Fix Scheduled Scripts Command

Repair scheduled scripts (cron jobs) when the plugin directory location changes. This command:

1. Creates/updates a stable symlink pointing to the current plugin location
2. Scans crontab for hardcoded plugin paths and replaces them with symlink paths

Step 1: Create/Update Stable Symlink

1. Define paths:

   • Symlink location: ~/.claude/research-system-config/plugin (stable, never changes)
   • Target: ${CLAUDE_PLUGIN_ROOT} (actual plugin location, may change)

2. Check config directory:

   • Run: test -d ~/.claude/research-system-config && echo "EXISTS" || echo "NOT_FOUND"
   • If NOT_FOUND: Run mkdir -p ~/.claude/research-system-config
   • If EXISTS: Continue (directory already exists)

3. Check if symlink exists:

   • Run: ls -la ~/.claude/research-system-config/plugin 2>/dev/null || echo "NOT_FOUND"

4. Handle existing path:

   • If symlink exists and points to correct location: "Symlink already up to date"
   • If symlink exists but points to wrong location: Remove and recreate
   • If regular directory exists: Show error - "Cannot create symlink: ~/.claude/research-system-config/plugin exists as a directory. Please remove or rename it."
   • If not found: Create new symlink

5. Create/update symlink:

   • Run: ln -sfn "${CLAUDE_PLUGIN_ROOT}" ~/.claude/research-system-config/plugin
   • Verify: ls -la ~/.claude/research-system-config/plugin
   • Report: "Created symlink: ~/.claude/research-system-config/plugin -> [actual path]"

Step 2: Scan Crontab for Hardcoded Paths

1. Get current crontab:

   • Run: crontab -l 2>/dev/null || echo "NO_CRONTAB"
   • If no crontab exists, skip to Step 4

2. Identify research-system related entries:

   • Look for lines containing:
     • fetch_papers.py
     • monitor_sources.py
     • Any path containing research-system

3. Check for hardcoded paths:

   • Pattern to find: Any path that is NOT ~/.claude/research-system-config/plugin/ but references research-system scripts
   • Common hardcoded patterns:
     • ~/.claude/plugins/cache/research-system/
     • ~/.claude/plugins/research-system/
     • Any absolute path containing /research-system/scripts/
   • Also check for the old symlink location ~/.claude/research-system/ (if we used that previously)

Step 3: Update Crontab Entries

1. For each hardcoded path found:

   • Extract the full cron entry
   • Replace the hardcoded path with ~/.claude/research-system-config/plugin/
   • Example:
     • Before: 0 6 * * * cd ~/.claude/plugins/cache/research-system/scripts/automation && python3 fetch_papers.py
     • After: 0 6 * * * cd ~/.claude/research-system-config/plugin/scripts/automation && python3 fetch_papers.py

2. Create updated crontab:

   • Build new crontab content with all replacements
   • Show diff to user: "Found [N] entries to update:"
   • Show before/after for each changed line

3. Apply updated crontab:

   • Run: echo "[new_crontab_content]" | crontab -
   • Verify: crontab -l | grep research-system

Step 4: Report Results

Provide summary:

Fix Scheduled Scripts Complete

Symlink Status:
- ~/.claude/research-system-config/plugin -> [actual plugin path]
- Status: [Created/Updated/Already correct]

Crontab Updates:
- Entries scanned: [N]
- Entries updated: [N]
- [List each updated entry if any]

Scheduled Scripts:
- fetch_papers.py: [Found at HH:MM daily / Not scheduled]
- monitor_sources.py: [Found at HH:MM daily / Not scheduled]

All scheduled scripts are now using stable paths.

If no crontab exists:

Fix Scheduled Scripts Complete

Symlink Status:
- ~/.claude/research-system-config/plugin -> [actual plugin path]
- Status: Created

Crontab Updates:
- No crontab found. Run /setup-research-automation to configure scheduled scripts.

Error Handling

• Cannot create symlink directory: Check ~/.claude/research-system-config/ exists and is writable
• Crontab permission denied: Show error, suggest checking user permissions
• Symlink target doesn't exist: Show error - plugin may not be properly installed
• Cannot read ${CLAUDE_PLUGIN_ROOT}: Show error - Claude Code environment variable not available

When to Run This Command

Run this command when:

• Scheduled scripts stop working after a Claude Code update
• You see errors about missing plugin scripts in cron logs
• After reinstalling or updating the research-system plugin
• When ~/.research-data/*.log shows "file not found" errors for Python scripts

Notes

• This command is safe to run multiple times - it's idempotent
• The symlink approach ensures cron jobs survive plugin directory changes
• After running this command, future plugin updates only require re-running this command to fix paths
• The symlink is created in ~/.claude/research-system-config/ alongside config.yaml