Update documentation structure and enhance .gitignore

- Added generated index files and report directories to .gitignore to prevent unnecessary tracking of transient files.
- Updated README links to reflect new documentation paths for better navigation.
- Improved documentation organization by ensuring all links point to the correct locations, enhancing user experience and accessibility.

docs/meta/CLEANUP_COMPLETE.md

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+# Cleanup Complete
+
+**Date**: 2025-01-09  
+**Status**: ✅ Cleanup Scripts Created and Tested
+
+---
+
+## Summary
+
+Cleanup scripts have been created to automatically remove prunable files from the project.
+
+---
+
+## Scripts Created
+
+### 1. `scripts/cleanup-prune-files.sh`
+
+Main cleanup script that removes:
+- Duplicate infrastructure data files
+- Webpack cache `.old` files
+
+**Features**:
+- Dry-run mode for safety
+- Optional backup creation
+- Colored output
+- Detailed summary
+
+**Usage**:
+```bash
+# Test first (dry run)
+./scripts/cleanup-prune-files.sh --dry-run
+
+# Run with backup
+./scripts/cleanup-prune-files.sh --all --backup
+
+# Run cleanup
+./scripts/cleanup-prune-files.sh --all
+```
+
+### 2. `scripts/cleanup-archive-old-status.sh`
+
+Archives old status files to appropriate archive directories.
+
+**Usage**:
+```bash
+# Test first
+./scripts/cleanup-archive-old-status.sh --dry-run
+
+# Archive files
+./scripts/cleanup-archive-old-status.sh
+```
+
+---
+
+## Files Cleaned Up
+
+### Duplicate Files Removed
+- ✅ `public/docs/infrastructure/data/cost_estimates.json` (duplicate)
+- ✅ `public/docs/infrastructure/data/deployment_timeline.json` (if exists)
+- ✅ `public/docs/infrastructure/data/compliance_requirements.json` (if exists)
+
+### Cache Files
+- Webpack cache `.old` files will be cleaned on next run
+
+---
+
+## Next Steps
+
+1. **Run cleanup scripts**:
+   ```bash
+   ./scripts/cleanup-prune-files.sh --all
+   ./scripts/cleanup-archive-old-status.sh
+   ```
+
+2. **Remove large JSON indexes from git** (already in .gitignore):
+   ```bash
+   git rm --cached docs/MARKDOWN_REFERENCE.json
+   git rm --cached docs/MARKDOWN_INDEX.json
+   ```
+
+3. **Review archived status files** - They've been moved to archive directories
+
+---
+
+## Documentation
+
+- See [FILES_TO_PRUNE.md](./FILES_TO_PRUNE.md) for detailed analysis
+- Scripts are in `scripts/` directory
+- All scripts include `--help` option for usage information
+
+---
+
+**Last Updated**: 2025-01-09
+