Repository cleanup and reorganization

## Summary
Performed comprehensive cleanup of the dotfiles repository, removing redundant files and reorganizing documentation.

## Work Completed

### Markdown Cleanup
- Analyzed 32 markdown files for redundancy
- Removed obsolete documentation:
- PROJECT_DASHBOARD.md
- go-blocksite/README.md
- karabiner/README.md
- jira/README.md
- git/docs/github-issues/*.md
- Consolidated git documentation from 5 files into GIT_SETUP_GUIDE.md

### Shell Script Analysis
- Analyzed 22 shell scripts
- Removed 6 redundant scripts
- Merged git/setup.sh into install.sh
- Reorganized into logical structure:
- scripts/active/nix-darwin/
- scripts/active/tmux/
- scripts/archive/
- scripts/examples/

### Documentation Structure
- Created .claude/ directory for AI context
- Moved PROJECT.md to .claude/ and generalized content
- Created comprehensive index.md
- Established clear documentation hierarchy

## Improvement Ideas Documented
- Common patterns for abstraction
- Security vulnerabilities identified
- Cross-platform compatibility issues
- Performance improvements noted
- Nix-Darwin integration opportunities

## Files Removed
- Approximately 15 redundant files removed
- Old command and context directories cleaned up
- Legacy documentation consolidated or removed