Codex History Ingest

Codex History Ingest — Conversation Mining

You are extracting knowledge from the user's past Codex sessions and distilling it into the Obsidian wiki. Session logs are rich but noisy: focus on durable knowledge, not operational telemetry.

This skill can be invoked directly or via the wiki-history-ingest router (/wiki-history-ingest codex).

Before You Start

1. Resolve config — follow the Config Resolution Protocol in llm-wiki/SKILL.md (walk up CWD for .env → ~/.obsidian-wiki/config → prompt setup). This gives OBSIDIAN_VAULT_PATH and CODEX_HISTORY_PATH (defaults to ~/.codex) 2. Read .manifest.json at the vault root to check what has already been ingested 3. Read index.md at the vault root to understand what the wiki already contains

Ingest Modes

Append Mode (default)

Check .manifest.json for each source file. Only process:

• Files not in the manifest (new session rollouts, new index files)
• Files whose modification time is newer than ingested_at in the manifest

Use this mode for regular syncs.

Full Mode

Process everything regardless of manifest. Use after wiki-rebuild or if the user explicitly asks for a full re-ingest.

Codex Data Layout

Codex stores local artifacts under ~/.codex/.

~/.codex/
├── sessions/                          # Session rollout logs by date
│   └── YYYY/MM/DD/
│       └── rollout-<timestamp>-<id>.jsonl
├── archived_sessions/                 # Archived rollout logs
├── session_index.jsonl                # Lightweight index of thread id/name/updated_at
├── history.jsonl                      # Local transcript history (if persistence enabled)
├── config.toml                        # User config (contains history settings)
└── state_*.sqlite / logs_*.sqlite     # Runtime DBs (usually skip)

Key data sources ranked by value

1. session_index.jsonl — best inventory source for IDs, titles, and freshness 2. sessions/**/rollout-*.jsonl — rich structured transcript events 3. history.jsonl — useful fallback/timeline aid if enabled

Avoid ingesting SQLite internals unless the user explicitly asks.

Step 1: Survey and Compute Delta

Scan CODEX_HISTORY_PATH and compare against .manifest.json:

• ~/.codex/session_index.jsonl
• ~/.codex/sessions/**/rollout-*.jsonl
• ~/.codex/archived_sessions/** (optional; only if user asks for archived history)
• ~/.codex/history.jsonl (optional fallback)

Classify each file:

• New — not in manifest
• Modified — in manifest but file is newer than ingested_at
• Unchanged — already ingested and unchanged

Report a concise delta summary before deep parsing.

Step 2: Parse Session Index First

session_index.jsonl typically has entries like:

{"id":"...","thread_name":"...","updated_at":"..."}

Use it to:

• Build a canonical session inventory
• Prioritize recent/high-signal sessions
• Map rollout IDs to human-readable thread names

Step 3: Parse Rollout JSONL Safely

Each rollout-*.jsonl line is an event envelope with:

{
  "timestamp": "...",
  "type": "session_meta|turn_context|event_msg|response_item",
  "payload": { ... }
}

Extraction rules

• Prioritize user intent and assistant-visible outputs
• Favor response_item records with user/assistant message content
• Use event_msg selectively for meaningful milestones; ignore pure telemetry
• Treat session_meta as metadata (cwd, model, ids), not user knowledge

Skip/noise filters

• Token accounting events
• Tool plumbing with no semantic content
• Raw command output unless it contains reusable decisions/patterns
• Repeated plan snapshots unless they add novel decisions

Critical privacy filter

Rollout logs can include injected instructions, tool payloads, and sensitive text. Do not ingest verbatim system/developer prompts or secrets.

• Remove API keys, tokens, passwords, credentials
• Redact private identifiers unless relevant and approved
• Summarize instead of quoting raw transcripts

Step 4: Cluster by Topic

Do not create one wiki page per session.

• Group by stable topics across many sessions
• Split mixed sessions into separate themes
• Merge recurring concepts across dates/projects
• Use cwd from metadata to infer project scope

Step 5: Distill into Wiki Pages

Route extracted knowledge using existing wiki conventions:

• Project-specific architecture/process -> projects/<name>/...
• General concepts -> concepts/
• Recurring techniques/debug playbooks -> skills/
• Tools/services -> entities/
• Cross-session patterns -> synthesis/

For each impacted project, create/update projects/<name>/<name>.md (project name as filename, never _project.md).

Writing rules

• Distill knowledge, not chronology
• Avoid "on date X we discussed..." unless date context is essential
• Add summary: frontmatter on each new/updated page (1-2 sentences, <= 200 chars)
• Add confidence and lifecycle fields to every new page:

  base_confidence: 0.42
  lifecycle: draft
  lifecycle_changed: <ISO date today>

Leave lifecycle unchanged on update.

• Add provenance markers:
• ^[extracted] when directly grounded in explicit session content
• ^[inferred] when synthesizing patterns across events/sessions
• ^[ambiguous] when sessions conflict
• Add/update provenance: frontmatter mix for each changed page

Step 6: Update Manifest, Log, and Index

Update .manifest.json

For each processed source file:

• ingested_at, size_bytes, modified_at
• source_type: codex_rollout | codex_index | codex_history
• project: inferred project name (when applicable)
• pages_created, pages_updated

Add/update a top-level project/session summary block:

{
  "project-name": {
    "source_path": "~/.codex/sessions/...",
    "last_ingested": "TIMESTAMP",
    "sessions_ingested": 12,
    "sessions_total": 40,
    "index_updated_at": "TIMESTAMP"
  }
}

Update special files

Update index.md and log.md:

- [TIMESTAMP] CODEX_HISTORY_INGEST sessions=N pages_updated=X pages_created=Y mode=append|full

`hot.md` — Read $OBSIDIAN_VAULT_PATH/hot.md (create from the template in wiki-ingest if missing). Update Recent Activity with a one-line summary — e.g. "Ingested 12 Codex sessions; surfaced recurring patterns in CLI tooling and shell scripting." Keep the last 3 operations. Update updated timestamp.

Privacy and Compliance

• Distill and synthesize; avoid raw transcript dumps
• Default to redaction for anything that looks sensitive
• Ask the user before storing personal/sensitive details
• Keep references to other people minimal and purpose-bound

Reference

See references/codex-data-format.md for field-level parsing notes and extraction guidance.

QMD Refresh After Vault Writes

QMD is a search index, not the source of truth. If $QMD_WIKI_COLLECTION is empty or unset, skip this step. Run it only after this skill has written or rewritten vault markdown. If QMD refresh fails, do not roll back the vault changes; report the QMD status separately.

Use $QMD_CLI if set; otherwise use qmd.

${QMD_CLI:-qmd} update

If the output says vectors are needed or embeddings may be stale, run:

${QMD_CLI:-qmd} embed

Verify the collection with either:

${QMD_CLI:-qmd} ls "$QMD_WIKI_COLLECTION"

or, when a specific page path is known:

${QMD_CLI:-qmd} get "qmd://$QMD_WIKI_COLLECTION/<page>.md" -l 5

Record one of:

• QMD refreshed: update + embed + verified
• QMD refreshed: update only + verified
• QMD skipped: QMD_WIKI_COLLECTION unset
• QMD skipped: qmd CLI unavailable
• QMD failed: <short error summary>

Codex Data Format — Detailed Reference

This reference describes practical, observed structures for Codex local history ingestion.

Root Layout

~/.codex/ usually contains:

• sessions/YYYY/MM/DD/rollout-*.jsonl — primary structured session logs
• archived_sessions/ — archived rollouts
• session_index.jsonl — session id/name/update index
• history.jsonl — transcript history (depends on config)
• config.toml — history persistence controls

Session Index

~/.codex/session_index.jsonl entries are one JSON object per line, commonly:

{"id":"<thread-id>","thread_name":"<title>","updated_at":"<timestamp>"}

Use this as the inventory backbone for append/full mode deltas.

Rollout JSONL

rollout-*.jsonl files are event streams with envelope fields:

{
  "timestamp": "2026-04-12T09:40:02.337Z",
  "type": "session_meta|turn_context|event_msg|response_item",
  "payload": { "...": "..." }
}

Common type values:

• session_meta — run metadata (id, cwd, model/provider, etc.)
• turn_context — turn-scoped context envelope
• event_msg — runtime events (task lifecycle, token/accounting, tool-call markers)
• response_item — model response items (messages, tool calls, reasoning blocks)

Typical payload subtypes

Observed examples include:

• event_msg.payload.type: task_started, user_message, agent_message, mcp_tool_call_end, exec_command_end, token_count
• response_item.payload.type: message, function_call, function_call_output, reasoning

Extraction Strategy

Keep

• User intent from user-message records
• Assistant conclusions/decisions from assistant message records
• High-signal tool outputs that encode reusable knowledge

Skip

• Pure telemetry (token_count, low-level plumbing events)
• Internal reasoning traces unless user explicitly asks to retain them
• Verbose execution dumps with no durable insight

Privacy Notes

Rollouts can contain sensitive data:

• Injected instruction layers
• Tool inputs/outputs
• Potential secrets in command output

Always redact secrets and summarize instead of copying raw transcript content.

Config Interaction

~/.codex/config.toml keys that affect ingestion completeness:

• history.persistence = "save-all" | "none"
• history.max_bytes = <int> (truncation/compaction cap)

codex exec --ephemeral runs may not persist rollout files.