diff --git a/Cargo.lock b/Cargo.lock
index 80ed409e8..7619ec293 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -139,6 +139,7 @@ dependencies = [
  "assert_cmd",
  "async-trait",
  "axum",
+ "base64",
  "chrono",
  "clap",
  "daytona-api-client",
diff --git a/crates/arc-attractor/Cargo.toml b/crates/arc-attractor/Cargo.toml
index 669be12e1..2988d63e1 100644
--- a/crates/arc-attractor/Cargo.toml
+++ b/crates/arc-attractor/Cargo.toml
@@ -44,6 +44,7 @@ dirs = "6"
 dialoguer.workspace = true
 daytona-sdk.workspace = true
 daytona-api-client.workspace = true
+base64.workspace = true
 scopeguard = "1"
 git2.workspace = true
 tokio-util.workspace = true
diff --git a/crates/arc-attractor/src/cli/run.rs b/crates/arc-attractor/src/cli/run.rs
index 2f38321a6..993d98f2a 100644
--- a/crates/arc-attractor/src/cli/run.rs
+++ b/crates/arc-attractor/src/cli/run.rs
@@ -8,7 +8,7 @@ use chrono::{Local, Utc};
 use arc_util::terminal::Styles;
 
 use crate::checkpoint::Checkpoint;
-use crate::engine::{PipelineEngine, RunConfig};
+use crate::engine::{GitCheckpointMode, PipelineEngine, RunConfig};
 use crate::event::EventEmitter;
 use crate::handler::default_registry;
 use crate::interviewer::auto_approve::AutoApproveInterviewer;
@@ -107,10 +107,11 @@ pub async fn run_command(args: RunArgs, styles: &'static Styles) -> anyhow::Resu
         args.execution_env.or(toml_exec).unwrap_or_default()
     };
     let original_cwd = std::env::current_dir()?;
-    let git_clean = if execution_env_kind_preview == ExecutionEnvKind::Local {
-        crate::git::ensure_clean(&original_cwd).is_ok()
-    } else {
-        false
+    let git_clean = match execution_env_kind_preview {
+        ExecutionEnvKind::Local | ExecutionEnvKind::Docker => {
+            crate::git::ensure_clean(&original_cwd).is_ok()
+        }
+        ExecutionEnvKind::Daytona => false,
     };
 
     // 3. Create logs directory
@@ -346,6 +347,22 @@ pub async fn run_command(args: RunArgs, styles: &'static Styles) -> anyhow::Resu
         }
     });
 
+    // Set up git inside Daytona sandbox (if applicable)
+    let (daytona_run_id, daytona_base_sha, daytona_branch) = if execution_env_kind == ExecutionEnvKind::Daytona {
+        match setup_daytona_git(&*execution_env).await {
+            Ok((rid, base, branch)) => (Some(rid), Some(base), Some(branch)),
+            Err(e) => {
+                eprintln!(
+                    "{yellow}Warning:{reset} Daytona git setup failed ({e}), running without git checkpoints.",
+                    yellow = styles.yellow, reset = styles.reset,
+                );
+                (None, None, None)
+            }
+        }
+    } else {
+        (None, None, None)
+    };
+
     // Run setup commands inside the execution environment (once, not per-stage)
     if !setup_commands.is_empty() {
         emitter.emit(&crate::event::PipelineEvent::SetupStarted { command_count: setup_commands.len() });
@@ -480,15 +497,24 @@ pub async fn run_command(args: RunArgs, styles: &'static Styles) -> anyhow::Resu
     let engine = PipelineEngine::with_interviewer(registry, Arc::clone(&emitter), interviewer, Arc::clone(&execution_env));
 
     // 7. Execute
-    let run_id = worktree_run_id.unwrap_or_else(|| ulid::Ulid::new().to_string());
+    let run_id = worktree_run_id
+        .or(daytona_run_id)
+        .unwrap_or_else(|| ulid::Ulid::new().to_string());
     let config = RunConfig {
         logs_root: logs_dir.clone(),
         cancel_token: None,
         dry_run: dry_run_mode,
         run_id,
-        work_dir: worktree_work_dir,
-        base_sha: worktree_base_sha,
-        run_branch: worktree_branch,
+        git_checkpoint: match execution_env_kind {
+            ExecutionEnvKind::Local | ExecutionEnvKind::Docker => {
+                worktree_work_dir.map(GitCheckpointMode::Host)
+            }
+            ExecutionEnvKind::Daytona => {
+                daytona_base_sha.as_ref().map(|_| GitCheckpointMode::Remote)
+            }
+        },
+        base_sha: worktree_base_sha.or(daytona_base_sha),
+        run_branch: worktree_branch.or(daytona_branch),
     };
 
     let run_start = Instant::now();
@@ -616,6 +642,33 @@ fn setup_worktree(
     Ok((run_id, worktree_path.clone(), worktree_path, branch_name, base_sha))
 }
 
+/// Set up git inside a Daytona sandbox for checkpoint commits.
+/// Returns (run_id, base_sha, branch_name) on success.
+async fn setup_daytona_git(
+    exec_env: &dyn arc_agent::ExecutionEnvironment,
+) -> anyhow::Result<(String, String, String)> {
+    // Get current HEAD as base SHA
+    let sha_result = exec_env.exec_command("git rev-parse HEAD", 10_000, None, None, None).await
+        .map_err(|e| anyhow::anyhow!("git rev-parse HEAD failed: {e}"))?;
+    if sha_result.exit_code != 0 {
+        anyhow::bail!("git rev-parse HEAD failed (exit {}): {}", sha_result.exit_code, sha_result.stderr);
+    }
+    let base_sha = sha_result.stdout.trim().to_string();
+
+    let run_id = ulid::Ulid::new().to_string();
+    let branch_name = format!("arc/run/{run_id}");
+
+    // Create and checkout a run branch
+    let checkout_cmd = format!("git checkout -b {branch_name}");
+    let checkout_result = exec_env.exec_command(&checkout_cmd, 10_000, None, None, None).await
+        .map_err(|e| anyhow::anyhow!("git checkout failed: {e}"))?;
+    if checkout_result.exit_code != 0 {
+        anyhow::bail!("git checkout -b failed (exit {}): {}", checkout_result.exit_code, checkout_result.stderr);
+    }
+
+    Ok((run_id, base_sha, branch_name))
+}
+
 #[cfg(test)]
 mod tests {
     #[test]
diff --git a/crates/arc-attractor/src/daytona_env.rs b/crates/arc-attractor/src/daytona_env.rs
index 70935a741..b6133ea69 100644
--- a/crates/arc-attractor/src/daytona_env.rs
+++ b/crates/arc-attractor/src/daytona_env.rs
@@ -667,9 +667,13 @@ impl ExecutionEnvironment for DaytonaExecutionEnvironment {
 ///
 /// The Daytona API uses direct exec (not a shell), so pipes, env vars,
 /// semicolons, etc. won't work without this wrapper.
+///
+/// Uses base64 encoding (matching the TypeScript/Python/Ruby Daytona SDKs)
+/// to avoid shell escaping issues with quotes and special characters.
 fn wrap_bash_command(command: &str) -> String {
-    // Shell-quote by replacing ' with '\'' then wrapping in single quotes.
-    format!("bash -c '{}'", command.replace('\'', "'\\''"))
+    use base64::Engine;
+    let encoded = base64::engine::general_purpose::STANDARD.encode(command);
+    format!("sh -c \"echo '{encoded}' | base64 -d | sh\"")
 }
 
 #[cfg(test)]
@@ -685,24 +689,29 @@ mod tests {
     }
 
     #[test]
-    fn wrap_bash_simple() {
-        assert_eq!(wrap_bash_command("echo hello"), "bash -c 'echo hello'");
+    fn wrap_bash_uses_base64_encoding() {
+        let wrapped = wrap_bash_command("echo hello");
+        // Should use base64 pipe to sh
+        assert!(wrapped.starts_with("sh -c \"echo '"), "should start with sh -c wrapper");
+        assert!(wrapped.ends_with("' | base64 -d | sh\""), "should end with base64 -d | sh");
+        // The base64 of "echo hello" is "ZWNobyBoZWxsbw=="
+        assert!(wrapped.contains("ZWNobyBoZWxsbw=="), "should contain base64 of 'echo hello'");
     }
 
     #[test]
-    fn wrap_bash_with_pipe() {
-        assert_eq!(
-            wrap_bash_command("ls | grep foo"),
-            "bash -c 'ls | grep foo'"
-        );
+    fn wrap_bash_handles_single_quotes_safely() {
+        // Single quotes in the original command are safely encoded in base64
+        let wrapped = wrap_bash_command("echo 'hello world'");
+        assert!(wrapped.starts_with("sh -c \"echo '"), "should use sh -c wrapper");
+        // No raw single quotes from the original command should appear in the base64
+        assert!(!wrapped.contains("hello world"), "original command should be base64 encoded, not literal");
     }
 
     #[test]
-    fn wrap_bash_escapes_single_quotes() {
-        assert_eq!(
-            wrap_bash_command("echo 'hello world'"),
-            "bash -c 'echo '\\''hello world'\\'''"
-        );
+    fn wrap_bash_handles_pipes() {
+        let wrapped = wrap_bash_command("ls | grep foo");
+        assert!(wrapped.starts_with("sh -c \"echo '"), "should use sh -c wrapper");
+        assert!(wrapped.ends_with("' | base64 -d | sh\""), "should end with base64 -d | sh");
     }
 
     #[test]
diff --git a/crates/arc-attractor/src/engine.rs b/crates/arc-attractor/src/engine.rs
index 9163eb051..f49c9e8ea 100644
--- a/crates/arc-attractor/src/engine.rs
+++ b/crates/arc-attractor/src/engine.rs
@@ -465,6 +465,70 @@ fn is_terminal(node: &Node) -> bool {
 
 // --- Pipeline engine ---
 
+/// How git checkpointing should be performed for a pipeline run.
+#[derive(Debug, Clone)]
+pub enum GitCheckpointMode {
+    /// Run git commands on the host filesystem (local & Docker bind-mount).
+    Host(PathBuf),
+    /// Run git commands inside the remote execution environment via `exec_command`.
+    Remote,
+}
+
+/// Run a git checkpoint commit on the host filesystem (local/Docker bind-mount).
+async fn git_checkpoint_host(work_dir: PathBuf, run_id: String, node_id: String, status: String) -> Option<String> {
+    match tokio::task::spawn_blocking(move || {
+        crate::git::checkpoint_commit(&work_dir, &run_id, &node_id, &status)
+    }).await {
+        Ok(Ok(sha)) => Some(sha),
+        Ok(Err(_)) | Err(_) => None,
+    }
+}
+
+/// Run a git diff on the host filesystem.
+async fn git_diff_host(work_dir: PathBuf, base: String) -> Option<String> {
+    match tokio::task::spawn_blocking(move || {
+        crate::git::diff_against(&work_dir, &base)
+    }).await {
+        Ok(Ok(patch)) => Some(patch),
+        Ok(Err(_)) | Err(_) => None,
+    }
+}
+
+/// Run a git checkpoint commit inside a remote execution environment.
+async fn git_checkpoint_remote(exec_env: &dyn ExecutionEnvironment, run_id: &str, node_id: &str, status: &str) -> Option<String> {
+    // Stage everything
+    let add_result = exec_env.exec_command("git add -A", 30_000, None, None, None).await;
+    if add_result.as_ref().map_or(true, |r| r.exit_code != 0) {
+        return None;
+    }
+
+    // Commit with arc identity
+    let message = format!("arc({run_id}): {node_id} ({status})");
+    let commit_cmd = format!(
+        "git -c user.name=arc -c user.email=arc@local commit --allow-empty -m '{message}'"
+    );
+    let commit_result = exec_env.exec_command(&commit_cmd, 30_000, None, None, None).await;
+    if commit_result.as_ref().map_or(true, |r| r.exit_code != 0) {
+        return None;
+    }
+
+    // Get the new HEAD SHA
+    let sha_result = exec_env.exec_command("git rev-parse HEAD", 10_000, None, None, None).await;
+    match sha_result {
+        Ok(r) if r.exit_code == 0 => Some(r.stdout.trim().to_string()),
+        _ => None,
+    }
+}
+
+/// Run a git diff inside a remote execution environment.
+async fn git_diff_remote(exec_env: &dyn ExecutionEnvironment, base: &str) -> Option<String> {
+    let cmd = format!("git diff {base} HEAD");
+    match exec_env.exec_command(&cmd, 30_000, None, None, None).await {
+        Ok(r) if r.exit_code == 0 => Some(r.stdout),
+        _ => None,
+    }
+}
+
 /// Configuration for a pipeline run.
 pub struct RunConfig {
     pub logs_root: PathBuf,
@@ -472,8 +536,8 @@ pub struct RunConfig {
     pub dry_run: bool,
     /// Unique identifier for this pipeline run.
     pub run_id: String,
-    /// Git worktree path for checkpoint commits.
-    pub work_dir: Option<PathBuf>,
+    /// Git checkpoint mode (None = no checkpointing).
+    pub git_checkpoint: Option<GitCheckpointMode>,
     /// SHA of the commit the worktree branched from.
     pub base_sha: Option<String>,
     /// Git branch name for the run (e.g. `arc/run/{run_id}`).
@@ -714,7 +778,10 @@ impl PipelineEngine {
             run_id: run_id.clone(),
             base_sha: config.base_sha.clone(),
             run_branch: config.run_branch.clone(),
-            worktree_dir: config.work_dir.as_ref().map(|p| p.display().to_string()),
+            worktree_dir: match config.git_checkpoint {
+                Some(GitCheckpointMode::Host(ref p)) => Some(p.display().to_string()),
+                _ => None,
+            },
         });
         self.inform(&format!("Pipeline started: {}", graph.name), "pipeline");
 
@@ -801,7 +868,7 @@ impl PipelineEngine {
 
         // Store run_id and work_dir in context for handlers
         context.set("internal.run_id", serde_json::json!(run_id));
-        if let Some(ref wd) = config.work_dir {
+        if let Some(GitCheckpointMode::Host(ref wd)) = config.git_checkpoint {
             context.set("internal.work_dir", serde_json::json!(wd.to_string_lossy().as_ref()));
         }
 
@@ -1029,58 +1096,57 @@ impl PipelineEngine {
                 });
             }
 
-            // Step 6b: Git checkpoint commit (when running in a worktree)
-            if let Some(ref work_dir) = config.work_dir {
-                let wd = work_dir.clone();
+            // Step 6b: Git checkpoint commit
+            if let Some(ref mode) = config.git_checkpoint {
                 let rid = run_id.clone();
                 let nid = node.id.clone();
                 let status_str = outcome.status.to_string();
-                match tokio::task::spawn_blocking(move || {
-                    crate::git::checkpoint_commit(&wd, &rid, &nid, &status_str)
-                })
-                .await
-                {
-                    Ok(Ok(sha)) => {
-                        checkpoint.git_commit_sha = Some(sha.clone());
-                        if let Err(e) = checkpoint.save(&checkpoint_path) {
-                            context.append_log(format!("checkpoint re-save with SHA failed: {e}"));
-                        }
-                        self.services.emitter.emit(&PipelineEvent::GitCheckpoint {
-                            run_id: run_id.clone(),
-                            node_id: node.id.clone(),
-                            status: outcome.status.to_string(),
-                            git_commit_sha: sha.clone(),
-                        });
 
-                        // Save diff.patch for this stage
-                        let prev = last_git_sha.as_deref()
-                            .or(config.base_sha.as_deref())
-                            .unwrap_or(&sha);
-                        let diff_base = prev.to_string();
-                        let diff_wd = work_dir.clone();
-                        let diff_dest = node_dir(&config.logs_root, &node.id, visit).join("diff.patch");
-                        match tokio::task::spawn_blocking(move || {
-                            crate::git::diff_against(&diff_wd, &diff_base)
-                        }).await {
-                            Ok(Ok(patch)) => {
-                                let _ = std::fs::write(&diff_dest, patch);
-                            }
-                            Ok(Err(e)) => {
-                                context.append_log(format!("git diff failed: {e}"));
-                            }
-                            Err(e) => {
-                                context.append_log(format!("git diff task panicked: {e}"));
-                            }
-                        }
+                let commit_result = match mode {
+                    GitCheckpointMode::Host(work_dir) => {
+                        git_checkpoint_host(work_dir.clone(), rid, nid, status_str).await
+                    }
+                    GitCheckpointMode::Remote => {
+                        git_checkpoint_remote(&*self.services.execution_env, &run_id, &node.id, &outcome.status.to_string()).await
+                    }
+                };
 
-                        last_git_sha = Some(sha);
+                if let Some(sha) = commit_result {
+                    checkpoint.git_commit_sha = Some(sha.clone());
+                    if let Err(e) = checkpoint.save(&checkpoint_path) {
+                        context.append_log(format!("checkpoint re-save with SHA failed: {e}"));
                     }
-                    Ok(Err(e)) => {
-                        context.append_log(format!("git checkpoint commit failed: {e}"));
-                    }
-                    Err(e) => {
-                        context.append_log(format!("git checkpoint commit task panicked: {e}"));
+                    self.services.emitter.emit(&PipelineEvent::GitCheckpoint {
+                        run_id: run_id.clone(),
+                        node_id: node.id.clone(),
+                        status: outcome.status.to_string(),
+                        git_commit_sha: sha.clone(),
+                    });
+
+                    // Save diff.patch for this stage
+                    let prev = last_git_sha.as_deref()
+                        .or(config.base_sha.as_deref())
+                        .unwrap_or(&sha);
+                    let diff_base = prev.to_string();
+                    let diff_dest = node_dir(&config.logs_root, &node.id, visit).join("diff.patch");
+
+                    let diff_result = match mode {
+                        GitCheckpointMode::Host(work_dir) => {
+                            git_diff_host(work_dir.clone(), diff_base).await
+                        }
+                        GitCheckpointMode::Remote => {
+                            git_diff_remote(&*self.services.execution_env, &diff_base).await
+                        }
+                    };
+                    if let Some(patch) = diff_result {
+                        let _ = std::fs::write(&diff_dest, patch);
+                    } else {
+                        context.append_log("git diff failed".to_string());
                     }
+
+                    last_git_sha = Some(sha);
+                } else {
+                    context.append_log("git checkpoint commit failed".to_string());
                 }
             }
 
@@ -1816,7 +1882,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -1834,7 +1900,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -1861,7 +1927,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -1883,7 +1949,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -1901,7 +1967,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -1932,7 +1998,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -1989,7 +2055,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2064,7 +2130,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2091,7 +2157,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2115,7 +2181,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2262,7 +2328,7 @@ mod tests {
         let dir = tempfile::tempdir().unwrap();
         let g = simple_graph();
         let engine = PipelineEngine::new(make_registry(), Arc::new(EventEmitter::new()), local_env());
-        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), work_dir: None, base_sha: None, run_branch: None };
+        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), git_checkpoint: None, base_sha: None, run_branch: None };
         engine.run(&g, &config).await.unwrap();
 
         let manifest_path = dir.path().join("manifest.json");
@@ -2284,7 +2350,7 @@ mod tests {
         g.edges.push(Edge::new("start", "exit"));
 
         let engine = PipelineEngine::new(make_registry(), Arc::new(EventEmitter::new()), local_env());
-        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), work_dir: None, base_sha: None, run_branch: None };
+        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), git_checkpoint: None, base_sha: None, run_branch: None };
         engine.run(&g, &config).await.unwrap();
 
         let manifest_path = dir.path().join("manifest.json");
@@ -2320,7 +2386,7 @@ mod tests {
         let mut registry = make_registry();
         registry.register("always_fail", Box::new(AlwaysFailHandler));
         let engine = PipelineEngine::new(registry, Arc::new(EventEmitter::new()), local_env());
-        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), work_dir: None, base_sha: None, run_branch: None };
+        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), git_checkpoint: None, base_sha: None, run_branch: None };
         let outcome = engine.run(&g, &config).await.unwrap();
 
         assert_eq!(outcome.status, StageStatus::Success);
@@ -2356,7 +2422,7 @@ mod tests {
         let mut registry = make_registry();
         registry.register("always_fail", Box::new(AlwaysFailHandler));
         let engine = PipelineEngine::new(registry, Arc::new(EventEmitter::new()), local_env());
-        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), work_dir: None, base_sha: None, run_branch: None };
+        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), git_checkpoint: None, base_sha: None, run_branch: None };
         let result = engine.run(&g, &config).await;
 
         assert!(result.is_ok());
@@ -2395,7 +2461,7 @@ mod tests {
         let mut registry = make_registry();
         registry.register("slow", Box::new(SlowHandler { sleep_ms: 500 }));
         let engine = PipelineEngine::new(registry, Arc::new(EventEmitter::new()), local_env());
-        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), work_dir: None, base_sha: None, run_branch: None };
+        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), git_checkpoint: None, base_sha: None, run_branch: None };
         let result = engine.run(&g, &config).await;
         assert!(result.is_ok());
 
@@ -2429,7 +2495,7 @@ mod tests {
         let mut registry = make_registry();
         registry.register("slow", Box::new(SlowHandler { sleep_ms: 10 }));
         let engine = PipelineEngine::new(registry, Arc::new(EventEmitter::new()), local_env());
-        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), work_dir: None, base_sha: None, run_branch: None };
+        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), git_checkpoint: None, base_sha: None, run_branch: None };
         let outcome = engine.run(&g, &config).await.unwrap();
         assert_eq!(outcome.status, StageStatus::Success);
     }
@@ -2460,7 +2526,7 @@ mod tests {
         let mut registry = make_registry();
         registry.register("slow", Box::new(SlowHandler { sleep_ms: 500 }));
         let engine = PipelineEngine::new(registry, Arc::new(EventEmitter::new()), local_env());
-        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), work_dir: None, base_sha: None, run_branch: None };
+        let config = RunConfig { logs_root: dir.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), git_checkpoint: None, base_sha: None, run_branch: None };
         let outcome = engine.run(&g, &config).await.unwrap();
 
         assert_eq!(outcome.status, StageStatus::Success);
@@ -2515,7 +2581,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2546,7 +2612,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2575,7 +2641,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2596,7 +2662,7 @@ mod tests {
             cancel_token: Some(cancel_token),
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2616,7 +2682,7 @@ mod tests {
             cancel_token: Some(cancel_token),
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2648,7 +2714,7 @@ mod tests {
             cancel_token: Some(cancel_token),
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2724,7 +2790,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2747,7 +2813,7 @@ mod tests {
             cancel_token: None,
             dry_run: true,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2774,7 +2840,7 @@ mod tests {
             cancel_token: None,
             dry_run: true,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -2862,7 +2928,7 @@ mod tests {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
diff --git a/crates/arc-attractor/src/server.rs b/crates/arc-attractor/src/server.rs
index a05f214d4..43a7da7ea 100644
--- a/crates/arc-attractor/src/server.rs
+++ b/crates/arc-attractor/src/server.rs
@@ -219,7 +219,7 @@ async fn start_pipeline(
     tokio::spawn(async move {
         let logs_root = std::env::temp_dir().join(format!("arc-{}", uuid::Uuid::new_v4()));
         std::fs::create_dir_all(&logs_root).expect("failed to create logs directory");
-        let config = RunConfig { logs_root, cancel_token: Some(cancel_token), dry_run: state_clone.dry_run, run_id: run_id_clone.clone(), work_dir: None, base_sha: None, run_branch: None };
+        let config = RunConfig { logs_root, cancel_token: Some(cancel_token), dry_run: state_clone.dry_run, run_id: run_id_clone.clone(), git_checkpoint: None, base_sha: None, run_branch: None };
 
         let result = tokio::select! {
             result = engine.run(&graph, &config) => result,
diff --git a/crates/arc-attractor/tests/daytona_integration.rs b/crates/arc-attractor/tests/daytona_integration.rs
index 694691466..8f8527716 100644
--- a/crates/arc-attractor/tests/daytona_integration.rs
+++ b/crates/arc-attractor/tests/daytona_integration.rs
@@ -271,7 +271,7 @@ async fn daytona_pipeline_artifact_offload_and_sync() {
         cancel_token: None,
         dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -317,6 +317,170 @@ async fn daytona_pipeline_artifact_offload_and_sync() {
 // CLI Backend on Daytona — real CLI tools via exec_command
 // ---------------------------------------------------------------------------
 
+use arc_attractor::engine::GitCheckpointMode;
+
+// ---------------------------------------------------------------------------
+// Git checkpoint E2E on Daytona (Remote mode)
+// ---------------------------------------------------------------------------
+
+/// Handler that writes a file via exec_command so git has something to commit.
+struct FileWriterHandler;
+
+#[async_trait::async_trait]
+impl Handler for FileWriterHandler {
+    async fn execute(
+        &self,
+        node: &Node,
+        _context: &Context,
+        _graph: &Graph,
+        _logs_root: &Path,
+        services: &arc_attractor::handler::EngineServices,
+    ) -> Result<Outcome, AttractorError> {
+        let content = format!("output from {}", node.id);
+        let cmd = format!("echo '{content}' > {}.txt", node.id);
+        let _ = services.execution_env.exec_command(&cmd, 10_000, None, None, None).await;
+        Ok(Outcome::success())
+    }
+}
+
+/// Set up git inside a Daytona sandbox for checkpoint commits.
+/// Returns (run_id, base_sha, branch_name) on success.
+async fn setup_daytona_git(
+    exec_env: &dyn ExecutionEnvironment,
+) -> (String, String, String) {
+    // Get current HEAD as base SHA
+    let sha_result = exec_env.exec_command("git rev-parse HEAD", 10_000, None, None, None).await
+        .expect("git rev-parse HEAD should succeed");
+    assert_eq!(sha_result.exit_code, 0, "git rev-parse HEAD failed: {}", sha_result.stderr);
+    let base_sha = sha_result.stdout.trim().to_string();
+
+    let run_id = ulid::Ulid::new().to_string();
+    let branch_name = format!("arc/run/{run_id}");
+
+    let checkout_cmd = format!("git checkout -b {branch_name}");
+    let checkout_result = exec_env.exec_command(&checkout_cmd, 10_000, None, None, None).await
+        .expect("git checkout should succeed");
+    assert_eq!(
+        checkout_result.exit_code, 0,
+        "git checkout -b failed (exit {}): stdout={} stderr={}",
+        checkout_result.exit_code, checkout_result.stdout, checkout_result.stderr
+    );
+
+    (run_id, base_sha, branch_name)
+}
+
+#[tokio::test]
+#[ignore]
+async fn daytona_git_checkpoint_remote_emits_events() {
+    let env = create_env().await;
+    env.initialize().await.unwrap();
+    let env: Arc<dyn ExecutionEnvironment> = Arc::new(env);
+
+    // Install git if not available (the default ubuntu:22.04 image may not have it)
+    let git_check = env.exec_command("git --version", 10_000, None, None, None).await;
+    if git_check.as_ref().map_or(true, |r| r.exit_code != 0) {
+        let install = env.exec_command(
+            "apt-get update -qq && apt-get install -y -qq git >/dev/null 2>&1",
+            120_000, None, None, None,
+        ).await.expect("apt-get install git should not error");
+        assert_eq!(install.exit_code, 0, "git install failed: {}", install.stderr);
+    }
+
+    // Set up git in the sandbox
+    let (run_id, base_sha, branch_name) = setup_daytona_git(&*env).await;
+
+    // Pipeline: start -> work -> exit
+    let mut graph = Graph::new("DaytonaGitCheckpoint");
+    graph.attrs.insert(
+        "goal".to_string(),
+        AttrValue::String("Test Remote git checkpoint".to_string()),
+    );
+
+    let mut start = Node::new("start");
+    start.attrs.insert("shape".to_string(), AttrValue::String("Mdiamond".to_string()));
+    graph.nodes.insert("start".to_string(), start);
+
+    let mut exit = Node::new("exit");
+    exit.attrs.insert("shape".to_string(), AttrValue::String("Msquare".to_string()));
+    graph.nodes.insert("exit".to_string(), exit);
+
+    let mut work = Node::new("work");
+    work.attrs.insert("label".to_string(), AttrValue::String("Work".to_string()));
+    graph.nodes.insert("work".to_string(), work);
+
+    graph.edges.push(Edge::new("start", "work"));
+    graph.edges.push(Edge::new("work", "exit"));
+
+    // Set up event collection
+    let dir = tempfile::tempdir().unwrap();
+    let mut emitter = EventEmitter::new();
+    let events = Arc::new(std::sync::Mutex::new(Vec::new()));
+    {
+        let events_clone = Arc::clone(&events);
+        emitter.on_event(move |event| {
+            events_clone.lock().unwrap().push(event.clone());
+        });
+    }
+
+    let mut registry = HandlerRegistry::new(Box::new(FileWriterHandler));
+    registry.register("start", Box::new(StartHandler));
+    registry.register("exit", Box::new(ExitHandler));
+
+    let engine = PipelineEngine::new(registry, Arc::new(emitter), env.clone());
+    let config = RunConfig {
+        logs_root: dir.path().to_path_buf(),
+        cancel_token: None,
+        dry_run: false,
+        run_id,
+        git_checkpoint: Some(GitCheckpointMode::Remote),
+        base_sha: Some(base_sha),
+        run_branch: Some(branch_name),
+    };
+
+    let outcome = engine.run(&graph, &config).await.expect("pipeline should succeed");
+    assert_eq!(outcome.status, StageStatus::Success);
+
+    // Assert GitCheckpoint events were emitted
+    let events = events.lock().unwrap();
+    let git_events: Vec<_> = events
+        .iter()
+        .filter_map(|e| {
+            if let arc_attractor::event::PipelineEvent::GitCheckpoint { node_id, git_commit_sha, .. } = e {
+                Some((node_id.clone(), git_commit_sha.clone()))
+            } else {
+                None
+            }
+        })
+        .collect();
+    assert!(
+        git_events.len() >= 2,
+        "expected at least 2 GitCheckpoint events, got {}",
+        git_events.len()
+    );
+    assert!(
+        git_events.iter().all(|(_, sha)| sha.len() == 40 && sha.chars().all(|c| c.is_ascii_hexdigit())),
+        "all SHAs should be 40-char hex, got: {git_events:?}"
+    );
+
+    // Assert diff.patch was written for the work node
+    let work_diff = dir.path().join("nodes").join("work").join("diff.patch");
+    assert!(work_diff.exists(), "diff.patch should exist for work node");
+
+    // Verify checkpoint.json has git_commit_sha
+    let checkpoint = Checkpoint::load(&dir.path().join("checkpoint.json"))
+        .expect("checkpoint should load");
+    assert!(
+        checkpoint.git_commit_sha.is_some(),
+        "checkpoint should have git_commit_sha"
+    );
+
+    env.cleanup().await.unwrap();
+}
+
+// ---------------------------------------------------------------------------
+// CLI Backend on Daytona — real CLI tools via exec_command
+// ---------------------------------------------------------------------------
+
 use arc_attractor::cli::cli_backend::CliBackend;
 use arc_attractor::handler::codergen::{CodergenBackend, CodergenResult};
 
diff --git a/crates/arc-attractor/tests/integration.rs b/crates/arc-attractor/tests/integration.rs
index 0178ea5d6..3058e4b61 100644
--- a/crates/arc-attractor/tests/integration.rs
+++ b/crates/arc-attractor/tests/integration.rs
@@ -187,7 +187,7 @@ async fn end_to_end_linear_pipeline() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -309,7 +309,7 @@ async fn end_to_end_branching_pipeline() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -418,7 +418,7 @@ async fn end_to_end_human_gate_pipeline() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -521,7 +521,7 @@ async fn goal_gate_routes_to_retry_target_on_failure() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -633,7 +633,7 @@ async fn goal_gate_routes_to_retry_target_when_present() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -945,7 +945,7 @@ async fn retry_on_failure_then_succeed() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -1011,7 +1011,7 @@ async fn pipeline_with_many_nodes() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -1329,7 +1329,7 @@ async fn smoke_test_with_mock_codergen_backend() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -1427,7 +1427,7 @@ async fn end_to_end_parallel_fan_out_fan_in() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -1534,7 +1534,7 @@ async fn resume_from_checkpoint_completes_pipeline() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -1626,7 +1626,7 @@ async fn resume_from_checkpoint_preserves_goal_gate_outcomes() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -1660,7 +1660,7 @@ async fn graph_goal_in_context() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -1690,7 +1690,7 @@ async fn event_streaming_lifecycle() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -1760,7 +1760,7 @@ async fn context_flow_between_stages() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -1803,7 +1803,7 @@ async fn tool_handler_e2e() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -1864,7 +1864,7 @@ async fn auto_approve_interviewer_e2e() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -1891,7 +1891,7 @@ async fn codergen_without_backend_simulated() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -1992,7 +1992,7 @@ async fn branching_loop_back_on_failure() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2076,7 +2076,7 @@ async fn human_gate_loops_back() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2128,7 +2128,7 @@ async fn scenario_ship_a_feature() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2208,7 +2208,7 @@ async fn scenario_parallel_expert_review() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2282,7 +2282,7 @@ async fn scenario_node_retries_on_retry_status() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2340,7 +2340,7 @@ async fn scenario_loop_restart_resets_context() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2402,7 +2402,7 @@ async fn scenario_bug_triage_router() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2452,7 +2452,7 @@ async fn scenario_crash_recovery() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2534,7 +2534,7 @@ async fn manager_loop_stop_condition_satisfied_e2e() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2584,7 +2584,7 @@ async fn manager_loop_max_cycles_exceeded_e2e() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2714,7 +2714,7 @@ async fn conditional_branching_success_fail_paths() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2762,7 +2762,7 @@ async fn edge_selection_condition_match_wins_over_weight() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2805,7 +2805,7 @@ async fn edge_selection_weight_breaks_ties() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2840,7 +2840,7 @@ async fn edge_selection_lexical_tiebreak() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2892,7 +2892,7 @@ async fn context_updates_visible_across_nodes() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2926,7 +2926,7 @@ async fn stylesheet_applies_model_override() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -2976,7 +2976,7 @@ async fn custom_handler_registration_and_execution() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -3037,7 +3037,7 @@ async fn integration_smoke_plan_implement_review_done() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -3526,7 +3526,7 @@ async fn sub_pipeline_e2e_through_engine() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -3672,7 +3672,7 @@ async fn manager_loop_with_child_observer_e2e() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -3795,7 +3795,7 @@ async fn graph_merge_e2e_through_engine() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -3939,7 +3939,7 @@ async fn fidelity_default_is_compact() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -3982,7 +3982,7 @@ async fn fidelity_graph_default_applied() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4024,7 +4024,7 @@ async fn fidelity_node_overrides_graph_default() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4072,7 +4072,7 @@ async fn fidelity_edge_overrides_node_and_graph() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4110,7 +4110,7 @@ async fn fidelity_full_produces_empty_preamble() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4155,7 +4155,7 @@ async fn fidelity_truncate_preamble_minimal() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4216,7 +4216,7 @@ async fn fidelity_summary_low_mode() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4272,7 +4272,7 @@ async fn fidelity_summary_medium_mode() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4328,7 +4328,7 @@ async fn fidelity_summary_high_mode() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4377,7 +4377,7 @@ async fn fidelity_full_sets_thread_id_in_context() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4437,7 +4437,7 @@ async fn fidelity_full_nodes_share_thread_id() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4504,7 +4504,7 @@ async fn fidelity_resume_degrades_full_to_summary_high() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4587,7 +4587,7 @@ async fn fidelity_resume_degrade_only_affects_first_hop() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4657,7 +4657,7 @@ async fn fidelity_resume_no_degrade_when_not_full() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4693,7 +4693,7 @@ async fn fidelity_stored_in_checkpoint_context() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4768,7 +4768,7 @@ async fn fidelity_precedence_multi_node_pipeline() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4825,7 +4825,7 @@ async fn fidelity_compact_preamble_includes_completed_stages_and_context() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -4873,7 +4873,7 @@ async fn fidelity_summary_low_excludes_context_values_in_pipeline() {
     registry_low.register("exit", Box::new(ExitHandler));
     registry_low.register("fidelity_capture", Box::new(FidelityCapturingHandler { captures: captures_low.clone() }));
     let engine_low = PipelineEngine::new(registry_low, Arc::new(EventEmitter::new()), local_env());
-    let config_low = RunConfig { logs_root: dir_low.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), work_dir: None, base_sha: None, run_branch: None };
+    let config_low = RunConfig { logs_root: dir_low.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), git_checkpoint: None, base_sha: None, run_branch: None };
     engine_low.run(&graph_low, &config_low).await.expect("run low");
 
     {
@@ -4907,7 +4907,7 @@ async fn fidelity_summary_low_excludes_context_values_in_pipeline() {
     registry_med.register("exit", Box::new(ExitHandler));
     registry_med.register("fidelity_capture", Box::new(FidelityCapturingHandler { captures: captures_med.clone() }));
     let engine_med = PipelineEngine::new(registry_med, Arc::new(EventEmitter::new()), local_env());
-    let config_med = RunConfig { logs_root: dir_med.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), work_dir: None, base_sha: None, run_branch: None };
+    let config_med = RunConfig { logs_root: dir_med.path().to_path_buf(), cancel_token: None, dry_run: false, run_id: "test-run".into(), git_checkpoint: None, base_sha: None, run_branch: None };
     engine_med.run(&graph_med, &config_med).await.expect("run med");
 
     let preambles_med = captures_med.preambles.lock().unwrap();
@@ -4961,7 +4961,7 @@ async fn fidelity_thread_id_fallback_to_previous_node_in_pipeline() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -5004,7 +5004,7 @@ async fn fidelity_thread_id_from_node_class_in_pipeline() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -5050,7 +5050,7 @@ async fn fidelity_edge_thread_id_override_in_pipeline() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -5097,7 +5097,7 @@ async fn fidelity_full_without_explicit_thread_id_uses_previous_node() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -5151,7 +5151,7 @@ async fn fidelity_from_parsed_dot_pipeline() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -5193,7 +5193,7 @@ async fn fidelity_checkpoint_roundtrip_preserves_fidelity() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -5252,7 +5252,7 @@ async fn fidelity_node_thread_id_overrides_edge_thread_id_in_pipeline() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -5325,7 +5325,7 @@ async fn fidelity_resume_preserves_context_values_across_checkpoint() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -5514,7 +5514,7 @@ mod real_llm {
             logs_root: dir.path().to_path_buf(),
             cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -5622,7 +5622,7 @@ mod real_llm {
             logs_root: dir.path().to_path_buf(),
             cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -5760,7 +5760,7 @@ mod real_llm {
             logs_root: dir.path().to_path_buf(),
             cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -5864,7 +5864,7 @@ mod real_llm {
             cancel_token: None,
             dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
         };
@@ -5948,7 +5948,7 @@ async fn human_gate_freeform_only_routes_text() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -6067,7 +6067,7 @@ async fn human_gate_freeform_with_fixed_choice_match() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -6171,7 +6171,7 @@ async fn human_gate_freeform_fallback_on_unmatched_text() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -6288,7 +6288,7 @@ async fn human_gate_freeform_sets_allow_freeform_on_question() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -6381,7 +6381,7 @@ async fn human_gate_without_freeform_sets_allow_freeform_false() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -6623,7 +6623,7 @@ async fn tool_hooks_pre_success_allows_pipeline_to_proceed() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -6662,7 +6662,7 @@ async fn tool_hooks_pre_failure_skips_tool_call() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -6704,7 +6704,7 @@ async fn tool_hooks_post_success_does_not_affect_outcome() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -6738,7 +6738,7 @@ async fn tool_hooks_post_failure_does_not_block_pipeline() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -6774,7 +6774,7 @@ async fn tool_hooks_graph_level_applies_to_all_nodes() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -6813,7 +6813,7 @@ async fn tool_hooks_node_level_overrides_graph_level() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -6862,7 +6862,7 @@ async fn tool_hooks_pre_receives_node_id_env_var() {
         logs_root: dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -6958,7 +6958,7 @@ async fn attractor_e2e_with_real_llm() {
         logs_root: logs_dir.path().to_path_buf(),
         cancel_token: None, dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -7065,7 +7065,7 @@ async fn run_fidelity_prompt_pipeline(fidelity: &str) -> String {
         cancel_token: None,
         dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -7208,7 +7208,7 @@ async fn large_context_values_are_offloaded_to_artifact_store() {
         cancel_token: None,
         dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -7383,7 +7383,7 @@ async fn artifact_pointers_rewritten_for_remote_execution_env() {
         cancel_token: None,
         dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -7497,7 +7497,7 @@ async fn node_dir_uses_visit_count_on_revisit() {
         cancel_token: None,
         dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -8063,7 +8063,7 @@ async fn full_pipeline_with_cli_backend_node() {
         cancel_token: None,
         dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -8151,7 +8151,7 @@ async fn stylesheet_backend_property_routes_to_cli() {
         cancel_token: None,
         dry_run: false,
         run_id: "test-run".into(),
-        work_dir: None,
+        git_checkpoint: None,
         base_sha: None,
         run_branch: None,
     };
@@ -8265,4 +8265,140 @@ fn parse_real_gemini_json() {
     assert_eq!(response.text, "4");
     assert_eq!(response.input_tokens, 123);
     assert_eq!(response.output_tokens, 1);
+}
+
+// ---------------------------------------------------------------------------
+// Git checkpoint e2e — Host mode (Docker / Local)
+// ---------------------------------------------------------------------------
+
+use arc_attractor::engine::GitCheckpointMode;
+
+/// End-to-end test: pipeline with `GitCheckpointMode::Host` emits `GitCheckpoint`
+/// events with valid commit SHAs and writes `diff.patch` per stage.
+#[tokio::test]
+async fn git_checkpoint_host_emits_events_and_diff_patch() {
+    // 1. Create a temporary git repo with an initial commit
+    let repo = tempfile::tempdir().unwrap();
+    std::process::Command::new("git")
+        .args(["init"])
+        .current_dir(repo.path())
+        .output()
+        .unwrap();
+    std::process::Command::new("git")
+        .args(["-c", "user.name=test", "-c", "user.email=test@test",
+               "commit", "--allow-empty", "-m", "init"])
+        .current_dir(repo.path())
+        .output()
+        .unwrap();
+
+    // 2. Create a branch and worktree (like cli/run.rs setup_worktree)
+    let base_sha = {
+        let out = std::process::Command::new("git")
+            .args(["rev-parse", "HEAD"])
+            .current_dir(repo.path())
+            .output()
+            .unwrap();
+        String::from_utf8_lossy(&out.stdout).trim().to_string()
+    };
+    std::process::Command::new("git")
+        .args(["branch", "arc/run/test-docker", "HEAD"])
+        .current_dir(repo.path())
+        .output()
+        .unwrap();
+    let worktree_path = repo.path().join("worktree");
+    std::process::Command::new("git")
+        .args(["worktree", "add"])
+        .arg(&worktree_path)
+        .arg("arc/run/test-docker")
+        .current_dir(repo.path())
+        .output()
+        .unwrap();
+
+    // Write a file in the worktree so there's something to commit
+    std::fs::write(worktree_path.join("hello.txt"), "from docker test").unwrap();
+
+    // 3. Build a simple pipeline: start -> work -> exit
+    let mut graph = Graph::new("DockerGitCheckpoint");
+    graph.attrs.insert("goal".to_string(), AttrValue::String("Test Host git checkpoint".to_string()));
+    let mut start = Node::new("start");
+    start.attrs.insert("shape".to_string(), AttrValue::String("Mdiamond".to_string()));
+    graph.nodes.insert("start".to_string(), start);
+    let mut exit = Node::new("exit");
+    exit.attrs.insert("shape".to_string(), AttrValue::String("Msquare".to_string()));
+    graph.nodes.insert("exit".to_string(), exit);
+    let mut work = Node::new("work");
+    work.attrs.insert("label".to_string(), AttrValue::String("Work".to_string()));
+    graph.nodes.insert("work".to_string(), work);
+    graph.edges.push(Edge::new("start", "work"));
+    graph.edges.push(Edge::new("work", "exit"));
+
+    // 4. Set up event collection and engine
+    let logs_dir = tempfile::tempdir().unwrap();
+    let mut emitter = EventEmitter::new();
+    let events = collect_events(&mut emitter);
+
+    let env: Arc<dyn arc_agent::ExecutionEnvironment> = Arc::new(
+        arc_agent::LocalExecutionEnvironment::new(worktree_path.clone()),
+    );
+    let mut registry = HandlerRegistry::new(Box::new(ContextSetterHandler));
+    registry.register("start", Box::new(StartHandler));
+    registry.register("exit", Box::new(ExitHandler));
+    let engine = PipelineEngine::new(registry, Arc::new(emitter), env);
+
+    let config = RunConfig {
+        logs_root: logs_dir.path().to_path_buf(),
+        cancel_token: None,
+        dry_run: false,
+        run_id: "test-docker".into(),
+        git_checkpoint: Some(GitCheckpointMode::Host(worktree_path.clone())),
+        base_sha: Some(base_sha.clone()),
+        run_branch: Some("arc/run/test-docker".to_string()),
+    };
+
+    // 5. Run pipeline
+    let outcome = engine.run(&graph, &config).await.expect("pipeline should succeed");
+    assert_eq!(outcome.status, StageStatus::Success);
+
+    // 6. Assert GitCheckpoint events were emitted
+    let events = events.lock().unwrap();
+    let git_events: Vec<_> = events
+        .iter()
+        .filter_map(|e| {
+            if let PipelineEvent::GitCheckpoint { node_id, git_commit_sha, .. } = e {
+                Some((node_id.clone(), git_commit_sha.clone()))
+            } else {
+                None
+            }
+        })
+        .collect();
+    // start, work, exit = 3 nodes, each gets a checkpoint commit
+    assert!(
+        git_events.len() >= 2,
+        "expected at least 2 GitCheckpoint events, got {}",
+        git_events.len()
+    );
+    // Each SHA should be a valid 40-char hex string
+    assert!(
+        git_events.iter().all(|(_, sha)| sha.len() == 40 && sha.chars().all(|c| c.is_ascii_hexdigit())),
+        "all SHAs should be 40-char hex, got: {git_events:?}"
+    );
+
+    // 7. Assert diff.patch was written for the "work" node
+    let work_diff = logs_dir.path().join("nodes").join("work").join("diff.patch");
+    assert!(work_diff.exists(), "diff.patch should exist for work node");
+
+    // 8. Verify checkpoint.json has git_commit_sha
+    let checkpoint = Checkpoint::load(&logs_dir.path().join("checkpoint.json"))
+        .expect("checkpoint should load");
+    assert!(
+        checkpoint.git_commit_sha.is_some(),
+        "checkpoint should have git_commit_sha"
+    );
+
+    // Cleanup worktree
+    let _ = std::process::Command::new("git")
+        .args(["worktree", "remove", "--force"])
+        .arg(&worktree_path)
+        .current_dir(repo.path())
+        .output();
 }
\ No newline at end of file