
+      - system-design/security-trust-model.md
   - Architecture:
       - architecture.md
       - workflows.md
+  - Developer:
+      - developer/index.md
+      - developer/editing-documentation.md
+      - developer/navigating-the-source.md
+      - developer/bun-bundle-and-feature-flags.md
+  - Guides:
+      - guides/building-an-agentic-cli-overview.md
+      - guides/mcp-and-tool-loop-patterns.md
+      - guides/documentation-and-ci-for-docs.md
   - Official docs map: official-docs-map.md
   - Reference:
       - reference/cli-entry.md
@@ -76,6 +89,7 @@ nav:
       - appendix/directory-structure.md
       - appendix/tool-packages.md
       - appendix/environment-variables.md
+      - appendix/glossary.md
 
 plugins:
   - search