Refactor Doxygen INPUT organization for better documentation flow with appendices at end

[Copilot]

The NetCDF-C documentation was poorly organized due to Doxygen's "first-in, first-out" processing behavior, where files listed in the INPUT section appear in the generated documentation in the same order they are specified. This resulted in users seeing advanced internal documentation before basic installation guides, API reference mixed arbitrarily with tutorials, and appendices scattered throughout instead of appearing at the end.

Changes Made

Reorganized the INPUT section in docs/Doxyfile.in to follow a logical progression that guides users from basic concepts to advanced topics, with all appendices properly positioned at the end:

1. Introduction & Overview - What is NetCDF, basic concepts (mainpage.dox, groups.dox)
2. Getting Started - Installation, building, quickstart guides (building-with-cmake.md, install-fortran.md, etc.)
3. User Guides - Tutorials and FAQ (tutorial.dox, FAQ.md)
4. Core API Reference - Primary header files (netcdf.h, netcdf_mem.h, etc.)
5. Advanced Topics - Specialized features (inmemory.md, quantize.md, byterange.md, auth.md, etc.)
6. Developer Documentation - Internals and architecture (internal.md, inmeminternal.dox, etc.)
7. Reference Materials - Release notes, specifications, credits
8. Implementation - Source code examples and internal implementation
9. Appendices - All documentation files containing appendix content:
   • cloud.md (Appendices A, B, C for S3 support)
   • dispatch.md (Appendices A, B for dispatch layer)
   • filters.md (Appendices A-I for filter mechanisms)
   • nczarr.md (Appendices A-E for Zarr format)
   • pluginpath.md (Appendix E.1 for plugin paths)

Impact

This reorganization addresses core usability issues where users would encounter:

• Release notes before knowing what NetCDF is
• Internal implementation details before learning how to install
• Advanced cloud authentication before basic tutorials
• Appendices scattered throughout the documentation instead of at the end

Now users follow a natural learning path: What is NetCDF? → How do I build it? → How do I use it? → Advanced features → Reference materials → Appendices.

Validation

• All 99 INPUT files verified to exist in the repository
• Documentation generation tested successfully with Doxygen
• Comparative testing confirms improved logical flow with proper appendix organization

This minimal change to a single configuration file significantly improves the organization and usability of the entire NetCDF-C documentation system.

Fixes #8.

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[WardF]

@copilot The Appendices should all appear at the end, in order.

[Copilot]

@copilot The Appendices should all appear at the end, in order.

Fixed in commit 04ca73a. Moved all files containing appendices to the end of the INPUT list in this order:

• cloud.md (Appendices A, B, C)
• dispatch.md (Appendices A, B)
• filters.md (Appendices A-I)
• nczarr.md (Appendices A-E)
• pluginpath.md (Appendix E.1)

All appendices now appear at the end in logical order.