# Pipeline & Infrastructure Commands

Reference for: `sync`, `ingest`, `generate-docs`, `embed`, `health`, `auth`, `doctor`, `status`, `stats`, `init`, `token`, `cron`, `migrate`, `version`, `completions`, `robot-docs`

---

## Data Pipeline

### `sync` (Full Pipeline)

Complete sync: ingest -> generate-docs -> embed.

| Flag | Type | Default | Purpose |
|---|---|---|---|
| `--full` | flag | — | Full re-sync (reset cursors) |
| `-f, --force` | flag | — | Override stale lock |
| `--no-embed` | flag | — | Skip embedding |
| `--no-docs` | flag | — | Skip doc generation |
| `--no-events` | flag | — | Skip resource events |
| `--no-file-changes` | flag | — | Skip MR file changes |
| `--no-status` | flag | — | Skip work-item status enrichment |
| `--dry-run` | flag | — | Preview without changes |
| `-t, --timings` | flag | — | Show timing breakdown |
| `--lock` | flag | — | Acquire file lock |
| `--issue` | int[] | — | Surgically sync specific issues (repeatable) |
| `--mr` | int[] | — | Surgically sync specific MRs (repeatable) |
| `-p, --project` | string | — | Required with `--issue`/`--mr` |
| `--preflight-only` | flag | — | Validate without DB writes |

**Stages:** GitLab REST ingest -> GraphQL status enrichment -> Document generation -> Ollama embedding

**Surgical sync:** `lore sync --issue 42 --mr 99 -p group/repo` fetches only specific entities.

### `ingest`

Fetch data from GitLab API only (no docs, no embeddings).

| Flag | Type | Default | Purpose |
|---|---|---|---|
| `[ENTITY]` | positional | — | `issues` or `mrs` (omit for all) |
| `-p, --project` | string | — | Single project |
| `-f, --force` | flag | — | Override stale lock |
| `--full` | flag | — | Full re-sync |
| `--dry-run` | flag | — | Preview |

**Fetches from GitLab:**
- Issues + discussions + notes
- MRs + discussions + notes
- Resource events (state, label, milestone)
- MR file changes (for DiffNote tracking)
- Work-item statuses (via GraphQL)

### `generate-docs`

Create searchable documents from ingested data.

| Flag | Type | Default | Purpose |
|---|---|---|---|
| `--full` | flag | — | Full rebuild |
| `-p, --project` | string | — | Single project rebuild |

**Writes:** `documents`, `document_labels`, `document_paths`

### `embed`

Generate vector embeddings via Ollama.

| Flag | Type | Default | Purpose |
|---|---|---|---|
| `--full` | flag | — | Re-embed all |
| `--retry-failed` | flag | — | Retry failed embeddings |

**Requires:** Ollama running with `nomic-embed-text`
**Writes:** `embeddings`, `embedding_metadata`

---

## Diagnostics

### `health`

Quick pre-flight check (~50ms). Exit 0 = healthy, exit 19 = unhealthy.

**Checks:** config found, DB found, schema version current.

```json
{
  "ok": true,
  "data": {
    "healthy": true,
    "config_found": true, "db_found": true,
    "schema_current": true, "schema_version": 28
  }
}
```

### `auth`

Verify GitLab authentication.

**Checks:** token set, GitLab reachable, user identity.

### `doctor`

Comprehensive environment check.

**Checks:** config validity, token, GitLab connectivity, DB health, migration status, Ollama availability + model status.

```json
{
  "ok": true,
  "data": {
    "config": { "valid": true, "path": "~/.config/lore/config.json" },
    "token": { "set": true, "gitlab": { "reachable": true, "user": "jdoe" } },
    "database": { "exists": true, "version": 28, "tables": 25 },
    "ollama": { "available": true, "model_ready": true }
  }
}
```

### `status` (alias: `st`)

Show sync state per project.

```json
{
  "ok": true,
  "data": {
    "projects": [
      {
        "project_path": "group/repo",
        "last_synced_at": "2026-02-26T10:00:00Z",
        "document_count": 5000, "discussion_count": 2000, "notes_count": 15000
      }
    ]
  }
}
```

### `stats` (alias: `stat`)

Document and index statistics with optional integrity checks.

| Flag | Type | Default | Purpose |
|---|---|---|---|
| `--check` | flag | — | Run integrity checks |
| `--repair` | flag | — | Fix issues (implies `--check`) |
| `--dry-run` | flag | — | Preview repairs |

```json
{
  "ok": true,
  "data": {
    "documents": { "total": 61652, "issues": 5000, "mrs": 2000, "notes": 50000 },
    "embeddings": { "total": 80000, "synced": 79500, "pending": 500, "failed": 0 },
    "fts": { "total_docs": 61652 },
    "queues": { "pending": 0, "in_progress": 0, "failed": 0, "max_attempts": 0 },
    "integrity": {
      "ok": true, "fts_doc_mismatch": 0, "orphan_embeddings": 0,
      "stale_metadata": 0, "orphan_state_events": 0
    }
  }
}
```

---

## Setup

### `init`

Initialize configuration and database.

| Flag | Type | Default | Purpose |
|---|---|---|---|
| `-f, --force` | flag | — | Skip overwrite confirmation |
| `--non-interactive` | flag | — | Fail if prompts needed |
| `--gitlab-url` | string | — | GitLab base URL (required in robot mode) |
| `--token-env-var` | string | — | Env var holding token (required in robot mode) |
| `--projects` | string | — | Comma-separated project paths (required in robot mode) |
| `--default-project` | string | — | Default project path |

### `token`

| Subcommand | Flags | Purpose |
|---|---|---|
| `token set` | `--token <TOKEN>` | Store token (reads stdin if omitted) |
| `token show` | `--unmask` | Display token (masked by default) |

### `cron`

| Subcommand | Flags | Purpose |
|---|---|---|
| `cron install` | `--interval <MINUTES>` (default: 8) | Schedule auto-sync |
| `cron uninstall` | — | Remove cron job |
| `cron status` | — | Check installation |

### `migrate`

Run pending database migrations. No flags.

---

## Meta

| Command | Purpose |
|---|---|
| `version` | Show version string |
| `completions <shell>` | Generate shell completions (bash/zsh/fish/powershell) |
| `robot-docs` | Machine-readable command manifest (`--brief` for ~60% smaller) |