Ensure settings$database defaults to NULL when absent

[AritraDey-Dev]

Description

Currently, both Demo notebooks use a workaround to set settings$database to NULL, even though the configuration is absent in the settings file.

pecan/documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd

Lines 123 to 125 in 381c450

	1. Disabling database write operations because we are not using a database
	```{r disable-db-write}
	settings$database <- NULL # Disable database operations for this demo

The issue arises because prepare.settings automatically adds settings$database$dbfiles even if settings$database is initially absent. (see #3701 (comment)).

This PR fixes the issue by modifying check.settings to only set settings$database$dbfiles if settings$database is already present (i.e., not NULL). This ensures that settings$database remains NULL when no database configuration is provided.
Also, after the fix, inspecting the settings object confirms that there is NO settings$database present.

Motivation and Context

Fixes #3701

Review Time Estimate

• Immediately
• Within one week
• When possible

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My change requires a change to the documentation.
• My name is in the list of CITATION.cff
• I agree that PEcAn Project may distribute my contribution under any or all of
  • the same license as the existing code,
  • and/or the BSD 3-clause license.
• I have updated the CHANGELOG.md.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.