Summary generation via `explain --generate` creates full Claude Code sessions that pollute /resume and entire status

[alexfosterinvisible]

Problem

When entire explain --generate runs, it spawns a full Claude Code session to generate AI summaries for checkpoints. These sessions:

1. Show up in Claude Code's /resume list - users see dozens of "This is your initialization prompt" entries alongside real work sessions
2. Show up in entire status as active sessions indefinitely (some persist 30+ days)
3. Contribute to the session count that drives post-commit hook latency (see ENCLI-123)
4. Cannot be distinguished from real interactive sessions

Evidence from my repo right now

After entire clean --force, I still have 12 active sessions. 7 of them are summary generation artifacts:

[Claude Code] 6d7acb6   started 27d ago  "This is your initialization prompt..."
[Claude Code] 79e5218   started 28d ago  "This is your initialization prompt..."
[Claude Code] 6e453d5   started 31d ago  "This is your initialization prompt..."
[Claude Code] 5ca15d9   started 31d ago  "This is your initialization prompt..."
[Claude Code] 7d2c429   started 31d ago  "This is your initialization prompt..."
[Claude Code] fcd3c15   started 32d ago  "This is your initialization prompt..."
[Claude Code] 5ee97fe   started 33d ago  "This is your initialization prompt..."

That's 58% of my active sessions being ghost summary sessions. They're stale (27-33 days old), never cleaned, and inflate session count.

Root cause

entire explain --generate appears to launch a full Claude Code session (with initialization prompt) rather than making a direct API call. This session gets tracked by Entire like any other, but it's ephemeral work that shouldn't persist.

Proposed fix

Use a direct LLM API call instead of spawning a Claude Code session. The user already has ANTHROPIC_API_KEY available. Summary generation is a simple prompt-in/text-out operation - it doesn't need tool use, file access, or session context. A direct API call would:

• Not create trackable sessions
• Not appear in /resume or entire status
• Be significantly faster (no session setup overhead)
• Not contribute to session count / latency scaling

If a full session is needed for some reason, at minimum spawn it as a sub-agent (Claude Code Task tool) rather than a top-level session - sub-agents don't appear in /resume by default.

Impact

• ENCLI-123 latency scales with session count - these ghost sessions directly worsen it
• /resume becomes unusable when 50%+ of entries are "initialization prompt" noise
• entire clean doesn't remove these since they're technically "active" sessions

Environment

• macOS Darwin 24.4.0
• Claude Code 2.1.58
• entire with manual-commit strategy
• Daily latency monitoring via cron (see ENCLI-123 for dataset)