Restructured deeply nested documentation files

[shreyannandanwar]

Description

This PR restructures documentation sections that had excessively deep heading hierarchies in order to improve navigation, readability, and conceptual clarity. The changes focus on correcting the document structure itself by aligning heading depth with conceptual importance.
Specifically, this PR:

• Removes skipped heading levels and eliminates level-6 headings
• Flattens non-structural sections such as examples, procedural variants, and step-specific notes
• Promotes conceptually important content to appropriate heading levels
• Improves consistency and parallelism across related sections
• Preserves all technical content while reorganizing its presentation
  This PR serves as a pilot restructuring that establishes a clear and reusable pattern for addressing similar structural issues elsewhere in the documentation.

Motivation and Context

Several PEcAn documentation files contained heading hierarchies 5–6 levels deep (e.g. section numbers like 15.2.3.4.1.2), leading to poor navigation, unreadable numbering, and structural inconsistencies such as skipped heading levels. Many deeply nested sections represented examples or procedural variants rather than true conceptual hierarchy.
Earlier discussion considered hiding deep section numbers via CSS, but this would only mask the underlying organizational problems. This PR addresses the root cause by restructuring the content hierarchy so numbering depth becomes manageable naturally.
Fixes #3741.

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.