Agents view Ctrl+X ×2 leaves orphaned .jsonl transcript on disk

Summary

In Claude Code 2.1.139–2.1.140, the Agents view's documented two-press delete (Ctrl+X stop, Ctrl+X again within 2s to delete) does not fully delete the session: the <uuid>/ subdirectory is removed, but the corresponding ~/.claude/projects/<encoded-cwd>/<uuid>.jsonl transcript file is left orphaned on disk.

This contradicts the Agent View docs which state: "To remove a session, press Ctrl+X to stop it and Ctrl+X again within two seconds to delete it." No carve-out for transcript preservation is mentioned.

Reproduction (macOS, claude --version 2.1.140)

1. Start a background agent session: claude --bg (or via Agents view), do one turn.
2. Note the session UUID and confirm both files exist:

• ~/.claude/projects/-Users-<you>/<uuid>.jsonl
• ~/.claude/projects/-Users-<you>/<uuid>/ (subdir, if any subagent/tool spilled)

1. From the Agents view, focus that session and press Ctrl+X twice within 2 seconds.
2. Confirm:

• The session vanishes from the Agents view ✓
• The <uuid>/ subdirectory is removed ✓
• The <uuid>.jsonl transcript file is still on disk ✗

Expected

Per the docs, Ctrl+X×2 deletes the session entirely — both the subdir and the .jsonl transcript.

Actual

Only the <uuid>/ subdir is deleted. The .jsonl file orphans, accumulating over time.

Root cause (from binary inspection)

The delete handler mHH (deleteJob) only rm -rfs the job state directory and never unlinks the matching .jsonl:

// mHH (deleteJob):
await BNH.rm(W4(H), {recursive:true, force:true}).catch(()=>{})
// W4(H) returns the job state dir; no matching unlinkSync on <uuid>.jsonl

The jsonl path is derivable elsewhere in the binary (e.g. in ioH / respawn: path.join(zG(await _Y(K.cwd)), ${w}.jsonl)), but mHH simply never calls it.

Related

• #45903 — mirror-image bug (jsonl deleted, subdirs orphaned)
• #41591, #48334 — auto-update cleanup leaves sessions-index.json entries stale
• Meta thread on cleanup gaps: #33979

Environment

• macOS 15 (Darwin 24.6.0), Apple Silicon
• Claude Code 2.1.139 and 2.1.140 (Mach-O arm64 native bundle)
• Reproduced multiple times

Impact

Disk usage accumulates indefinitely. Users believe their sessions are deleted but transcripts persist. Third-party cleaners (CC-Cleaner, claude-code-cleaner) exist precisely because of this class of orphan accumulation.