debug

name	debug
description	Debug container agent issues. Use when things aren't working, container fails, authentication problems, or to understand how the container system works. Covers logs, environment variables, mounts, and common issues.

BioClaw Container Debugging

This guide covers debugging the containerized agent execution system.

Architecture Overview

Host (macOS)                          Container (Linux VM)
─────────────────────────────────────────────────────────────
src/container-runner.ts               container/agent-runner/
    │                                      │
    │ spawns Apple Container               │ runs Claude Agent SDK
    │ with volume mounts                   │ with MCP servers
    │                                      │
    ├── data/env/env ──────────────> /workspace/env-dir/env
    ├── groups/{folder} ───────────> /workspace/group
    ├── data/ipc/{folder} ────────> /workspace/ipc
    ├── data/sessions/{folder}/.claude/ ──> /home/node/.claude/ (isolated per-group)
    └── (main only) project root ──> /workspace/project

Important: The container runs as user node with HOME=/home/node. Session files must be mounted to /home/node/.claude/ (not /root/.claude/) for session resumption to work.

Log Locations

Log	Location	Content
Main app logs	logs/bioclaw.log	Host-side WhatsApp, routing, container spawning
Main app errors	logs/bioclaw.error.log	Host-side errors
Container run logs	groups/{folder}/logs/container-*.log	Per-run: input, mounts, stderr, stdout
Claude sessions	~/.claude/projects/	Claude Code session history

Enabling Debug Logging

Set LOG_LEVEL=debug for verbose output:

# For development
LOG_LEVEL=debug npm run dev

# For launchd service, add to plist EnvironmentVariables:
<key>LOG_LEVEL</key>
<string>debug</string>

Debug level shows:

• Full mount configurations
• Container command arguments
• Real-time container stderr

Common Issues

1. "Claude Code process exited with code 1"

Check the container log file in groups/{folder}/logs/container-*.log

Common causes:

Missing Authentication

Invalid API key · Please run /login

Fix: Ensure .env file exists with either OAuth token or API key:

cat .env  # Should show one of:
# CLAUDE_CODE_OAUTH_TOKEN=sk-ant-oat01-...  (subscription)
# ANTHROPIC_API_KEY=sk-ant-api03-...        (pay-per-use)

Root User Restriction

--dangerously-skip-permissions cannot be used with root/sudo privileges

Fix: Container must run as non-root user. Check Dockerfile has USER node.

2. Environment Variables Not Passing

Apple Container Bug: Environment variables passed via -e are lost when using -i (interactive/piped stdin).

Workaround: The system extracts only authentication variables (CLAUDE_CODE_OAUTH_TOKEN, ANTHROPIC_API_KEY) from .env and mounts them for sourcing inside the container. Other env vars are not exposed.

To verify env vars are reaching the container:

echo '{}' | container run -i \
  --mount type=bind,source=$(pwd)/data/env,target=/workspace/env-dir,readonly \
  --entrypoint /bin/bash bioclaw-agent:latest \
  -c 'export $(cat /workspace/env-dir/env | xargs); echo "OAuth: ${#CLAUDE_CODE_OAUTH_TOKEN} chars, API: ${#ANTHROPIC_API_KEY} chars"'

3. Mount Issues

Apple Container quirks:

• Only mounts directories, not individual files
• -v syntax does NOT support :ro suffix - use --mount for readonly:

  # Readonly: use --mount
  --mount "type=bind,source=/path,target=/container/path,readonly"
  
  # Read-write: use -v
  -v /path:/container/path
  

To check what's mounted inside a container:

container run --rm --entrypoint /bin/bash bioclaw-agent:latest -c 'ls -la /workspace/'

Expected structure:

/workspace/
├── env-dir/env           # Environment file (CLAUDE_CODE_OAUTH_TOKEN or ANTHROPIC_API_KEY)
├── group/                # Current group folder (cwd)
├── project/              # Project root (main channel only)
├── global/               # Global CLAUDE.md (non-main only)
├── ipc/                  # Inter-process communication
│   ├── messages/         # Outgoing WhatsApp messages
│   ├── tasks/            # Scheduled task commands
│   ├── current_tasks.json    # Read-only: scheduled tasks visible to this group
│   └── available_groups.json # Read-only: WhatsApp groups for activation (main only)
└── extra/                # Additional custom mounts

4. Permission Issues

The container runs as user node (uid 1000). Check ownership:

container run --rm --entrypoint /bin/bash bioclaw-agent:latest -c '
  whoami
  ls -la /workspace/
  ls -la /app/
'

All of /workspace/ and /app/ should be owned by node.

5. Session Not Resuming / "Claude Code process exited with code 1"

If sessions aren't being resumed (new session ID every time), or Claude Code exits with code 1 when resuming:

Root cause: The SDK looks for sessions at $HOME/.claude/projects/. Inside the container, HOME=/home/node, so it looks at /home/node/.claude/projects/.

Check the mount path:

# In container-runner.ts, verify mount is to /home/node/.claude/, NOT /root/.claude/
grep -A3 "Claude sessions" src/container-runner.ts

Verify sessions are accessible:

container run --rm --entrypoint /bin/bash \
  -v ~/.claude:/home/node/.claude \
  bioclaw-agent:latest -c '
echo "HOME=$HOME"
ls -la $HOME/.claude/projects/ 2>&1 | head -5
'

Fix: Ensure container-runner.ts mounts to /home/node/.claude/:

mounts.push({
  hostPath: claudeDir,
  containerPath: '/home/node/.claude',  // NOT /root/.claude
  readonly: false
});

6. MCP Server Failures

If an MCP server fails to start, the agent may exit. Check the container logs for MCP initialization errors.

Manual Container Testing

Test the full agent flow:

# Set up env file
mkdir -p data/env groups/test
cp .env data/env/env

# Run test query
echo '{"prompt":"What is 2+2?","groupFolder":"test","chatJid":"[e-mail]","isMain":false}' | \
  container run -i \
  --mount "type=bind,source=$(pwd)/data/env,target=/workspace/env-dir,readonly" \
  -v $(pwd)/groups/test:/workspace/group \
  -v $(pwd)/data/ipc:/workspace/ipc \
  bioclaw-agent:latest

Test Claude Code directly:

container run --rm --entrypoint /bin/bash \
  --mount "type=bind,source=$(pwd)/data/env,target=/workspace/env-dir,readonly" \
  bioclaw-agent:latest -c '
  export $(cat /workspace/env-dir/env | xargs)
  claude -p "Say hello" --dangerously-skip-permissions --allowedTools ""
'

Interactive shell in container:

container run --rm -it --entrypoint /bin/bash bioclaw-agent:latest

SDK Options Reference

The agent-runner uses these Claude Agent SDK options:

query({
  prompt: input.prompt,
  options: {
    cwd: '/workspace/group',
    allowedTools: ['Bash', 'Read', 'Write', ...],
    permissionMode: 'bypassPermissions',
    allowDangerouslySkipPermissions: true,  // Required with bypassPermissions
    settingSources: ['project'],
    mcpServers: { ... }
  }
})

Important: allowDangerouslySkipPermissions: true is required when using permissionMode: 'bypassPermissions'. Without it, Claude Code exits with code 1.

Rebuilding After Changes

# Rebuild main app
npm run build

# Rebuild container (use --no-cache for clean rebuild)
./container/build.sh

# Or force full rebuild
container builder prune -af
./container/build.sh

Checking Container Image

# List images
container images

# Check what's in the image
container run --rm --entrypoint /bin/bash bioclaw-agent:latest -c '
  echo "=== Node version ==="
  node --version

  echo "=== Claude Code version ==="
  claude --version

  echo "=== Installed packages ==="
  ls /app/node_modules/
'

Session Persistence

Claude sessions are stored per-group in data/sessions/{group}/.claude/ for security isolation. Each group has its own session directory, preventing cross-group access to conversation history.

Critical: The mount path must match the container user's HOME directory:

• Container user: node
• Container HOME: /home/node
• Mount target: /home/node/.claude/ (NOT /root/.claude/)

To clear sessions:

# Clear all sessions for all groups
rm -rf data/sessions/

# Clear sessions for a specific group
rm -rf data/sessions/{groupFolder}/.claude/

# Also clear the session ID from BioClaw's tracking (stored in SQLite)
sqlite3 store/messages.db "DELETE FROM sessions WHERE group_folder = '{groupFolder}'"

To verify session resumption is working, check the logs for the same session ID across messages:

grep "Session initialized" logs/bioclaw.log | tail -5
# Should show the SAME session ID for consecutive messages in the same group

IPC Debugging

The container communicates back to the host via files in /workspace/ipc/:

# Check pending messages
ls -la data/ipc/messages/

# Check pending task operations
ls -la data/ipc/tasks/

# Read a specific IPC file
cat data/ipc/messages/*.json

# Check available groups (main channel only)
cat data/ipc/main/available_groups.json

# Check current tasks snapshot
cat data/ipc/{groupFolder}/current_tasks.json

IPC file types:

• messages/*.json - Agent writes: outgoing WhatsApp messages
• tasks/*.json - Agent writes: task operations (schedule, pause, resume, cancel, refresh_groups)
• current_tasks.json - Host writes: read-only snapshot of scheduled tasks
• available_groups.json - Host writes: read-only list of WhatsApp groups (main only)

Quick Diagnostic Script

Run this to check common issues:

echo "=== Checking BioClaw Container Setup ==="

echo -e "\n1. Authentication configured?"
[ -f .env ] && (grep -q "CLAUDE_CODE_OAUTH_TOKEN=sk-" .env || grep -q "ANTHROPIC_API_KEY=sk-" .env) && echo "OK" || echo "MISSING - add CLAUDE_CODE_OAUTH_TOKEN or ANTHROPIC_API_KEY to .env"

echo -e "\n2. Env file copied for container?"
[ -f data/env/env ] && echo "OK" || echo "MISSING - will be created on first run"

echo -e "\n3. Apple Container system running?"
container system status &>/dev/null && echo "OK" || echo "NOT RUNNING - BioClaw should auto-start it; check logs"

echo -e "\n4. Container image exists?"
echo '{}' | container run -i --entrypoint /bin/echo bioclaw-agent:latest "OK" 2>/dev/null || echo "MISSING - run ./container/build.sh"

echo -e "\n5. Session mount path correct?"
grep -q "/home/node/.claude" src/container-runner.ts 2>/dev/null && echo "OK" || echo "WRONG - should mount to /home/node/.claude/, not /root/.claude/"

echo -e "\n6. Groups directory?"
ls -la groups/ 2>/dev/null || echo "MISSING - run setup"

echo -e "\n7. Recent container logs?"
ls -t groups/*/logs/container-*.log 2>/dev/null | head -3 || echo "No container logs yet"

echo -e "\n8. Session continuity working?"
SESSIONS=$(grep "Session initialized" logs/bioclaw.log 2>/dev/null | tail -5 | awk '{print $NF}' | sort -u | wc -l)
[ "$SESSIONS" -le 2 ] && echo "OK (recent sessions reusing IDs)" || echo "CHECK - multiple different session IDs, may indicate resumption issues"