Clean Codex Archives

Use the bundled scripts/clean_codex_archives.py script as the cross-platform entry point. It uses only Python's standard library and preserves active sessions.

Safety contract

• Resolve the Codex data root from an explicit --codex-home argument, then the CODEX_HOME environment variable, then the current user's .codex directory.
• Treat state_5.sqlite as the source of truth. Only rows with threads.archived = 1 are eligible for deletion.
• Preserve all unarchived threads, their logs, and their session-index entries.
• Run without --apply first. Use --apply only after the user explicitly authorizes deletion.
• Delete associated logs and goals before deleting archived thread rows, because the archived IDs are needed to select related records safely.
• Delete related thread_dynamic_tools and thread_spawn_edges rows when those tables are present.
• Remove only archived_sessions/*.jsonl files. Do not delete the archive directory itself or unrelated files.
• Rewrite session_index.jsonl only after database cleanup, retaining entries whose IDs still exist in state_5.sqlite and rejecting malformed JSON instead of silently dropping it.
• If a database is locked, ask the user to close Codex or otherwise stop the process holding the database, then retry.

Workflow

1. Run a dry run and inspect the counts for archive files, archived threads, related logs, goals, and stale index entries.
2. If the user confirms deletion, rerun with --apply.
3. Use --vacuum only when the user also wants SQLite files compacted; it may require exclusive database access and is not needed for logical deletion.
4. Verify that archived-thread count is zero, archive-file count is zero, remaining index IDs all exist in the state database, and SQLite quick_check reports ok for modified databases.

Commands

# Inventory only; no changes. Use python3 on Unix-like systems.
python3 ./scripts/clean_codex_archives.py

# Apply the explicitly authorized cleanup.
python3 ./scripts/clean_codex_archives.py --apply

# Use a specific Codex data root.
python3 ./scripts/clean_codex_archives.py --codex-home "$HOME/.codex" --apply

# Optional physical compaction after deletion.
python3 ./scripts/clean_codex_archives.py --apply --vacuum

On Windows, use python instead of python3.