Update docs, build tools, and add validation caching

[IB-Tool]

Summary

This pull request includes the following changes:

1. Documentation Updates:

   • Expanded description of IB-Tool 3 in README.md.
   • Added context for ArcGIS adaptation.
   • Refined details about building density analysis.

2. Build System Improvements:

   • Replaced deprecated PEP8 tool with Flake8 in the Makefile for style checks.
   • Updated Pylint comments for improved clarity.

3. Validation Optimization:

   • Implemented a per-file caching mechanism for validation results.
   • Optimized validation to reuse checks for unchanged files, improving performance.

Checklist

• Tests added/updated, if applicable.
• Documentation updated, if applicable.
• Build system improvements functional.
• Code changes reviewed and approved.