Remove duplicate images and clean repo config

- Remove 12 unreferenced files from images/ (10 PDFs duplicated in
  R/docs/articles/figures/, 1 PDF duplicate of PNG, 1 unused QR code)
- Rewrite .gitignore: remove fake API-key filename patterns that
  cannot prevent secret leaks, deduplicate entries, organize by category
- Clean .gitattributes: remove unconfigured filter=remove-sensitive
  rules, remove redundant text declarations covered by text=auto

Author: cafferychen777

.gitattributes

@@ -1,13 +1,5 @@
-# Git attributes for mLLMCelltype
-
-# Ensure consistent line endings
+# Line endings
 * text=auto
-*.md text
-*.py text
-*.R text
-*.json text
-*.yml text
-*.yaml text
 
 # Binary files
 *.png binary
@@ -17,18 +9,6 @@
 *.rds binary
 *.RData binary
 
-# Files that should never be committed (additional safety)
-**/api_keys.* filter=remove-sensitive
-**/secrets.* filter=remove-sensitive
-**/*_key.* filter=remove-sensitive
-**/*_secret.* filter=remove-sensitive
-**/credentials.* filter=remove-sensitive
-**/*test_report*.md filter=remove-sensitive
-**/*test_results*.json filter=remove-sensitive
-
-# Archive directory (if it gets recreated)
-archive/** filter=remove-sensitive
-
-# Language-specific settings
+# Language-specific diff
 *.py diff=python
 *.R diff=r

.gitignore

@@ -1,137 +1,65 @@
-# R related
+# R
 .Rproj.user
 .Rhistory
 .RData
 .Ruserdata
 *.Rcheck
 *.tar.gz
-.build_files
-logs/
-test_logs/
-.DS_Store
-
-# R package build files
 R/Meta/
 R/doc/
 R/inst/doc/
 R/vignettes/*.html
 R/vignettes/*.pdf
-
-# R cache and temporary files
 R/consensus_cache/
 R/cache/
 R/*_cache/
 R/*.rds
 R/*.pdf
 R/*.png
 R/*.jpg
-R/*.jpeg
-
-# API keys and sensitive files
-R/api_keys.env
 R/examples/
-*.env
-*api_key*
-*secret*
+R/.Rcheck-ignore
 
-# Python related
+# Python
 __pycache__/
 *.py[cod]
 *$py.class
 *.so
-.Python
-env/
+*.egg-info/
+*.egg
 build/
-develop-eggs/
 dist/
-downloads/
+sdist/
+develop-eggs/
 eggs/
 .eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
-*.egg
+
+# Environments & secrets
 .env
-logs/
-cache/
+*.env
+!.env.template
+venv*/
+env/
 
-# 通用
+# IDE & OS
 .DS_Store
 .idea/
 .vscode/
-test_pbmc3k.R
+.playwright-mcp/
+.pytest_cache/
+.ruff_cache/
 
-# Large files and visualizations
-mLLMCelltype_visualizations/
-mLLMCelltype-poster/
-
-# Test files and results
+# Project-specific
+logs/
+cache/
+demos/
+examples/
 tests/
 R/tests/
-R/.Rcheck-ignore
 test_scripts/
-
-# Web application
-mllmcelltype-web/
-
-# Additional sensitive patterns
-**/api_keys.*
-**/secrets.*
-**/*_key.*
-**/*_secret.*
-**/token.*
-**/*token*
-**/.env.*
-!**/.env.example
-!**/.env.template
-**/config/local.*
-**/credentials.*
-
-# API Key patterns (comprehensive)
-*sk-*
-*sk_*
-*api_key_*
-*apikey*
-*API_KEY*
-*OPENAI_API_KEY*
-*ANTHROPIC_API_KEY*
-*GOOGLE_API_KEY*
-*GEMINI_API_KEY*
-*QWEN_API_KEY*
-*GROK_API_KEY*
-*OPENROUTER_API_KEY*
-*DEEPSEEK_API_KEY*
-*MINIMAX_API_KEY*
-*ZHIPU_API_KEY*
-*STEPFUN_API_KEY*
-
-# Files that might contain API keys
-**/test_report*.md
-**/test_results*.json
-**/langextract_test*.json
-**/*_test_report.md
-**/*_test_results.json
-**/api_test*.py
-**/api_test*.R
-**/test_api*.py
-**/test_api*.R
-
-# Archive and documentation that might contain sensitive info
 archive/
-docs/test_reports/
-docs/api_tests/
-**/LANGEXTRACT_TEST_REPORT.md
-**/API_TEST_*.md
-
-# Demo and development directories
-demos/
-examples/
-test_scripts/
+mllmcelltype-web/
+mLLMCelltype_visualizations/
+mLLMCelltype-poster/
 dev_tools/
-
-# Claude Code
 CLAUDE.md