Cleanup: Fix CI formula, reorganize shell scripts and test files
- Fixed CI calculation: changed from NDVI (NIR-Red)/(NIR+Red) to correct NIR/Green-1 formula in:
* process_single_tile() function
* create_ci_band() utility function
* Updated create_mask_and_crop() documentation
- Renamed numbered shell scripts for clarity (matching R script numbering):
* 01_run_planet_download -> 10_planet_download.sh
* 02_run_ci_extraction -> 20_ci_extraction.sh
* 03_run_growth_model -> 30_growth_model.sh
* 04_run_mosaic_creation -> 40_mosaic_creation.sh
* 09_run_calculate_kpis -> 80_calculate_kpis.sh
* 10_run_kpi_report -> 90_kpi_report.sh
- Archived obsolete shell scripts to old_sh/:
* build_mosaic.sh, build_report.sh, interpolate_growth_model.sh
* 05_run_dashboard_report.sh, 06_run_crop_messaging.sh
* 11_run_yield_prediction.sh/ps1
* runcane.sh, runpython.sh, smartcane.sh, update_RDS.sh
- Deleted test/debug files and temporary outputs:
* analyze_*.R, benchmark_gpu_vs_cpu.py, convert_angata_harvest.py
* debug_mosaic.R, examine_kpi_results.R, generate_sar_report.R
* inspect_8band_structure.R, inspect_tif_bands.R
* old_working_utils.R, predict_harvest_operational.R
* run_kpi_calculation.R, run_report.R, simple_sar_test.R
* data_validation_tool/, harvest_ci_pattern_analysis.png, kpi_debug.out
- Enhanced harvest prediction: Added threshold tuning (0.40-0.45) and field type handling
- Enhanced mosaic creation: Improved tile detection and routing logic
Timon
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