# 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.

Start with the path that matches the work you need to do:

| I need to… | Start here |
| --- | --- |
| Install or operate one instance | [Install and first start](install/first-start.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) |

## How the documentation is organised

- **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 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.