Clean up root directory and update README

This commit cleans up the repository by removing 183 temporary/debug files
from the root directory and completely refreshing the README to accurately
reflect SeqRush's current functionality.

Changes:

Root Directory Cleanup:
- Removed temporary test data files (.fa, .fai, .paf, .odgi, .html, etc.)
- Removed debug scripts and analysis tools (Python, shell scripts)
- Removed development notes and historical documentation
- Removed compiled artifacts and temp directories
- Removed pafcheck submodule (no longer used)
- Kept only essential files: source code, submodules, config files

README Refresh:
- Updated description to reflect actual implemented features
- Removed "Planned" markers for completed features:
  * AllWave and SweepGA aligners (implemented)
  * Bidirected union-find (implemented)
  * Graph layout pipeline (implemented)
  * Iterative alignment (implemented)
- Added comprehensive usage examples for all features
- Documented iterative alignment with two-phase processing
- Added sparsification strategies documentation
- Included validation results from HLA-Zoo testing
- Updated project structure to match actual codebase
- Corrected repository URL to pangenome organization
- Updated acknowledgments to reflect actual dependencies

The repository now presents a clean, professional interface that accurately
documents the tool's capabilities.

All tests pass. Build verified.

Author: ekg

*Messages*

@@ -1,9 +1,6 @@
 [submodule "HLA-zoo"]
 	path = HLA-zoo
 	url = https://github.com/ekg/HLA-zoo.git
-[submodule "pafcheck"]
-	path = pafcheck
-	url = https://github.com/ekg/pafcheck.git
 [submodule "allwave"]
 	path = allwave
 	url = https://github.com/pangenome/allwave.git