Issue #1743 fix clip_box with transient states_at_boundary

[JoerivanEngelen]

Fixes #1743, #1746 and #1747

Description

Fixes the following problems to the Modflow6Simulation.clip_box :

• A mistake in the template ConstantConcentration package, which makes it unable to write transient packages
• Enforce dimension order before creating the clipped boundary package, as ValidationErrors could be thrown when the model already contained a ConstantConcentration or ConstantHead package.
• Align layers with an outer align to prevent layers being dropped when ConstantConcentration or ConstantHead was assigned to less layers.
• Reindex timesteps with a forward fill to properly filter out cells present in ConstantConcentration or ConstantHead packages with different time domains.

Furthermore a bit of maintenance:

• Declutter tests a bit
• Add some missing type annotations for return types and fix mypy errors

Checklist

• Links to correct issue
• Update changelog, if changes affect users
• PR title starts with Issue #nr, e.g. Issue #737
• Unit tests were added
• If feature added: Added/extended example
• If feature added: Added feature to API documentation
• If pixi.lock was changed: Ran pixi run generate-sbom and committed changes

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud