feat: Replace git worktree with git clone for workspace management

[CarlJi]

Summary

Replace git worktree approach with direct git clone for managing temporary workspaces. This solves the container mounting issues where git commands fail due to missing parent repository references.

Key Changes

• Replaced RepoManager+worktree system with direct git clone approach
• Updated workspace creation methods to use git clone instead of worktree
• Simplified cleanup by removing entire cloned directories
• Each workspace now has complete, independent git repository

Benefits

• ✅ Containers can now use git commands without issues
• ✅ Simplified architecture with no worktree complexity
• ✅ Network efficient with --depth 1 clones
• ✅ Full git functionality available in containers

Closes #321

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