fix: Align Makefile, README, and Examples Structure

[aygp-dr]

Inconsistencies between Makefile, README, and Examples\n\n## Numbering and Structure Issues\n\n### Makefile ESSENTIAL_EXAMPLES Variable\nCurrently only includes examples 00-02, missing later examples listed in README\n\n### Examples Directory Structure\n- Has examples 00-06 (continuous)\n- Then jumps to 50-51 (SQLite queries)\n- Ends with 99 (feature requests)\n- No clear separation between essential and advanced examples\n\n### README Learning Path\n- Lists examples 00-03 as essential\n- Lists 04-06 under advanced topics\n- No mention of examples 50-51\n\n## Path References\n1. Embeddings example path mismatch:\n - README refers to: 04-embeddings-intro.org\n - Makefile variable expects: 04-embeddings.org\n\n## Missing Makefile Targets\n1. No explicit targets for:\n - 04-embeddings-intro.org\n - 05-photo-embeddings.org\n - 06-advanced-usage.org\n\n## Proposed Changes\n\n1. Update Makefile variables to include all example types\n2. Reorganize examples directory with clear categories:\n - essential/ (00-03)\n - advanced/ (04-06)\n - tools/ (50-51)\n - roadmap/ (99)\n\n3. Update README to:\n - Document all example categories\n - Clarify learning progression\n - Include tools and roadmap sections\n\n## Success Criteria\n- All example paths are consistent across files\n- Clear separation between example types\n- All examples have corresponding Makefile targets\n- README accurately reflects directory structure\n- Learning path is clearly documented