Organism Maintenance

Run maintenance checks and repairs on the Samara organism.

Quick Check

Run a quick health status:

~/.claude-mind/system/bin/sync-organism --check && echo "No drift detected" || echo "Drift detected"

Full Maintenance Checklist

1. System Drift Check

~/.claude-mind/system/bin/sync-organism --check

If drift detected, review and sync:

~/.claude-mind/system/bin/sync-organism

2. Launchd Services

launchctl list | grep com.claude

Expected: 4+ services (wake-adaptive, dream, message-watcher, etc.)

If missing, reload:

launchctl load ~/Library/LaunchAgents/com.claude.*.plist

3. Samara.app Status

launchctl list co.organelle.Samara 2>/dev/null | grep -q 'PID' && echo "Running" || echo "Not running"

If not running:

open /Applications/Samara.app

4. FDA Status

# Check for recent FDA issues
tail -20 ~/.claude-mind/system/logs/samara.log | grep -i "denied\|permission"

5. Lock File

# Check for stale locks
if [ -f ~/.claude-mind/state/locks/system-cli.lock ]; then
    cat ~/.claude-mind/state/locks/system-cli.lock | python3 -c "import sys,json; d=json.load(sys.stdin); print(f\"Lock held by: {d.get('task')} (PID: {d.get('pid')})\")"
fi

6. Symlink Integrity

# Check critical symlinks
for link in ~/.claude-mind/system/bin ~/.claude-mind/.claude ~/.claude-mind/system/instructions; do
    if [ -L "$link" ]; then
        if [ -e "$link" ]; then
            echo "$link -> $(readlink "$link") [OK]"
        else
            echo "$link -> $(readlink "$link") [BROKEN]"
        fi
    fi
done

Repair Commands

Sync from repo

~/.claude-mind/system/bin/sync-organism

Rebuild Samara.app

~/.claude-mind/system/bin/update-samara

Clear stale lock

rm -f ~/.claude-mind/state/locks/system-cli.lock

Reload all launchd services

for f in ~/Library/LaunchAgents/com.claude.*.plist; do
    launchctl unload "$f" 2>/dev/null
    launchctl load "$f"
done

When to Use

• After updating samara-main repo
• After system restart
• When wake cycles seem stuck
• When messages aren't being processed
• After Xcode rebuild of Samara.app