diff --git a/.gitignore b/.gitignore
index 924a8d8..d4c5b38 100644
--- a/.gitignore
+++ b/.gitignore
@@ -65,10 +65,8 @@ config/config.conf
 local_config.yaml
 user_settings.yaml
 
-# Reference hardlinks
-config/config.conf.template.txt
-scripts/dock-cleanup.command.txt
-config/config.conf.txt
+# User-modified scripts
+app-setup/templates/transmission-done.sh
 
 # Claude Code runtime files
 .claude/
diff --git a/app-setup/app-setup-templates/mount-nas-media.sh b/app-setup/templates/mount-nas-media.sh
similarity index 100%
rename from app-setup/app-setup-templates/mount-nas-media.sh
rename to app-setup/templates/mount-nas-media.sh
diff --git a/app-setup/app-setup-templates/start-plex.sh b/app-setup/templates/start-plex.sh
similarity index 100%
rename from app-setup/app-setup-templates/start-plex.sh
rename to app-setup/templates/start-plex.sh
diff --git a/app-setup/app-setup-templates/start-rclone.sh b/app-setup/templates/start-rclone.sh
similarity index 100%
rename from app-setup/app-setup-templates/start-rclone.sh
rename to app-setup/templates/start-rclone.sh
diff --git a/app-setup/templates/transmission-done-template.sh b/app-setup/templates/transmission-done-template.sh
new file mode 100755
index 0000000..8b13435
--- /dev/null
+++ b/app-setup/templates/transmission-done-template.sh
@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+#
+# transmission-done.sh - Transmission completion script
+# Called when a torrent finishes downloading
+#
+# Environment variables provided by Transmission:
+# TR_APP_VERSION, TR_TIME_LOCALTIME, TR_TORRENT_DIR, TR_TORRENT_HASH,
+# TR_TORRENT_ID, TR_TORRENT_NAME
+
+# Log completion
+LOG_FILE="${HOME}/.local/state/transmission-completion.log"
+mkdir -p "$(dirname "${LOG_FILE}")"
+timestamp=$(date '+%Y-%m-%d %H:%M:%S')
+echo "${timestamp} - Torrent completed: ${TR_TORRENT_NAME:-unknown}" >>"${LOG_FILE}"
+
+# Future: FileBot integration will be added here
+# filebot -rename "${TR_TORRENT_DIR}/${TR_TORRENT_NAME}" --output /path/to/media/library
+
+exit 0
diff --git a/app-setup/transmission-setup.sh b/app-setup/transmission-setup.sh
index 806059d..5ae3e0c 100755
--- a/app-setup/transmission-setup.sh
+++ b/app-setup/transmission-setup.sh
@@ -316,30 +316,12 @@ log "✅ Magnet link handler configuration completed successfully"
 # Create completion script (for FileBot integration later)
 section "Creating Completion Script"
 
-log "Creating transmission-done.sh completion script..."
+log "Copying transmission-done.sh completion script from template..."
 OPERATOR_LOCAL_BIN="$(dirname "${TRANSMISSION_DONE_SCRIPT}")"
-mkdir -p "${OPERATOR_LOCAL_BIN}"
-sudo -iu "${OPERATOR_USERNAME}" tee "${TRANSMISSION_DONE_SCRIPT}" >/dev/null <<'EOF'
-#!/usr/bin/env bash
-#
-# transmission-done.sh - Transmission completion script
-# Called when a torrent finishes downloading
-#
-# Environment variables provided by Transmission:
-# TR_APP_VERSION, TR_TIME_LOCALTIME, TR_TORRENT_DIR, TR_TORRENT_HASH,
-# TR_TORRENT_ID, TR_TORRENT_NAME
-
-# Log completion
-LOG_FILE="${HOME}/.local/state/transmission-completion.log"
-mkdir -p "$(dirname "${LOG_FILE}")"
-echo "$(date '+%Y-%m-%d %H:%M:%S') - Torrent completed: ${TR_TORRENT_NAME:-unknown}" >> "${LOG_FILE}"
-
-# Future: FileBot integration will be added here
-# filebot -rename "${TR_TORRENT_DIR}/${TR_TORRENT_NAME}" --output /path/to/media/library
-
-exit 0
-EOF
+sudo mkdir -p "${OPERATOR_LOCAL_BIN}"
 
+# Copy template script to destination
+sudo cp "${SCRIPT_DIR}/templates/transmission-done.sh" "${TRANSMISSION_DONE_SCRIPT}"
 sudo chmod +x "${TRANSMISSION_DONE_SCRIPT}"
 sudo chown -v "${OPERATOR_USERNAME}" "${TRANSMISSION_DONE_SCRIPT}"
 log "✅ Completion script creation completed successfully"
diff --git a/docs/apps/transmission-setup-README.md b/docs/apps/transmission-setup-README.md
index f61c850..8406606 100644
--- a/docs/apps/transmission-setup-README.md
+++ b/docs/apps/transmission-setup-README.md
@@ -169,6 +169,41 @@ defaults read com.apple.LaunchServices/com.apple.launchservices.secure LSHandler
 - **FileBot**: Completion script prepared for media processing integration
 - **Plex**: Downloads organized for media library integration
 
+### User Customization
+
+#### **Custom Completion Scripts**
+
+The setup creates a default `transmission-done.sh` completion script that logs torrent completion. Users can customize this behavior:
+
+1. **Before Setup**: Create your own `app-setup/templates/transmission-done.sh` script
+   - The setup will use your custom script instead of the default template
+   - Your script will be preserved across repository updates (gitignored)
+
+2. **After Setup**: Modify the deployed script directly
+   - Location: `~/.local/bin/transmission-done.sh` (on the server)
+   - Changes take effect for new torrent completions
+   - Script runs with full user environment and Transmission variables
+
+**Available Environment Variables**:
+
+```bash
+TR_APP_VERSION      # Transmission version
+TR_TIME_LOCALTIME   # Completion timestamp
+TR_TORRENT_DIR      # Download directory path
+TR_TORRENT_HASH     # Torrent hash identifier
+TR_TORRENT_ID       # Transmission internal ID
+TR_TORRENT_NAME     # Torrent display name
+```
+
+**Common Customizations**:
+
+- FileBot automatic processing
+- Email/notification integration  
+- Cloud sync triggers
+- Custom file organization
+- Statistics logging
+- Integration with external APIs
+
 ## Research and Development
 
 ### Preference Key Research
diff --git a/prep-airdrop.sh b/prep-airdrop.sh
index e25fbbe..3b69950 100755
--- a/prep-airdrop.sh
+++ b/prep-airdrop.sh
@@ -746,9 +746,13 @@ if [[ -d "${SCRIPT_SOURCE_DIR}" ]]; then
   done
 
   # Copy template scripts to app-setup/templates
-  copy_with_manifest "${SCRIPT_SOURCE_DIR}/app-setup/app-setup-templates/mount-nas-media.sh" "app-setup/templates/mount-nas-media.sh" "REQUIRED" || echo "Warning: mount-nas-media.sh not found in app-setup-templates directory"
-  copy_with_manifest "${SCRIPT_SOURCE_DIR}/app-setup/app-setup-templates/start-plex.sh" "app-setup/templates/start-plex.sh" "OPTIONAL" || echo "Warning: start-plex.sh not found in app-setup-templates directory"
-  copy_with_manifest "${SCRIPT_SOURCE_DIR}/app-setup/app-setup-templates/start-rclone.sh" "app-setup/templates/start-rclone.sh" "REQUIRED" || echo "Warning: start-rclone.sh not found in app-setup-templates directory"
+  copy_with_manifest "${SCRIPT_SOURCE_DIR}/app-setup/templates/mount-nas-media.sh" "app-setup/templates/mount-nas-media.sh" "REQUIRED" || echo "Warning: mount-nas-media.sh not found in templates directory"
+  copy_with_manifest "${SCRIPT_SOURCE_DIR}/app-setup/templates/start-plex.sh" "app-setup/templates/start-plex.sh" "OPTIONAL" || echo "Warning: start-plex.sh not found in templates directory"
+  copy_with_manifest "${SCRIPT_SOURCE_DIR}/app-setup/templates/start-rclone.sh" "app-setup/templates/start-rclone.sh" "REQUIRED" || echo "Warning: start-rclone.sh not found in templates directory"
+  if [[ ! -f "${SCRIPT_SOURCE_DIR}/app-setup/templates/transmission-done.sh" ]]; then
+    cp "${SCRIPT_SOURCE_DIR}/app-setup/templates/transmission-done-template.sh" "${SCRIPT_SOURCE_DIR}/app-setup/templates/transmission-done.sh"
+  fi
+  copy_with_manifest "${SCRIPT_SOURCE_DIR}/app-setup/templates/transmission-done.sh" "app-setup/templates/transmission-done.sh" "OPTIONAL" || echo "Warning: transmission-done.sh not found in templates directory"
 
   # Copy app setup scripts to app-setup directory
   echo "Copying app setup scripts..."