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

HOME=/home/node

/home/node/.claude/

/root/.claude/

Log Locations

logs/bioclaw.log

logs/bioclaw.error.log

groups/{folder}/logs/container-*.log

~/.claude/projects/

Enabling Debug Logging

Set

LOG_LEVEL=debug

# 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

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

-i

Workaround: The system extracts only authentication variables (

CLAUDE_CODE_OAUTH_TOKEN

ANTHROPIC_API_KEY

.env

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

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

All of

/workspace/

/app/

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/

HOME=/home/node

/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

/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":"test@g.us","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

permissionMode: 'bypassPermissions'

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/

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"