E2E Path Resolution Fix

When to Use This Skill

Use this skill when you encounter:

1. •E2E experiments with 0% pass rates and $0.00 costs despite configuration appearing correct
2. •Agent execution completing in 0.0s with exit code 1 (immediate failure)
3. •"cd: No such file or directory" errors in agent stderr logs
4. •Relative paths in subprocess execution causing directory navigation failures
5. •Generated scripts (replay.sh) failing to navigate to workspace directories

Problem Indicators

Symptoms

• •All tiers return 0% pass rate
• •Total cost: $0.00 (no API calls made)
• •Agent stage completes in 0.0s
• •Exit code: 1 (error)
• •Token counts: 0 input / 0 output

Error Message Pattern

cd: results/2026-01-17T13-50-51-test-001/T0/00/run_01/workspace: No such file or directory

Root Cause Location

The error occurs in subtest_executor.py at two critical locations:

1. •Line 809 - cwd=workspace passes relative path to subprocess.run()
2. •Line 1022 - cwd=str(workspace) logs relative path in command logger

Verified Workflow

1. Identify the Problem

Read agent stderr logs:

cat results/*/T*/*/run_01/agent/stderr.log

Look for:

• •"cd: No such file or directory" errors
• •Relative paths in cd commands
• •Empty stdout with immediate exit

Check exit codes:

jq '.exit_code' results/*/T*/*/run_01/run_result.json
# Exit code 1 = execution error
# Exit code -2 = timeout

2. Locate the Bug

Search for relative path usage:

grep -n "cwd=workspace" scylla/e2e/subtest_executor.py

Expected matches:

• •Line 809: cwd=workspace, in _run_via_replay_script()
• •Line 1022: cwd=str(workspace), in _run_agent_execution()

3. Apply the Fix

Change 1 - Line 809 (subprocess cwd):

# Before:
result = subprocess.run(
    ["bash", str(replay_script.resolve())],
    capture_output=True,
    text=True,
    timeout=adapter_config.timeout,
    cwd=workspace,  # ❌ Relative path
)

# After:
result = subprocess.run(
    ["bash", str(replay_script.resolve())],
    capture_output=True,
    text=True,
    timeout=adapter_config.timeout,
    cwd=workspace.resolve(),  # ✅ Absolute path
)

Change 2 - Line 1022 (command logger cwd):

# Before:
command_logger.log_command(
    cmd=cmd,
    stdout="",
    stderr="",
    exit_code=0,
    duration=0.0,
    cwd=str(workspace),  # ❌ Relative path
)

# After:
command_logger.log_command(
    cmd=cmd,
    stdout="",
    stderr="",
    exit_code=0,
    duration=0.0,
    cwd=str(workspace.resolve()),  # ✅ Absolute path
)

4. Verify the Fix

Run failing E2E test:

pixi run python scripts/run_e2e_experiment.py \
    --tiers-dir tests/fixtures/tests/test-001 \
    --tiers T0 --runs 1 -v --max-subtests 1 --fresh

Expected after fix:

• •Agent execution time > 0.0s (e.g., 25.5s)
• •Token counts > 0 (e.g., 54 input, 1,308 output)
• •Cost > $0.00 (e.g., $0.1650)
• •Pass rate > 0% (e.g., 89%)
• •Exit code: 0 (success)

Verify replay.sh contains absolute paths:

cat results/*/T0/00/run_01/agent/replay.sh | head -25

Expected output:

cd /home/mvillmow/ProjectScylla/results/2026-01-17T14-44-38-test-001/T0/00/run_01/workspace

Run unit tests:

pixi run pytest tests/unit/e2e/test_subtest_executor.py -v

Failed Attempts

❌ Attempt 1: Fixing Only the Subprocess CWD

What was tried:

• •Fixed only line 809 (cwd=workspace.resolve())
• •Left line 1022 unchanged (cwd=str(workspace))

Why it failed:

• •The command logger still logged relative paths
• •Generated replay.sh contained relative cd commands
• •When replay.sh executed, it couldn't navigate to the directory

Lesson learned: Both locations must be fixed together - the subprocess execution AND the command logging must use absolute paths.

❌ Attempt 2: Investigating Worktree Creation

What was tried:

• •Initially suspected worktree creation was the issue
• •Checked for "fatal: a branch named 'T6_01_run_01' already exists" errors

Why it failed:

• •This was a red herring from a different run (T6)
• •The real issue was path resolution, not worktree creation
• •T6's failure was actually due to timeout, not path issues

Lesson learned: Don't get distracted by errors from different tier runs - focus on the pattern across all failed runs.

Results & Parameters

Before Fix

{
  "pass_rate": 0.0,
  "cost_usd": 0.00,
  "agent_duration_seconds": 0.0,
  "exit_code": 1,
  "tokens_input": 0,
  "tokens_output": 0
}

After Fix

{
  "pass_rate": 0.89,
  "cost_usd": 0.1650,
  "agent_duration_seconds": 25.5,
  "exit_code": 0,
  "tokens_input": 54,
  "tokens_output": 1308
}

Configuration Used

• •Mojo version: 0.26.1
• •Python version: 3.14.2
• •Test fixture: tests/fixtures/tests/test-001
• •Timeout: 300 seconds
• •Model: claude-sonnet-4-5-20250929

Key Insights

1. Path Resolution in Subprocess Execution

When passing cwd to subprocess.run(), Python resolves the path relative to the current working directory of the parent process, NOT the subprocess. Using .resolve() ensures absolute paths.

2. Command Logger Path Consistency

The command logger generates replay.sh scripts that will be executed later. These scripts must use absolute paths because they may be run from different working directories.

3. Silent Failure Detection

This bug caused 100% silent failures - experiments appeared to complete successfully (exit code 0 at the experiment level) but all subtests failed immediately with exit code 1.

4. Diagnostic Importance

The agent stderr logs were crucial for diagnosis - they showed the exact cd command that was failing with the relative path.

Related Skills

• •e2e-checkpoint-resume - Documents proper path handling patterns in E2E
• •e2e-rate-limit-detection - Shows how to debug E2E execution failures
• •debug-evaluation-logs - Patterns for improving diagnostic messages

Files Modified

Testing Evidence

E2E Test Success

============================================================
EXPERIMENT COMPLETE
============================================================
Duration: 103.3s
Total Cost: $0.1650

Best Tier: T0
Best Sub-test: 00
Frontier CoP: $0.1650

Tier Results:
------------------------------------------------------------
  T0: PASS (score: 0.890, cost: $0.1650)
============================================================

replay.sh Verification

#!/bin/bash
# Generated: 2026-01-17T14:44:47.338423+00:00
# Total commands: 1

# Command 1/1 at 2026-01-17T14:44:47.338324+00:00
cd /home/mvillmow/ProjectScylla/results/2026-01-17T14-44-38-test-001/T0/00/run_01/workspace
claude --model claude-sonnet-4-5-20250929 --print --output-format json --dangerously-skip-permissions /home/mvillmow/ProjectScylla/results/2026-01-17T14-44-38-test-001/T0/00/run_01/agent/prompt.md

Unit Test Success

============================= test session starts ==============================
tests/unit/e2e/test_subtest_executor.py::TestMoveToFailed::test_move_creates_failed_dir PASSED [ 20%]
tests/unit/e2e/test_subtest_executor.py::TestMoveToFailed::test_move_increments_attempt PASSED [ 40%]
tests/unit/e2e/test_subtest_executor.py::TestMoveToFailed::test_move_preserves_contents PASSED [ 60%]
tests/unit/e2e/test_subtest_executor.py::TestMoveToFailed::test_move_with_custom_attempt PASSED [ 80%]
tests/unit/e2e/test_subtest_executor.py::TestMoveToFailed::test_move_multiple_increments PASSED [100%]

============================== 5 passed in 0.14s

Bonus Finding: T6 Timeout Analysis

While debugging this issue, we also discovered why T6 (maximum capability tier) failed:

T6 Configuration:

• •73 sub-agents enabled
• •63 skills enabled
• •9 MCP servers enabled
• •Task: Simple "Hello World" script

Result:

• •Exit code: -2 (timeout)
• •Duration: 187.45s (approaching 300s limit)
• •Cost: $0.00 (no completion)

Key Insight: More tools/agents/complexity ≠ better performance. T6 failed on the simplest task because having "everything enabled" created cognitive overhead that prevented task completion within the timeout.