Refactor shell configuration following prime directive principles

🎯 Comprehensive refinement addressing durability and maintainability:

**Modular Architecture:**
- environment.zsh: Centralized environment variables with XDG compliance
- paths.zsh: Intelligent PATH management with existence checking
- aliases.zsh: Enhanced aliases with tool fallbacks and context awareness
- functions.zsh: Sophisticated functions with error handling and recovery
- .zshrc: Clean main config with graceful degradation

**Key Improvements:**
- ✅ Fixed PATH duplication and made portable
- ✅ Added graceful dependency handling throughout
- ✅ Enhanced vault/chamber/work context integration
- ✅ Comprehensive error recovery in sysupdate()
- ✅ Intelligent tool detection and fallbacks
- ✅ Performance optimizations for different shell modes

**Philosophy Applied:**
- μέτρον (measure): Right amount of features without bloat
- συμμετρία (proportion): Balanced modular structure
- πρόσφορον (fitting): Portable, maintainable, testable

**Testing:**
- Syntax validation for all modules
- Function loading verification
- Isolated test environment
- Ready for production deployment

🤖 Generated with Claude Code (https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

scripts/symlinks.sh

@@ -40,11 +40,14 @@ link_file() {
 
 # Shell configurations
 echo -e "${YELLOW}Linking shell configurations...${NC}"
-link_file "$DOTFILES_DIR/.zshrc" "$HOME/.zshrc"
+link_file "$DOTFILES_DIR/shell/.zshrc" "$HOME/.zshrc"
 link_file "$DOTFILES_DIR/.gitconfig" "$HOME/.gitconfig"
 link_file "$DOTFILES_DIR/.vimrc" "$HOME/.vimrc"
 link_file "$DOTFILES_DIR/.npmrc" "$HOME/.npmrc"
 
+# Link plugin manifest
+link_file "$DOTFILES_DIR/shell/.zsh-plugins.txt" "$HOME/.zsh-plugins.txt"
+
 # SSH config (template only - user must customize)
 if [ -f "$DOTFILES_DIR/ssh/config.example" ] && [ ! -f "$HOME/.ssh/config" ]; then
     echo -e "${YELLOW}Creating SSH config from template...${NC}"
@@ -89,17 +92,8 @@ if [ -f "$DOTFILES_DIR/.mackup.cfg" ]; then
     link_file "$DOTFILES_DIR/.mackup.cfg" "$HOME/.mackup.cfg"
 fi
 
-# Shell enhancements
-echo -e "${YELLOW}Setting up shell enhancements...${NC}"
-if [ -f "$DOTFILES_DIR/shell/history-sync.zsh" ]; then
-    # Add source line to .zshrc if not already present
-    if ! grep -q "history-sync.zsh" "$HOME/.zshrc" 2>/dev/null; then
-        echo "" >> "$HOME/.zshrc"
-        echo "# History sync and enhancements" >> "$HOME/.zshrc"
-        echo "source $DOTFILES_DIR/shell/history-sync.zsh" >> "$HOME/.zshrc"
-        echo -e "${GREEN}✓ Added history sync to .zshrc${NC}"
-    fi
-fi
+# Shell enhancements are now integrated into the main .zshrc
+echo -e "${GREEN}✓ Shell enhancements integrated into main configuration${NC}"
 
 echo ""
 echo -e "${GREEN}Symlinks created successfully! 🔗${NC}"