docs: separate public manual from internal project documentation

docs/index.md

@@ -1,35 +1,33 @@
 # ThothII documentation
 
-ThothII is a human-reviewed datamart builder. It turns a question into validated SQL through an
-eight-phase workflow: the model proposes; a reviewer makes the decisions that are persisted.
+ThothII turns a natural-language question into reviewed SQL. The model proposes;
+a human reviewer decides which interpretations, sources and results to accept.
 
-Start with the path that matches the work you need to do:
+This is the public product manual. Start with the task you need to perform:
 
 | I need to… | Start here |
 | --- | --- |
-| Install or operate one instance | [Install and first start](install/first-start.md) |
-| Clone and manually install on macOS, Windows, or Linux | [Italian procedure](install/standalone-manual-it.md) · [English procedure](install/standalone-manual-en.md) |
-| Upgrade the server and integrate Omics Portal | [Codex server handoff](operations/server-codex-handoff.md) |
-| Choose full/embedded and configure the shell | [Shell and localization](operations/shell-and-localization.md) |
-| Reuse an authenticated server portal without a second login | [Upstream authentication](install/authentication-upstream.md) |
-| Understand how the two renderings share the same application | [Rendering architecture](architecture/application-shell.md) |
-| Validate login, logout and portal integration before release | [Acceptance matrix](testing/authentication-manual-acceptance.md) |
-| Add, update, or prepare a workspace | [Workspace operations](operations/workspaces.md) |
-| Ask a question and review the SQL workflow | [User guide](guida-utente.md) |
-| Configure and refresh an authoritative database catalog | [Database management](operations/database-management.md) |
-| Author and publish domain Evidence | [Evidence](evidence.md) |
-| Understand boundaries and persistence | [Architecture overview](architecture/overview.md) |
+| Understand the product and its boundaries | [What ThothII does](product-overview.md) |
+| Install on Mac, Windows through WSL2, or Linux | [Italian procedure](install/standalone-manual-it.md) · [English procedure](install/standalone-manual-en.md) |
+| Choose display mode and language | [Display mode and language](install/shell-and-language.md) |
+| Configure login | [Local accounts](install/authentication-local.md) · [OIDC](install/authentication-oidc.md) |
+| Configure model providers | [Model configuration](general/pi-configuration.md) |
+| Prepare a domain workspace | [Workspaces](operations/workspaces.md) |
+| Configure databases and reviewed descriptions | [Database management](operations/database-management.md) |
+| Ask a question and review SQL | [User guide](guida-utente.md) · [Workflow](skills.md) |
+| Maintain domain knowledge | [Evidence](evidence.md) · [Memory](usage/memory.md) |
 
-## How the documentation is organised
+## Scope of this manual
 
-- **Install and operate** documents host-side setup, authentication, lifecycle, workspaces, and
-  Pi administration.
-- **Use ThothII** documents the two application paths: reviewed NL→SQL sessions and administrative
-  database management.
-- **Architecture and contracts** explain why the system behaves as it does and define the
-  machine-facing boundaries. Consult them when integrating or changing an implementation; they
-  are not a substitute for an operator runbook.
+The manual covers the product, installation, use and administration. Architecture,
+code contracts, design decisions, implementation plans, test reports and site-specific
+deployment handoffs are developer/project material maintained in the repository;
+they are not pages of this site and are not included in its search index.
 
-The host-side `tht` command is the operator interface. The Python `tht` inside `harness/` is a
-different, internal workflow CLI invoked by the core. In examples, use an absolute installation
-descriptor path whenever discovery is not unambiguous.
+The installation procedures distinguish checked documentation from platform and
+functional tests that still require execution. A clone does not transfer another
+installation's credentials, data or network access.
+
+The host-side `tht` command operates an installation. The Python workflow CLI inside
+the runtime is a separate internal interface; do not substitute its commands for
+the host installation procedure.