Reorganize src directory into subdirectories with automatic CMake detection

[debog]

Summary

This PR reorganizes the src directory into logical subdirectories and updates the CMake build system to automatically discover and compile source files. It also renames Utils.H/cpp to RuntimeParams.H/cpp for better clarity.

Directory Structure

Source files have been organized into 6 subdirectories:

• agents/ - Agent containers and core agent definitions (3 files)
• disease/ - Disease modeling components (5 files: parameters, status, hospital model, disease coupling)
• init/ - Initialization and runtime parameters (13 files)
  • census/ - Census data loading and processing
  • infections/ - Initial infection setup and case data
  • urbanpop/ - Urban population data structures
  • RuntimeParams.H/cpp - Runtime parameter management
• interactions/ - All interaction models (8 files: home, school, work, neighborhoods, air travel)
• io/ - Input/output operations (2 files)
• travel/ - Air travel flow data and logic (2 files)

CMake Build System Improvements

The CMake build system has been enhanced to:

• Automatically discover all subdirectories in src/
• Automatically detect and compile all .cpp and .H files in each subdirectory
• Eliminate the need for manual file listing in CMakeLists.txt
• Support adding new files or subdirectories without CMake configuration changes

File Renaming and Reorganization

• Renamed Utils.H/cpp to RuntimeParams.H/cpp for better clarity
• Moved RuntimeParams files from utils/ to init/ directory
• Removed empty utils/ directory
• Updated all include statements throughout the codebase (7 files)
• Updated header guard from UTILS_H_ to RUNTIME_PARAMS_H_
• Updated documentation comments

Changes

• 33 files reorganized into subdirectories (using git mv to preserve history)
• Utils.H/cpp renamed to RuntimeParams.H/cpp with all references updated
• RuntimeParams files moved to init/ directory
• src/CMakeLists.txt simplified from 42 lines to 30 lines
• Build verified to work correctly with all files compiled

Test plan

• CMake configuration succeeds
• Full build completes successfully
• All source files (11 .cpp files + headers) are compiled
• Executable links correctly
• All include statements reference correct file names

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