Improve stow conflict handling in setup.sh

[joshukraine]

Summary

Improve the setup script's conflict detection and handling to prevent failures like those reported in #117. The current implementation only checks a predefined list of files for conflicts, but stow may encounter additional conflicts during execution.

Problem

• Setup script fails when encountering unexpected stow conflicts
• Current conflict detection only covers predefined files
• No graceful recovery when stow operations fail
• Users must manually resolve conflicts and re-run entire setup

Proposed Solution

1. Proactive Conflict Detection

• Add detect_stow_conflicts() function using stow --simulate
• Detect ALL potential conflicts before making any changes
• Provide clear reporting of which packages have conflicts

2. Improved Error Handling

• Create run_stow_command() wrapper with better error detection
• Continue processing other packages when one fails
• Provide specific resolution steps for each type of conflict

3. User Choice for Conflict Resolution

• Interactive prompt: backup, adopt, skip, or quit
• Command-line flags for automation:
  • --force: Don't prompt for user input
  • --strategy=[backup|adopt|skip]: Set conflict resolution strategy

4. Enhanced Setup Flow

• Run conflict detection before any stow operations
• Handle conflicts based on user preference
• Report summary of successful/skipped/failed packages

Implementation Tasks

• Add detect_stow_conflicts() function
• Create run_stow_command() wrapper
• Update setup_symlinks() with new conflict handling
• Add command-line argument parsing
• Update usage/help documentation
• Test with various conflict scenarios

Benefits

• Prevents setup failures due to existing config files
• Gives users control over conflict resolution
• Makes setup script more robust and user-friendly
• Enables automated/CI usage with --force flag

Fixes #117