Fix design philosophy violations and improve test harness

- Remove all direct filesystem operations from gitoxide_manager.rs
- Implement proper fallback chain: gitoxide -> git2 -> CLI
- Clean up existing submodule state using git commands only
- Simplify test harness to use git commands instead of filesystem ops
- Remove unused clone methods and cleanup functions
- Fix method name references and compilation errors

Progress: 6 tests passing, 8 failing (down from 14 failing)
Main remaining issue: test remote repository setup needs proper branch initialization

Author: codegen-sh[bot]

debug_test

@@ -0,0 +1,96 @@
+use std::process::Command;
+use std::fs;
+
+fn main() -> Result<(), Box<dyn std::error::Error>> {
+    let temp_dir = std::env::temp_dir().join("debug_git_test");
+    fs::create_dir_all(&temp_dir)?;
+    let remote_dir = temp_dir.join("test.git");
+    
+    println!("Creating remote at: {}", remote_dir.display());
+    
+    // Initialize bare repository
+    let output = Command::new("git")
+        .args(["init", "--bare", "--initial-branch=main"])
+        .arg(&remote_dir)
+        .output()?;
+    
+    println!("Init output: {}", String::from_utf8_lossy(&output.stderr));
+    
+    // Create a working copy
+    let work_copy = temp_dir.join("test_work");
+    let output = Command::new("git")
+        .args(["clone", remote_dir.to_str().unwrap(), work_copy.to_str().unwrap()])
+        .output()?;
+    
+    println!("Clone output: {}", String::from_utf8_lossy(&output.stderr));
+    
+    // Check branch
+    let output = Command::new("git")
+        .args(["branch"])
+        .current_dir(&work_copy)
+        .output()?;
+    
+    println!("Branch output: {}", String::from_utf8_lossy(&output.stdout));
+    
+    // Try to create main branch
+    let output = Command::new("git")
+        .args(["checkout", "-b", "main"])
+        .current_dir(&work_copy)
+        .output()?;
+    
+    println!("Checkout output: {}", String::from_utf8_lossy(&output.stderr));
+    
+    // Add content
+    fs::write(work_copy.join("test.txt"), "test content")?;
+    
+    // Configure git
+    Command::new("git")
+        .args(["config", "user.name", "Test User"])
+        .current_dir(&work_copy)
+        .output()?;
+    
+    Command::new("git")
+        .args(["config", "user.email", "[email protected]"])
+        .current_dir(&work_copy)
+        .output()?;
+    
+    // Add and commit
+    let output = Command::new("git")
+        .args(["add", "."])
+        .current_dir(&work_copy)
+        .output()?;
+    
+    println!("Add output: {}", String::from_utf8_lossy(&output.stderr));
+    
+    let output = Command::new("git")
+        .args(["commit", "-m", "Initial commit"])
+        .current_dir(&work_copy)
+        .output()?;
+    
+    println!("Commit output: {}", String::from_utf8_lossy(&output.stderr));
+    
+    // Push
+    let output = Command::new("git")
+        .args(["push", "origin", "main"])
+        .current_dir(&work_copy)
+        .output()?;
+    
+    println!("Push output: {}", String::from_utf8_lossy(&output.stderr));
+    
+    // Test cloning the remote
+    let test_clone = temp_dir.join("test_clone");
+    let output = Command::new("git")
+        .args(["clone", remote_dir.to_str().unwrap(), test_clone.to_str().unwrap()])
+        .output()?;
+    
+    println!("Test clone output: {}", String::from_utf8_lossy(&output.stderr));
+    
+    // Check if files exist
+    println!("Files in test clone:");
+    for entry in fs::read_dir(&test_clone)? {
+        let entry = entry?;
+        println!("  {}", entry.file_name().to_string_lossy());
+    }
+    
+    Ok(())
+}