Synchronize Documentation for V4

[ParticularlyPythonicBS]

synchronizes the user-facing documentation across the root README and Sphinx docs to reflect the Version 4 codebase and the transition to the Typer-based CLI. It resolves several inconsistencies where guides still referenced legacy commands, outdated help text, or non-existent file paths.

Summary by CodeRabbit

• Documentation
  • Updated CLI tutorial examples to reflect simplified command syntax (no model name argument required).
  • Updated default output filenames in tutorials and examples to tutorial_config.toml.
  • Added instructions for migrating existing databases to the V4 schema.
  • Refreshed data validation guidance to use the temoa validate command.
  • Updated help output formatting and command descriptions.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: ASSERTIVE

Plan: Pro

Run ID: 50600fd6-79d5-4fdd-b3d9-24a7705d231e

📥 Commits

Reviewing files that changed from the base of the PR and between 1156792 and f83bfe0.

📒 Files selected for processing (4)

• README.md
• docs/README.md
• docs/source/database.rst
• docs/source/quick_start.rst

Walkthrough

The changes update documentation across multiple files to reflect updated CLI command usage: temoa tutorial without model name arguments and temoa run tutorial_config.toml for running the generated configuration, replacing previous conventions of specifying model names.

Changes

Cohort / File(s)	Summary
Tutorial CLI Examples README.md, docs/source/quick_start.rst	Updated tutorial invocation examples from temoa tutorial my_first_model to temoa tutorial (no model argument) and run command from temoa run my_first_model.toml to temoa run tutorial_config.toml. Also refreshed help output snapshot and updated command descriptions.
Database & Migration Documentation docs/source/database.rst	Updated tutorial help reference to remove model name placeholder, added migration instructions using temoa migrate command, and replaced data quality guidance with temoa validate instructions (BUILD_ONLY mode).
Documentation Build Configuration docs/README.md	Updated static documentation sources from single source/Documentation.rst file to multiple .rst files under source/ directory including mathematical_formulation.rst and database.rst.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~12 minutes

Possibly related PRs

• adding a tutorial command to the cli #198: Documents the CLI tutorial command defaults and filenames that are reflected in these updated examples.
• update readme with pypi based instructions #247: Both PRs update tutorial invocation examples and related quick_start documentation to use simplified CLI commands.
• docs: restructure for better sidebar #290: Both PRs modify the same documentation files (database.rst and quick_start.rst) to update CLI/tutorial command references.

Suggested reviewers

• jdecarolis

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title directly describes the main objective of the pull request—synchronizing documentation to match the V4 codebase and Typer CLI migration.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch docs/fix_discrepancies

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@README.md`:
- Around line 40-45: The README mixes example filenames (tutorial_config.toml,
my_project.toml, my_project_config.toml); pick one canonical example name (e.g.,
tutorial_config.toml) and replace all occurrences so examples are consistent —
update the instances currently showing my_project.toml and
my_project_config.toml to match tutorial_config.toml (search for the symbols
"tutorial_config.toml", "my_project.toml", and "my_project_config.toml" to
locate and edit the examples), and ensure the CLI examples (temoa tutorial,
temoa run ...) use the chosen filename consistently.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: ASSERTIVE

Plan: Pro

Run ID: 8fbfcab1-0ef4-4bfe-8333-54004fc4d6f3

📥 Commits

Reviewing files that changed from the base of the PR and between b12237e and 1156792.

📒 Files selected for processing (4)

• README.md
• docs/README.md
• docs/source/database.rst
• docs/source/quick_start.rst