diff --git a/.gitignore b/.gitignore
index 611e363..7b94e27 100644
--- a/.gitignore
+++ b/.gitignore
@@ -35,3 +35,6 @@ crontab/crontab-backups/*/archive/
 # backblaze cli <https://www.backblaze.com/docs/cloud-storage-command-line-tools>
 #   can be downloaded from <https://github.com/Backblaze/B2_Command_Line_Tool/releases/latest/download/b2-linux>
 immich/b2-linux
+
+# Generated dotfiles - these are created dynamically by bootstrap process
+dotfiles/my-aliases.zsh
diff --git a/cleanup-alias-tracking.sh b/cleanup-alias-tracking.sh
new file mode 100755
index 0000000..f18b71d
--- /dev/null
+++ b/cleanup-alias-tracking.sh
@@ -0,0 +1,176 @@
+#!/bin/bash
+
+# Cleanup script for removing my-aliases.zsh from git tracking
+# This script handles the repository cleanup needed after the alias file
+# was changed from tracked to dynamically generated
+
+set -e
+
+# Colors for output
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+RED='\033[0;31m'
+BLUE='\033[0;34m'
+NC='\033[0m' # No Color
+
+# Script directory and repository root
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$SCRIPT_DIR"
+
+echo -e "${BLUE}=== Alias File Tracking Cleanup Script ===${NC}"
+echo -e "${YELLOW}This script will remove my-aliases.zsh from git tracking${NC}"
+echo -e "${YELLOW}and update .gitignore to prevent future conflicts.${NC}"
+echo ""
+
+# Verify we're in a git repository
+if [ ! -d "$REPO_ROOT/.git" ]; then
+    echo -e "${RED}Error: Not in a git repository${NC}"
+    echo "Please run this script from the root of your shell repository"
+    exit 1
+fi
+
+# Change to repository root
+cd "$REPO_ROOT"
+
+# Check current git status
+echo -e "${BLUE}=== Current Git Status ===${NC}"
+git status --porcelain
+
+# Check if my-aliases.zsh is currently tracked
+if git ls-files --error-unmatch dotfiles/my-aliases.zsh >/dev/null 2>&1; then
+    echo -e "${YELLOW}my-aliases.zsh is currently tracked by git${NC}"
+    ALIASES_TRACKED=true
+else
+    echo -e "${GREEN}my-aliases.zsh is already untracked${NC}"
+    ALIASES_TRACKED=false
+fi
+
+# Check if .gitignore already has the entry
+if grep -q "dotfiles/my-aliases.zsh" .gitignore 2>/dev/null; then
+    echo -e "${GREEN}.gitignore already contains entry for my-aliases.zsh${NC}"
+    GITIGNORE_UPDATED=true
+else
+    echo -e "${YELLOW}.gitignore needs to be updated${NC}"
+    GITIGNORE_UPDATED=false
+fi
+
+# Prompt for confirmation
+echo ""
+echo -e "${YELLOW}Actions that will be performed:${NC}"
+if [ "$ALIASES_TRACKED" = true ]; then
+    echo "  1. Remove dotfiles/my-aliases.zsh from git tracking"
+fi
+if [ "$GITIGNORE_UPDATED" = false ]; then
+    echo "  2. Add dotfiles/my-aliases.zsh to .gitignore"
+fi
+if [ "$ALIASES_TRACKED" = true ] || [ "$GITIGNORE_UPDATED" = false ]; then
+    echo "  3. Commit the changes"
+else
+    echo "  → No changes needed - cleanup already complete"
+fi
+
+echo ""
+read -p "Continue? (y/N): " -n 1 -r
+echo
+if [[ ! $REPLY =~ ^[Yy]$ ]]; then
+    echo -e "${YELLOW}Cleanup cancelled${NC}"
+    exit 0
+fi
+
+# Step 1: Remove from git tracking if needed
+if [ "$ALIASES_TRACKED" = true ]; then
+    echo -e "${BLUE}=== Removing my-aliases.zsh from git tracking ===${NC}"
+
+    # Check if file exists and remove from tracking
+    if [ -f "dotfiles/my-aliases.zsh" ]; then
+        git rm --cached dotfiles/my-aliases.zsh
+        echo -e "${GREEN}✓ Removed dotfiles/my-aliases.zsh from git tracking${NC}"
+    else
+        # File doesn't exist but is tracked - remove from index anyway
+        git rm --cached dotfiles/my-aliases.zsh 2>/dev/null || true
+        echo -e "${GREEN}✓ Removed non-existent dotfiles/my-aliases.zsh from git index${NC}"
+    fi
+fi
+
+# Step 2: Update .gitignore if needed
+if [ "$GITIGNORE_UPDATED" = false ]; then
+    echo -e "${BLUE}=== Updating .gitignore ===${NC}"
+
+    # Check if the "Generated dotfiles" section already exists
+    if grep -q "Generated dotfiles" .gitignore 2>/dev/null; then
+        # Add to existing section
+        if ! grep -q "dotfiles/my-aliases.zsh" .gitignore; then
+            sed -i '/# Generated dotfiles/a dotfiles/my-aliases.zsh' .gitignore
+            echo -e "${GREEN}✓ Added entry to existing Generated dotfiles section${NC}"
+        fi
+    else
+        # Create new section
+        echo "" >> .gitignore
+        echo "# Generated dotfiles - these are created dynamically by bootstrap process" >> .gitignore
+        echo "dotfiles/my-aliases.zsh" >> .gitignore
+        echo -e "${GREEN}✓ Added new Generated dotfiles section to .gitignore${NC}"
+    fi
+fi
+
+# Step 3: Check if we have changes to commit
+if git diff --cached --quiet && git diff --quiet; then
+    echo -e "${GREEN}=== No changes to commit - cleanup already complete ===${NC}"
+else
+    echo -e "${BLUE}=== Committing changes ===${NC}"
+
+    # Add .gitignore changes if any
+    git add .gitignore
+
+    # Create commit message
+    COMMIT_MSG="Remove my-aliases.zsh from tracking, add to .gitignore
+
+- Remove dotfiles/my-aliases.zsh from git tracking to prevent conflicts
+- Add to .gitignore as it's now dynamically generated by bootstrap
+- Aliases are now created from my-aliases.zsh.original template"
+
+    # Commit the changes
+    git commit -m "$COMMIT_MSG"
+    echo -e "${GREEN}✓ Changes committed successfully${NC}"
+fi
+
+# Step 4: Verify the cleanup
+echo -e "${BLUE}=== Verification ===${NC}"
+
+# Check that file is no longer tracked
+if ! git ls-files --error-unmatch dotfiles/my-aliases.zsh >/dev/null 2>&1; then
+    echo -e "${GREEN}✓ dotfiles/my-aliases.zsh is no longer tracked${NC}"
+else
+    echo -e "${RED}✗ dotfiles/my-aliases.zsh is still tracked${NC}"
+fi
+
+# Check that .gitignore contains the entry
+if grep -q "dotfiles/my-aliases.zsh" .gitignore; then
+    echo -e "${GREEN}✓ .gitignore contains entry for dotfiles/my-aliases.zsh${NC}"
+else
+    echo -e "${RED}✗ .gitignore missing entry for dotfiles/my-aliases.zsh${NC}"
+fi
+
+# Show final git status
+echo -e "${BLUE}=== Final Git Status ===${NC}"
+git status --porcelain
+
+# Check if we need to push
+if git log --oneline origin/main..HEAD 2>/dev/null | grep -q "Remove my-aliases.zsh"; then
+    echo ""
+    echo -e "${YELLOW}=== Push Required ===${NC}"
+    echo -e "${YELLOW}You have local commits that need to be pushed to the remote repository.${NC}"
+    echo "Run: ${BLUE}git push origin main${NC}"
+elif ! git remote >/dev/null 2>&1; then
+    echo -e "${YELLOW}No remote repository configured${NC}"
+else
+    echo -e "${GREEN}Repository is up to date with remote${NC}"
+fi
+
+echo ""
+echo -e "${GREEN}=== Cleanup Complete! ===${NC}"
+echo -e "${GREEN}The my-aliases.zsh file is now properly configured as a generated file.${NC}"
+echo ""
+echo -e "${YELLOW}Next steps:${NC}"
+echo "1. Push changes if needed: ${BLUE}git push origin main${NC}"
+echo "2. Run bootstrap/setup on this system to regenerate aliases"
+echo "3. The aliases file will now be created dynamically without git conflicts"
diff --git a/docs/cleanup-alias-tracking.md b/docs/cleanup-alias-tracking.md
new file mode 100644
index 0000000..61fec57
--- /dev/null
+++ b/docs/cleanup-alias-tracking.md
@@ -0,0 +1,148 @@
+# Alias File Tracking Cleanup
+
+## Overview
+
+The `cleanup-alias-tracking.sh` script is designed to clean up the git repository on systems where `dotfiles/my-aliases.zsh` was previously tracked but should now be treated as a dynamically generated file.
+
+## Problem Context
+
+Originally, `my-aliases.zsh` was tracked in git, but this caused conflicts when the bootstrap process tried to update it with system-specific aliases. The file is now:
+
+- **Generated dynamically** from `my-aliases.zsh.original` template
+- **Customized per system** (debian vs ubuntu vs fedora)
+- **Should not be tracked** in git to prevent conflicts
+
+## What This Script Does
+
+1. **Removes git tracking** of `dotfiles/my-aliases.zsh`
+2. **Updates .gitignore** to ignore the file
+3. **Commits the changes** with a descriptive message
+4. **Verifies the cleanup** was successful
+5. **Provides next steps** for pushing and regenerating aliases
+
+## Usage
+
+### On Each System You Manage
+
+```bash
+# Navigate to your shell repository
+cd ~/shell
+
+# Run the cleanup script
+./cleanup-alias-tracking.sh
+```
+
+### What You'll See
+
+The script will:
+- Show current git status
+- Check if the file is currently tracked
+- Check if .gitignore already has the entry
+- Ask for confirmation before making changes
+- Perform the cleanup
+- Verify the results
+
+### Example Output
+
+```
+=== Alias File Tracking Cleanup Script ===
+This script will remove my-aliases.zsh from git tracking
+and update .gitignore to prevent future conflicts.
+
+=== Current Git Status ===
+M  dotfiles/my-aliases.zsh
+
+my-aliases.zsh is currently tracked by git
+.gitignore needs to be updated
+
+Actions that will be performed:
+  1. Remove dotfiles/my-aliases.zsh from git tracking
+  2. Add dotfiles/my-aliases.zsh to .gitignore
+  3. Commit the changes
+
+Continue? (y/N): y
+
+=== Removing my-aliases.zsh from git tracking ===
+✓ Removed dotfiles/my-aliases.zsh from git tracking
+
+=== Updating .gitignore ===
+✓ Added new Generated dotfiles section to .gitignore
+
+=== Committing changes ===
+✓ Changes committed successfully
+
+=== Verification ===
+✓ dotfiles/my-aliases.zsh is no longer tracked
+✓ .gitignore contains entry for dotfiles/my-aliases.zsh
+
+=== Final Git Status ===
+(clean working directory)
+
+=== Cleanup Complete! ===
+```
+
+## After Running the Script
+
+1. **Push the changes** to your repository:
+   ```bash
+   git push origin main
+   ```
+
+2. **Regenerate the aliases** on the system:
+   ```bash
+   # Run setup to regenerate aliases from template
+   ~/shell/setup/setup.sh
+   ```
+
+3. **Verify aliases work**:
+   ```bash
+   # Source your shell config or start a new terminal
+   source ~/.zshrc
+
+   # Test aliases
+   ll  # Should work if aliases were generated correctly
+   ```
+
+## Safety Features
+
+- **Confirmation prompt** before making any changes
+- **Git status checks** to show what will be affected
+- **Verification steps** to ensure cleanup was successful
+- **No data loss** - the script only removes tracking, not the actual file
+- **Idempotent** - safe to run multiple times
+
+## Troubleshooting
+
+### Script Says "No changes needed"
+
+This means the cleanup was already done on this system. You can verify by checking:
+```bash
+git ls-files | grep my-aliases.zsh  # Should return nothing
+grep "my-aliases.zsh" .gitignore    # Should show the ignore entry
+```
+
+### File Still Shows as Modified
+
+If `my-aliases.zsh` still shows as modified after cleanup:
+1. This is normal - the file exists locally but is now ignored
+2. Delete the local file: `rm dotfiles/my-aliases.zsh`
+3. Run setup to regenerate: `~/shell/setup/setup.sh`
+
+### Merge Conflicts on Other Systems
+
+If you get merge conflicts when pulling:
+1. Run this cleanup script first
+2. Then pull the latest changes
+3. The conflicts should be resolved automatically
+
+## Files Modified
+
+- **dotfiles/my-aliases.zsh** - Removed from git tracking
+- **.gitignore** - Added ignore entry with explanatory comment
+- **Git history** - One commit documenting the change
+
+## Related Files
+
+- **dotfiles/my-aliases.zsh.original** - Template file (remains tracked)
+- **setup/setup.sh** - Script that generates aliases from template
+- **~/.oh-my-zsh/custom/aliases.zsh** - Final generated aliases location