chore: project-wide cleanup — consolidate docs, remove obsolete code, update .gitignore

- Remove obsolete docs (OID_handover, SR_analysis_results, ccd_* handover)
- Remove CCD legacy output_redux and old scripts
- Remove SR old sindy scripts and compare modules
- Update .gitignore to cover all analysis-generated outputs
- Retain all active code in OID/SR/CCD analysis directories

Co-authored-by: Cursor <cursoragent@cursor.com>

.gitignore

@@ -75,6 +75,17 @@ tensorboard/
 *.h5
 *.hdf5
 *.npz
+*.npy
+
+# Analysis outputs (generated)
+src/OID_analysis/data/derived/
+src/OID_analysis/data/*/vorticity_*.png
+src/OID_analysis/data/*/*/vorticity_*.png
+src/OID_analysis/data/*/*/ddf_checkpoint.npy
+src/OID_analysis/data/*/*/fifo_checkpoint.npy
+src/CCD_analysis/data/
+src/SR_analysis/data/*/*/fields.npz
+outputs/
 
 # Logs
 *.log