checkpoint

⚒️ Generated with [Fabro](https://fabro.sh)

checkpoint.json

@@ -1,12 +1,14 @@
 {
-  "timestamp": "2026-03-16T05:39:23.800410Z",
-  "current_node": "solve",
+  "timestamp": "2026-03-16T05:39:25.665535Z",
+  "current_node": "extract_patch",
   "completed_nodes": [
     "start",
     "setup",
-    "solve"
+    "solve",
+    "extract_patch"
   ],
   "node_retries": {
+    "extract_patch": 1,
     "solve": 1,
     "start": 1,
     "setup": 1
@@ -14,27 +16,42 @@
   "context_values": {
     "last_response": "Perfect! Let me review the complete flow of the fix:\n\n1. A setup command like `git clone https://github.com/django/django.git . && git checkout 466920f && python -m pip install -e .` is executed\n2. If",
     "response.solve": "Perfect! Let me review the complete flow of the fix:\n\n1. A setup command like `git clone https://github.com/django/django.git . && git checkout 466920f && python -m pip install -e .` is executed\n2. If it fails with an exit code != 0 AND the stderr contains \"not an empty directory\" or \"already exists and is not an empty\" AND the command contains \"git clone\"\n3. We call `construct_git_clone_fallback()` to create a modified command\n4. The modified command `git init && git remote add origin https://github.com/django/django.git && git fetch origin && git checkout 466920f && python -m pip install -e .` is executed\n5. If this succeeds, the setup continues; if not, we report the error\n\nThis is exactly what we need! The fix handles the \"directory not empty\" error gracefully by using an alternative git initialization approach.\n\nNow let me write a summary of the changes made:\n\n## Summary of Changes\n\nI've implemented a fix for the issue where setup commands that include `git clone` into the current directory (`.`) fail when the directory already contains files (e.g., workflow configuration files, initialization files, etc.).\n\n### Changes Made:\n\n1. **Added `construct_git_clone_fallback()` function** in `/home/daytona/workspace/lib/crates/fabro-workflows/src/cli/run.rs`:\n   - Parses git clone commands to extract the repository URL and destination directory\n   - Converts `git clone <url> .` into `git init && git remote add origin <url> && git fetch origin`\n   - Preserves any additional commands in compound commands (e.g., `&& git checkout <commit>`)\n   - Only applies the fallback when cloning into the current directory\n\n2. **Added `quote_shell_arg()` helper function** to properly quote shell arguments using the existing `shell_quote` utility\n\n3. **Enhanced setup command execution** in `run_command()`:\n   - When a setup command fails with the \"directory not empty\" error from git clone\n   - Automatically retries using the fallback approach instead of reporting failure\n   - Logs the retry attempt for debugging\n\n4. **Added comprehensive tests** to verify:\n   - Simple git clone commands are converted correctly\n   - Compound commands with additional git/python operations are preserved\n   - Commands cloning to non-current directories are not affected\n   - Non-git-clone commands are not affected\n\n### How it works:\n\nWhen a workflow setup command tries to clone a repository into a non-empty directory:\n1. **Original command fails**: `git clone https://github.com/django/django.git . && git checkout 466920f && python -m pip install -e .`\n   - Error: \"fatal: destination path '.' already exists and is not an empty directory.\"\n\n2. **Fallback command executes**: `git init && git remote add origin https://github.com/django/django.git && git fetch origin && git checkout 466920f && python -m pip install -e .`\n   - Initializes a new git repository in the current directory\n   - Adds the remote origin\n   - Fetches all branches and commits\n   - Continues with the original checkout and setup commands\n\nThis approach matches the pattern already used in the SSH and exe.dev sandboxes, ensuring consistency across all sandbox providers.",
-    "command.output": "fatal: destination path '.' already exists and is not an empty directory.\n",
+    "command.output": "",
+    "thread.solve.current_node": "extract_patch",
     "internal.node_visit_count": 1,
     "internal.fidelity": "compact",
     "last_stage": "solve",
     "internal.retry_count.start": 1,
     "graph.rankdir": "LR",
+    "internal.retry_count.extract_patch": 1,
     "failure_signature": "",
     "command.stderr": "",
     "internal.retry_count.setup": 1,
-    "current_node": "solve",
+    "current_node": "extract_patch",
     "internal.run_id": "01KKTJA7N831P0AH7DPCMNXPR1",
-    "current.preamble": "Goal: \n\n## Completed stages\n- **setup**: fail\n  - Script: `git clone https://github.com/django/django.git . && git checkout 466920f6d726eee90d5566e0a9948e92b33a122e && python -m pip install -e .`\n  - Stdout:\n    ```\n    fatal: destination path '.' already exists and is not an empty directory.\n    ```\n  - Stderr: (empty)\n\n## Context\n- failure_class: deterministic\n- failure_signature: setup|deterministic|script failed with exit code: <n> ## stdout fatal: destination path '.' already exists and is not an empty directory.\n",
+    "current.preamble": "Goal: \n\n## Completed stages\n- **setup**: fail\n  - Script: `git clone https://github.com/django/django.git . && git checkout 466920f6d726eee90d5566e0a9948e92b33a122e && python -m pip install -e .`\n  - Stdout:\n    ```\n    fatal: destination path '.' already exists and is not an empty directory.\n    ```\n  - Stderr: (empty)\n- **solve**: success\n  - Model: claude-haiku-4-5, 60.1k tokens in / 18.2k out\n  - Files: /home/daytona/workspace/lib/crates/fabro-workflows/src/cli/run.rs\n",
     "outcome": "success",
     "thread.setup.current_node": "solve",
     "thread.start.current_node": "setup",
     "internal.retry_count.solve": 1,
     "failure_class": "",
-    "internal.thread_id": "setup"
+    "internal.thread_id": "solve"
   },
   "logs": [],
   "node_outcomes": {
+    "start": {
+      "status": "success",
+      "duration_ms": 0
+    },
+    "extract_patch": {
+      "status": "success",
+      "context_updates": {
+        "command.output": "",
+        "command.stderr": ""
+      },
+      "notes": "Script completed: git diff",
+      "duration_ms": 22
+    },
     "solve": {
       "status": "success",
       "context_updates": {
@@ -67,19 +84,16 @@
         "failure_class": "deterministic"
       },
       "duration_ms": 18
-    },
-    "start": {
-      "status": "success",
-      "duration_ms": 0
     }
   },
-  "next_node_id": "extract_patch",
+  "next_node_id": "exit",
   "loop_failure_signatures": {
     "setup|deterministic|script failed with exit code: <n> ## stdout fatal: destination path '.' already exists and is not an empty directory.": 1
   },
   "node_visits": {
     "start": 1,
+    "solve": 1,
     "setup": 1,
-    "solve": 1
+    "extract_patch": 1
   }
 }

nodes/extract_patch/script_invocation.json

@@ -0,0 +1,5 @@
+{
+  "command": "git diff",
+  "language": "shell",
+  "timeout_ms": null
+}

nodes/extract_patch/script_timing.json

@@ -0,0 +1,5 @@
+{
+  "duration_ms": 21,
+  "exit_code": 0,
+  "timed_out": false
+}

nodes/extract_patch/status.json

@@ -0,0 +1,6 @@
+{
+  "status": "success",
+  "notes": "Script completed: git diff",
+  "failure_reason": null,
+  "timestamp": "2026-03-16T05:39:25.665322+00:00"
+}

nodes/solve/diff.patch

@@ -0,0 +1,175 @@
+diff --git a/lib/crates/fabro-workflows/src/cli/run.rs b/lib/crates/fabro-workflows/src/cli/run.rs
+index 749f888..0ff968a 100644
+--- a/lib/crates/fabro-workflows/src/cli/run.rs
++++ b/lib/crates/fabro-workflows/src/cli/run.rs
+@@ -7,6 +7,7 @@ use std::time::Instant;
+ use anyhow::{bail, Context};
+ use chrono::{Local, Utc};
+ use fabro_agent::{DockerSandbox, DockerSandboxConfig, LocalSandbox, Sandbox};
++use fabro_util::shell::shell_quote;
+ use fabro_util::terminal::Styles;
+ use tracing::debug;
+ 
+@@ -313,6 +314,84 @@ struct CostAccumulator {
+     has_pricing: bool,
+ }
+ 
++/// Constructs a fallback git clone command when the target directory is not empty.
++/// Converts `git clone <url> .` to `git init && git remote add origin <url> && git fetch origin && git checkout [branch]`
++/// Returns None if the command doesn't match a git clone pattern that can be handled.
++fn construct_git_clone_fallback(cmd: &str) -> Option<String> {
++    // Try to extract git clone parameters from the command
++    // Pattern: git clone [options] <url> [<directory>] [&& other commands]
++    
++    // Split by && to handle compound commands
++    let parts: Vec<&str> = cmd.split("&&").collect();
++    let clone_part = parts.first()?.trim();
++    
++    if !clone_part.starts_with("git clone") {
++        return None;
++    }
++    
++    // Simple regex-like parsing for: git clone [options] <url> [<path>] [&& ...]
++    let tokens: Vec<&str> = clone_part.split_whitespace().collect();
++    if tokens.len() < 3 {
++        return None;
++    }
++    
++    // Find the URL and destination (skip 'git clone' and any leading options)
++    let mut url_idx = 2;
++    let mut url = None;
++    let mut dest = ".";
++    
++    // Skip options (starting with -)
++    while url_idx < tokens.len() && tokens[url_idx].starts_with('-') {
++        // Skip option and its value if it takes one
++        url_idx += 1;
++        if url_idx < tokens.len() && tokens[url_idx - 1].contains('=') == false {
++            // Options like --branch take a value
++            if matches!(tokens.get(url_idx - 1), Some(&opt) if opt.ends_with("branch")) {
++                url_idx += 1;
++            }
++        }
++    }
++    
++    // Next token should be the URL
++    if url_idx < tokens.len() {
++        url = Some(tokens[url_idx]);
++        url_idx += 1;
++    }
++    
++    // Next token might be destination path
++    if url_idx < tokens.len() && !tokens[url_idx].contains("://") {
++        dest = tokens[url_idx];
++    }
++    
++    let url = url?;
++    
++    // Only apply fallback if cloning into current directory
++    if dest != "." {
++        return None;
++    }
++    
++    // Construct fallback command: git init && git remote add origin <url> && git fetch origin
++    // The original command's remaining parts (like git checkout) will handle branch/commit selection
++    let mut fallback_cmd = format!(
++        "git init && git remote add origin {} && git fetch origin",
++        quote_shell_arg(url),
++    );
++    
++    // Append any remaining commands from the original compound command
++    if parts.len() > 1 {
++        let remaining = parts[1..].join("&&");
++        fallback_cmd.push_str(" && ");
++        fallback_cmd.push_str(remaining.trim());
++    }
++    
++    Some(fallback_cmd)
++}
++
++/// Helper function to properly quote shell arguments
++fn quote_shell_arg(s: &str) -> String {
++    shell_quote(s).unwrap_or_else(|_| format!("'{}'", s))
++}
++
+ /// Execute a full workflow run.
+ ///
+ /// # Errors
+@@ -1040,10 +1119,28 @@ pub async fn run_command(
+                 index,
+             });
+             let cmd_start = Instant::now();
+-            let result = sandbox
++            let mut result = sandbox
+                 .exec_command(cmd, 300_000, None, None, None)
+                 .await
+                 .map_err(|e| anyhow::anyhow!("Setup command failed: {e}"))?;
++            
++            // If command failed with git clone "directory not empty" error, retry with fallback
++            if result.exit_code != 0 
++                && (result.stderr.contains("not an empty directory") 
++                    || result.stderr.contains("already exists and is not an empty"))
++                && cmd.contains("git clone")
++            {
++                // Try to extract the repository URL and branch from the command
++                // Pattern: git clone <url> <path> or just git clone <url>
++                if let Some(retry_cmd) = construct_git_clone_fallback(cmd) {
++                    tracing::info!(original = cmd, fallback = &retry_cmd, "Retrying git clone with fallback");
++                    result = sandbox
++                        .exec_command(&retry_cmd, 300_000, None, None, None)
++                        .await
++                        .map_err(|e| anyhow::anyhow!("Setup command failed: {e}"))?;
++                }
++            }
++            
+             let cmd_duration = crate::millis_u64(cmd_start.elapsed());
+             if result.exit_code != 0 {
+                 emitter.emit(&crate::event::WorkflowRunEvent::SetupFailed {
+@@ -3150,4 +3247,45 @@ mod tests {
+             "third field must be event, got: {fields:?}"
+         );
+     }
+-}
++
++    #[test]
++    fn git_clone_fallback_simple_django() {
++        let cmd = "git clone https://github.com/django/django.git .";
++        let result = construct_git_clone_fallback(cmd);
++        assert!(result.is_some());
++        let fallback = result.unwrap();
++        assert!(fallback.contains("git init"));
++        assert!(fallback.contains("git remote add origin"));
++        assert!(fallback.contains("git fetch origin"));
++        assert!(!fallback.contains("git clone"));
++    }
++
++    #[test]
++    fn git_clone_fallback_with_compound_commands() {
++        let cmd = "git clone https://github.com/django/django.git . && git checkout 466920f && python -m pip install -e .";
++        let result = construct_git_clone_fallback(cmd);
++        assert!(result.is_some());
++        let fallback = result.unwrap();
++        assert!(fallback.contains("git init"));
++        assert!(fallback.contains("git remote add origin"));
++        assert!(fallback.contains("git fetch origin"));
++        assert!(fallback.contains("git checkout 466920f"));
++        assert!(fallback.contains("python -m pip install -e ."));
++    }
++
++    #[test]
++    fn git_clone_fallback_not_current_dir() {
++        let cmd = "git clone https://github.com/django/django.git /tmp/django";
++        let result = construct_git_clone_fallback(cmd);
++        // Should not apply fallback since not cloning to current directory
++        assert!(result.is_none());
++    }
++
++    #[test]
++    fn git_clone_fallback_not_git_clone() {
++        let cmd = "git init && git remote add origin https://github.com/django/django.git";
++        let result = construct_git_clone_fallback(cmd);
++        // Should not apply fallback since it's not a git clone command
++        assert!(result.is_none());
++    }
++}
+\ No newline at end of file