omicsx 1.0.2

# Rust
/target/

Cargo.lock

**/*.rs.bk

*.pdb


# IDE
.vscode/

.idea/

*.swp

*.swo

*~

.DS_Store

*.iml


# Build artifacts
/dist/

/build/

*.o

*.a

*.so

*.dylib


# Criterion benchmarks
/target/criterion/


# Environment
.env

.env.local


# Temporary files
*.tmp

*.log

test_output.txt

test_*.txt

*.bak

*.backup

*.swp~

*.orig

*~


# Build and test output files
build_output.txt

build_output_kernel.txt

build_release.txt

test_output.log

test_after_fixes.txt

test_final_validation.txt

test_halo_output.txt

test_halo_run.txt

test_halo_unit.txt

test_integration_run.txt

test_kernel_final.txt

test_large_seq.txt

test_output_kernel.txt

test_push_final.txt

test_results_final.txt

test_tiling_run.txt

test_final.txt


# Audit and report files (generated during development)
*_AUDIT.md

*_AUDIT_REPORT.md

*_AUDIT_DETAILED.md

*_REPORT.md

*_TEST_REPORT.md

*_VERIFICATION.md

*_VERIFICATION_REPORT.md

*_FIXES.md

*_FIXES_APPLIED.md

*_FIXES_VALIDATION*.md

*_SUMMARY.md

*_COMPLETION*.md

*_DIAGNOSTIC*.md

*_STATUS_REPORT.md

*_PROGRESS*.md

*_OPTIMIZATIONS.md

*_INTEGRATION*.md

*_EXECUTION*.md

*_IMPLEMENTATION*.md

*_REGISTRY.md

*_GUIDE*.md

*_BRIDGE*.md


# Enhanced implementation backups (Phase 3)
src/futures/*_original.rs

src/alignment/*_old.rs

src/futures/*_enhanced.rs

src/alignment/*_enhanced.rs


# GPU simulation backups (replaced with real hardware implementation)
src/futures/gpu_simulated.rs

src/futures/gpu_old.rs

src/futures/gpu_mock.rs

src/alignment/gpu_simulation.rs


# Redundant documentation files (kept for reference only, not tracked)
CHANGELOG_OLD_BACKUP.md

README_OLD_BACKUP.md

*_OLD_BACKUP.md

*_DEPRECATED.md

*_ARCHIVE.md

*_BACKUP.md


# Archived phase documentation (consolidate into ADVANCED_IMPLEMENTATION_SUMMARY.md)
PHASE1_IMPLEMENTATION.md

PHASE1_STATUS.md

PHASE2_COMPLETION_REPORT.md

PHASE3_ENHANCEMENT_COMPLETION.md

PHASE3_ENHANCEMENT_PLAN.md

PHASE3_FINAL_COMPLETION.md

PHASE4_GPU_PLAN.md

PHASE4_PROGRESS_REPORT.md


# Duplicate integration summaries (use ST_JUDE_BRIDGE.md as canonical)
STJUDE_EXECUTIVE_SUMMARY.md

ST_JUDE_INTEGRATION_SUMMARY.md


# Redundant enhancement/completion documents
GPU_JIT_COMPILER_ENHANCED.md

IMPLEMENTATION_SUMMARY.md

COMPLETION_REPORT.md

ENHANCEMENT_ROADMAP.md

ROADMAP_ENHANCEMENTS.md

SESSION_SUMMARY.md


# Release notes archives (keep current RELEASE_NOTES_v1.0.2.md only)
RELEASE_NOTES_v*.md

!RELEASE_NOTES_v1.0.2.md


# Generated documentation
/doc/

docs/_build/

.doctrees/


# Node and JavaScript (if used with web components)
/node_modules/

/.npm/

package-lock.json

npm-debug.log


# Redundant Phase files (keep current phase docs only)
PHASE1_IMPLEMENTATION.md

PHASE2_COMPLETION_REPORT.md

PHASE3_ENHANCEMENT_PLAN.md

PHASE3_ENHANCEMENT_COMPLETION.md

PHASE3_FINAL_COMPLETION.md

PHASE4_GPU_PLAN.md

PHASE4_PROGRESS_REPORT.md

PHASE_1_STATUS.md


# Redundant summary files
COMPLETION_REPORT.md

IMPLEMENTATION_SUMMARY.md

SESSION_SUMMARY.md

ROADMAP_ENHANCEMENTS.md

ENHANCEMENT_ROADMAP.md

DOCUMENTATION_INDEX.md


# Duplicate integration files
STJUDE_EXECUTIVE_SUMMARY.md

ST_JUDE_INTEGRATION_SUMMARY.md


# Redundant GPU files
GPU_JIT_COMPILER_ENHANCED.md


# Build and Benchmark Output
benchmark_results.txt

test_output.txt

*.csv

perf_results.json


# IDE and Editor Configuration (if created locally)
.vscode/settings.json

.vscode/launch.json

.idea/workspace.xml


# Dependency Caches
.cargo/

Cargo.lock


# Python cache
__pycache__/

*.pyc

*.pyo

*.egg-info/

.pytest_cache/


# macOS specific
.AppleDouble

.LSOverride

.Spotlight-V100

.Trashes


# Windows specific
Thumbs.db

Desktop.ini

ehthumbs.db


# JetBrains IDE additional
.idea/

*.iml

*.pem


# Visual Studio Code additional
.vscode/settings.json

.vscode/launch.json

.vscode/extensions.json


# Temporary scripts and notebooks
*.ipynb_checkpoints/

*.ipynb

scratch/

temp/

.tmp/


# Benchmark and profiling artifacts
*.prof

*.flame

perf.data*

callgrind.out*


# Cargo local overrides
.cargo/local.json


# OS temp files
.Tmp/

$RECYCLE.BIN/