fix: Remove trailing whitespace and add end-of-file newlines

- Fix trailing whitespace in configuration and documentation files
- Add missing newlines at end of files to comply with pre-commit hooks
- Ensure GitHub Actions pre-commit checks will pass

This addresses the CI/CD pipeline failure caused by whitespace formatting issues.

.flake8

@@ -1,11 +1,11 @@
 [flake8]
 max-line-length = 88
-extend-ignore = 
+extend-ignore =
     # E203: whitespace before ':' (conflicts with black)
     E203,
     # W503: line break before binary operator (conflicts with black)
     W503
-exclude = 
+exclude =
     venv,
     .venv,
     __pycache__,
@@ -13,4 +13,4 @@ exclude =
     .pytest_cache
 per-file-ignores =
     # Allow unused imports in __init__.py files
-    __init__.py:F401
+    __init__.py:F401

CHANGELOG.md

@@ -27,11 +27,11 @@ Each entry includes:
 - **Action Type**: ANALYSIS
 - **Component**: Repository Structure
 - **Description**: Conducted comprehensive repository review to understand current state and development requirements
-- **Files Changed**: 
+- **Files Changed**:
   - Created: `planning/repository-review-and-development-roadmap.md`
 - **Tests**: N/A (analysis only)
 - **CI/CD**: No changes
-- **Notes**: 
+- **Notes**:
   - Repository has solid foundation with Flask app, CI/CD, and 22 policy documents
   - Ready to begin Phase 1: Data Ingestion and Processing
   - Current milestone: Task 4 from project-plan.md
@@ -40,7 +40,7 @@ Each entry includes:
 - **Action Type**: CREATE
 - **Component**: Project Structure
 - **Description**: Created planning directory and added to gitignore for private development documents
-- **Files Changed**: 
+- **Files Changed**:
   - Created: `planning/` directory
   - Modified: `.gitignore` (added planning/ entry)
 - **Tests**: N/A
@@ -51,11 +51,11 @@ Each entry includes:
 - **Action Type**: CREATE
 - **Component**: Development Planning
 - **Description**: Created detailed TDD implementation plan for Data Ingestion and Processing milestone
-- **Files Changed**: 
+- **Files Changed**:
   - Created: `planning/tdd-implementation-plan.md`
 - **Tests**: Plan includes comprehensive test strategy
 - **CI/CD**: No changes
-- **Notes**: 
+- **Notes**:
   - Step-by-step TDD approach defined
   - Covers document parser, chunker, and integration pipeline
   - Follows project requirements for reproducibility and error handling
@@ -64,11 +64,11 @@ Each entry includes:
 - **Action Type**: CREATE
 - **Component**: Project Management
 - **Description**: Created comprehensive changelog system for tracking all development actions
-- **Files Changed**: 
+- **Files Changed**:
   - Created: `planning/development-changelog.md`
 - **Tests**: N/A
 - **CI/CD**: No changes
-- **Notes**: 
+- **Notes**:
   - Will be updated after every action taken
   - Provides complete audit trail of development process
   - Includes impact analysis for tests and CI/CD
@@ -77,11 +77,11 @@ Each entry includes:
 - **Action Type**: ANALYSIS
 - **Component**: Development Strategy
 - **Description**: Validated TDD implementation plan against project requirements and current repository state
-- **Files Changed**: 
+- **Files Changed**:
   - Modified: `planning/development-changelog.md`
 - **Tests**: N/A (strategic analysis)
 - **CI/CD**: No changes
-- **Notes**: 
+- **Notes**:
   - Confirmed TDD plan aligns perfectly with project-plan.md milestone 4
   - Verified approach supports all rubric requirements for grade 5
   - Plan follows copilot-instructions.md principles (TDD, plan-driven, CI/CD)
@@ -90,7 +90,7 @@ Each entry includes:
 - **Action Type**: CREATE
 - **Component**: Data Ingestion Pipeline
 - **Description**: Implemented complete document ingestion pipeline using TDD approach
-- **Files Changed**: 
+- **Files Changed**:
   - Created: `tests/test_ingestion/__init__.py`
   - Created: `tests/test_ingestion/test_document_parser.py` (5 tests)
   - Created: `tests/test_ingestion/test_document_chunker.py` (6 tests)
@@ -102,11 +102,11 @@ Each entry includes:
   - Created: `src/ingestion/ingestion_pipeline.py`
 - **Tests**: ✅ 19/19 tests passing
   - Document parser: 5/5 tests pass
-  - Document chunker: 6/6 tests pass  
+  - Document chunker: 6/6 tests pass
   - Integration pipeline: 8/8 tests pass
   - Real corpus test included and passing
 - **CI/CD**: No pipeline run yet (local development)
-- **Notes**: 
+- **Notes**:
   - Full TDD workflow followed: failing tests → implementation → passing tests
   - Supports .txt and .md file formats
   - Character-based chunking with configurable overlap
@@ -119,7 +119,7 @@ Each entry includes:
 - **Action Type**: UPDATE
 - **Component**: Flask Application
 - **Description**: Integrated ingestion pipeline with Flask application and added /ingest endpoint
-- **Files Changed**: 
+- **Files Changed**:
   - Modified: `app.py` (added /ingest endpoint)
   - Created: `src/config.py` (centralized configuration)
   - Modified: `tests/test_app.py` (added ingest endpoint test)
@@ -128,7 +128,7 @@ Each entry includes:
   - All existing tests still pass
   - Manual testing confirms 98 chunks processed from 22 documents
 - **CI/CD**: Ready to test pipeline
-- **Notes**: 
+- **Notes**:
   - /ingest endpoint successfully processes entire corpus
   - Returns JSON with processing statistics
   - Proper error handling implemented
@@ -139,14 +139,14 @@ Each entry includes:
 - **Action Type**: DEPLOY
 - **Component**: CI/CD Pipeline
 - **Description**: Committed and pushed data ingestion pipeline implementation to trigger CI/CD
-- **Files Changed**: 
+- **Files Changed**:
   - All files committed to git
 - **Tests**: ✅ 22/22 tests passing locally
 - **CI/CD**: ✅ Branch pushed to GitHub (feat/data-ingestion-pipeline)
   - Repository has branch protection requiring PRs
   - CI/CD pipeline will run on branch
   - Ready for PR creation and merge
-- **Notes**: 
+- **Notes**:
   - Created feature branch due to repository rules
   - Comprehensive commit message documenting all changes
   - Ready to create PR: https://github.com/sethmcknight/msse-ai-engineering/pull/new/feat/data-ingestion-pipeline
@@ -156,12 +156,12 @@ Each entry includes:
 - **Action Type**: CREATE
 - **Component**: Phase 2 Planning
 - **Description**: Created new feature branch and comprehensive implementation plan for embedding and vector storage
-- **Files Changed**: 
+- **Files Changed**:
   - Created: `planning/phase2-embedding-vector-storage-plan.md`
   - Modified: `planning/development-changelog.md`
 - **Tests**: N/A (planning phase)
 - **CI/CD**: New branch created (`feat/embedding-vector-storage`)
-- **Notes**: 
+- **Notes**:
   - Comprehensive task breakdown with 5 major tasks and 12 subtasks
   - Technical requirements defined (ChromaDB, HuggingFace embeddings)
   - Success criteria established (25+ new tests, performance benchmarks)
@@ -173,13 +173,13 @@ Each entry includes:
 - **Action Type**: CREATE
 - **Component**: Phase 2A Implementation - Embedding Service
 - **Description**: Successfully implemented EmbeddingService with comprehensive TDD approach, fixed dependency issues, and achieved full test coverage
-- **Files Changed**: 
+- **Files Changed**:
   - Created: `src/embedding/embedding_service.py` (94 lines)
   - Created: `tests/test_embedding/test_embedding_service.py` (196 lines, 12 tests)
   - Modified: `requirements.txt` (updated sentence-transformers to v2.7.0)
 - **Tests**: ✅ 12/12 embedding tests passing, 42/42 total tests passing
 - **CI/CD**: All tests pass in local environment, ready for PR
-- **Notes**: 
+- **Notes**:
   - **EmbeddingService Implementation**: Singleton pattern with model caching, batch processing, similarity calculations
   - **Dependency Resolution**: Fixed sentence-transformers import issues by upgrading from v2.2.2 to v2.7.0
   - **Test Coverage**: Comprehensive test suite covering initialization, embeddings, consistency, performance, edge cases
@@ -191,13 +191,13 @@ Each entry includes:
 - **Action Type**: CREATE + TEST
 - **Component**: Phase 2A Integration Testing & Completion
 - **Description**: Created comprehensive integration tests and validated complete Phase 2A foundation layer with full test coverage
-- **Files Changed**: 
+- **Files Changed**:
   - Created: `tests/test_integration.py` (95 lines, 3 integration tests)
   - Created: `planning/phase2a-completion-summary.md` (comprehensive completion documentation)
   - Modified: `planning/development-changelog.md` (this entry)
 - **Tests**: ✅ 45/45 total tests passing (100% success rate)
 - **CI/CD**: All tests pass, system ready for Phase 2B
-- **Notes**: 
+- **Notes**:
   - **Integration Validation**: Complete text → embedding → storage → search workflow tested and working
   - **End-to-End Testing**: Successfully validated EmbeddingService + VectorDatabase integration
   - **Performance Verification**: Model caching working efficiently, operations observed to be fast (no timing recorded)
@@ -209,13 +209,13 @@ Each entry includes:
 - **Action Type**: DEPLOY + COLLABORATE
 - **Component**: Project Documentation & Team Collaboration
 - **Description**: Moved development changelog to root directory and committed to git for better team collaboration and visibility
-- **Files Changed**: 
+- **Files Changed**:
   - Moved: `planning/development-changelog.md` → `CHANGELOG.md` (root directory)
   - Modified: `README.md` (added Development Progress section)
   - Committed: All Phase 2A changes to `feat/embedding-vector-storage` branch
 - **Tests**: N/A (documentation/collaboration improvement)
 - **CI/CD**: Branch pushed to GitHub with comprehensive commit history
-- **Notes**: 
+- **Notes**:
   - **Team Collaboration**: CHANGELOG.md now visible in repository for partner collaboration
   - **Comprehensive Commit**: All Phase 2A changes committed with detailed descriptions
   - **Documentation Enhancement**: README updated to reference changelog for development tracking
@@ -227,14 +227,14 @@ Each entry includes:
 - **Action Type**: FIX + CI/CD
 - **Component**: Code Quality & CI/CD Pipeline
 - **Description**: Fixed code formatting and linting issues to ensure CI/CD pipeline passes successfully
-- **Files Changed**: 
+- **Files Changed**:
   - Modified: 22 Python files (black formatting, isort import ordering)
   - Removed: Unused imports (pytest, pathlib, numpy, Union types)
   - Fixed: Line length issues, whitespace, end-of-file formatting
   - Merged: Remote pre-commit hook changes with local fixes
 - **Tests**: ✅ 45/45 tests still passing after formatting changes
 - **CI/CD**: ✅ Branch ready to pass pre-commit hooks and automated checks
-- **Notes**: 
+- **Notes**:
   - **Formatting Compliance**: All Python files now conform to black, isort, and flake8 standards
   - **Import Cleanup**: Removed unused imports to eliminate F401 errors
   - **Line Length**: Fixed E501 errors by splitting long lines appropriately
@@ -246,7 +246,7 @@ Each entry includes:
 - **Action Type**: CREATE + TOOLING
 - **Component**: Local CI/CD Testing Infrastructure
 - **Description**: Created comprehensive local CI/CD testing infrastructure to prevent GitHub Actions pipeline failures
-- **Files Changed**: 
+- **Files Changed**:
   - Created: `scripts/local-ci-check.sh` (complete CI/CD pipeline simulation)
   - Created: `scripts/format.sh` (quick formatting utility)
   - Created: `Makefile` (convenient development commands)
@@ -254,7 +254,7 @@ Each entry includes:
   - Modified: `pyproject.toml` (added tool configurations for black, isort, pytest)
 - **Tests**: ✅ 45/45 tests passing, all formatting checks pass
 - **CI/CD**: ✅ Local infrastructure mirrors GitHub Actions pipeline perfectly
-- **Notes**: 
+- **Notes**:
   - **Local Testing**: Can now run full CI/CD checks before pushing to prevent failures
   - **Developer Workflow**: Simple commands (`make ci-check`, `make format`) for daily development
   - **Tool Configuration**: Centralized configuration for black (88-char lines), isort (black-compatible), flake8
@@ -267,7 +267,7 @@ Each entry includes:
 - **Action Type**: ORGANIZE + UPDATE
 - **Component**: Development Infrastructure Organization & Documentation
 - **Description**: Organized development tools into proper structure and updated project documentation
-- **Files Changed**: 
+- **Files Changed**:
   - Moved: `scripts/*` → `dev-tools/` (better organization)
   - Created: `dev-tools/README.md` (comprehensive tool documentation)
   - Modified: `Makefile` (updated paths to dev-tools)
@@ -276,7 +276,7 @@ Each entry includes:
   - Modified: `CHANGELOG.md` (this entry)
 - **Tests**: ✅ 45/45 tests passing, all tools working after reorganization
 - **CI/CD**: ✅ All tools function correctly from new locations
-- **Notes**: 
+- **Notes**:
   - **Better Organization**: Development tools now in dedicated `dev-tools/` folder with documentation
   - **Team Onboarding**: Clear documentation for new developers in dev-tools/README.md
   - **Improved .gitignore**: Added coverage for testing artifacts, IDE files, OS files

Makefile

@@ -54,4 +54,4 @@ clean:
 	@echo "🧹 Cleaning cache and temporary files..."
 	@find . -type d -name "__pycache__" -exec rm -rf {} +
 	@find . -type d -name ".pytest_cache" -exec rm -rf {} +
-	@find . -type f -name "*.pyc" -delete
+	@find . -type f -name "*.pyc" -delete

README.md

@@ -82,7 +82,7 @@ make format && make ci-check
 
 # 3. If everything passes, commit and push
 git add .
-git commit -m "Your commit message"  
+git commit -m "Your commit message"
 git push origin your-branch
 ```
 
@@ -93,7 +93,7 @@ For detailed information about the development tools, see [`dev-tools/README.md`
 For detailed development progress, implementation decisions, and technical changes, see [`CHANGELOG.md`](./CHANGELOG.md). The changelog provides:
 
 - Chronological development history
-- Technical implementation details  
+- Technical implementation details
 - Test results and coverage metrics
 - Component integration status
 - Performance benchmarks and optimization notes

dev-tools/README.md

@@ -77,4 +77,4 @@ git push origin your-branch
 - All tools respect the project's virtual environment (`./venv/`)
 - Configuration matches GitHub Actions pre-commit hooks exactly
 - Scripts provide helpful error messages and suggested fixes
-- Designed to be run frequently during development
+- Designed to be run frequently during development

dev-tools/format.sh

@@ -28,4 +28,4 @@ else
 fi
 
 echo ""
-echo -e "${GREEN}🎉 Formatting complete! Your code is ready.${NC}"
+echo -e "${GREEN}🎉 Formatting complete! Your code is ready.${NC}"

dev-tools/local-ci-check.sh

@@ -55,7 +55,7 @@ echo "Running: isort --check-only ."
 if isort --check-only .; then
     print_success "Import sorting check passed"
 else
-    print_error "Import sorting check failed" 
+    print_error "Import sorting check failed"
     echo "💡 Fix with: isort ."
     FAILED=1
 fi
@@ -108,4 +108,4 @@ else
     echo "Please fix the issues above before pushing."
     echo "This will prevent CI/CD pipeline failures on GitHub."
     exit 1
-fi
+fi

pyproject.toml

@@ -38,4 +38,4 @@ addopts = "-v --tb=short"
 filterwarnings = [
     "ignore::DeprecationWarning",
     "ignore::PendingDeprecationWarning",
-]
+]