Knowledge Bootstrap

# Skill: Knowledge Bootstrap

## Purpose
Initialize all 7 knowledge subsystems for a new session. Loads setup state,
dataset, user profile, integrations, org context, corrections, learnings,
query archaeology, and analysis archive into working memory.

## When to Use
- At the start of any session
- After `/connect-data` or `/switch-dataset`
- When the system detects missing or stale knowledge files

## Instructions

Load each subsystem in order. Every file read MUST gracefully degrade: if the
file does not exist, skip silently and note "not yet populated" in the summary.
Never block the session on a missing subsystem.

### Step 1: Setup State
Read `.knowledge/setup-state.yaml`.
- Parse `setup_complete` and count phases with `status: "complete"`.
- If `setup_complete: false`, note incomplete phases to offer `/setup`.
- **If missing:** Note "Setup: not initialized -- offer /setup".

### Step 2: Active Dataset
Read `.knowledge/active.yaml`.
- If `active_dataset` is null or missing, note "No active dataset" and continue.
- If set, load from `.knowledge/datasets/{active}/`:

| File | Required | If Missing |
|------|----------|------------|
| `manifest.yaml` | Yes | Note "manifest missing -- not usable" |
| `schema.md` | Yes | Generate via `schema_to_markdown()` or profiling |
| `quirks.md` | No | Create empty template |
| `metrics/index.yaml` | No | Count as 0 |

Schema generation if `schema.md` is missing:
1. Check `data/schemas/{active}.yaml` -- use `schema_to_markdown()` if found.
2. Otherwise fall back to `get_connection_for_profiling()`.
3. Staleness: if `last_profile.md` is newer, regenerate.

Extract system variables from manifest: `{{SCHEMA}}`, `{{DISPLAY_NAME}}`,
`{{DATE_RANGE}}`, `{{DATABASE}}`.

### Step 3: User Profile
Read `.knowledge/user/profile.md`.
- **If exists:** Apply `Detail level`, `Chart preference`, `Narrative style`.
- **If missing:** Create from template (see below), note "Profile: new".

On explicit user corrections during session, update the profile:
append `YYYY-MM-DD | Assumed [X] | User prefers [Y]` to the Corrections Log
section. Never infer from silence.

### Step 4: User Integrations
Read `.knowledge/user/integrations.yaml`.
- Extract `preferred_export_format`, `communication.detail_level`.
- Count configured channels (`configured: true`).
- **If missing:** Note "Integrations: not configured -- defaults apply".

### Step 5: Organization Context
Check for org ID in `setup-state.yaml` (`phases.phase_3_business.data.organization_id`)
or in the active dataset manifest's `organization` field.

If an org ID exists and is not `_example`:
- Read `.knowledge/organizations/{org_id}/manifest.yaml` for name, industry.
- Read `.knowledge/organizations/{org_id}/business/index.yaml` for section counts
  (glossary terms, products, metrics, objectives, teams).
- **If org dir missing:** Note "Org: linked but not found".

If no org linked: Note "Org: not configured".

### Step 6: Corrections
Read `.knowledge/corrections/index.yaml`.
- Extract `total_corrections` and `by_severity` counts.
- If `total_corrections > 0`, highlight critical/high counts so agents check
  the full log before writing SQL.
- **If missing:** Note "Corrections: not yet populated".

### Step 7: Learnings
Read `.knowledge/learnings/index.md`.
- Scan for category headings (`### N. Category Name`).
- Note which categories have content entries vs are empty.
- Do NOT load full content -- just category presence.
- **If missing:** Note "Learnings: not yet populated".

### Step 8: Query Archaeology
Read `.knowledge/query-archaeology/curated/index.yaml`.
- Extract `cookbook_entries`, `table_cheatsheets`, `join_patterns` counts.
- **If missing:** Note "Archaeology: not yet populated".

### Step 9: Analysis Archive
Read `.knowledge/analyses/index.yaml`:
- Extract `total_analyses` and last 5 entries (title, date, findings count, level).
- If most recent analysis was <24h ago, flag for continuity.

Read `.knowledge/analyses/_patterns.yaml`:
- Count `patterns[]` entries and note pattern names if any.
- **If missing:** Note "Patterns: not yet populated".

### Step 10: Report Readiness

Compile an **internal context summary** (held in working memory, not shown raw):

```
Setup: {complete (N/M phases) | incomplete (list missing) | not initialized}
Dataset: {display_name} ({source_type}, {N} tables, ~{rows} rows, {date_range}) | not configured
Profile: {role}, {detail_level} | new
Integrations: {preferred_format}, {N} channels | not configured
Org: {company} ({industry}), {N} glossary, {N} products, {N} metrics | not configured
Corrections: {N} logged ({N} critical, {N} high) | none
Learnings: {N}/{6} categories populated | not yet populated
Archaeology: {N} cookbook, {N} cheatsheets, {N} join patterns | not yet populated
Archive: {N} analyses, {N} recurring patterns | none
```

Then output the **user-facing status**:

```
Dataset: {display_name} ({source_type})
Tables: {N} tables, ~{row_count} rows
Date range: {date_range}
Metrics: {M} defined
Profile: {loaded | new}
Status: Ready for analysis
```

If a critical subsystem is missing (no dataset, no manifest), adjust the status
and suggest `/connect-data` or `/setup`.

---

## User Profile Template

```markdown
# User Profile

Auto-created by knowledge bootstrap. Updated as the system learns preferences.

## Role & Expertise
- **Role:** _[auto-detected or user-specified]_
- **Technical level:** _[beginner | intermediate | advanced]_
- **SQL comfort:** _[none | basic | intermediate | advanced]_
- **Statistics comfort:** _[none | basic | intermediate | advanced]_
- **Domain:** _[e-commerce | fintech | saas | marketplace | other]_

## Communication Preferences
- **Detail level:** _[executive-summary | standard | deep-dive]_
- **Chart preference:** _[minimal | standard | chart-heavy]_
- **Narrative style:** _[bullet-points | prose | mixed]_

## Corrections Log
_Records of times the user corrected the system's assumptions._
<!-- Format: YYYY-MM-DD | What was wrong | What was right -->
```

## Edge Cases
- **No `.knowledge/` dir:** Create full tree and prompt `/connect-data`.
- **Empty schema.md:** Regenerate via profiling.
- **No data files:** Suggest checking connection or falling back to CSV.
- **Multiple datasets:** Report active, remind about `/switch-dataset`.
- **Setup incomplete:** Note phases, do not block. Suggest `/setup`.

## Anti-Patterns
1. **Never skip bootstrap.** Always read manifest -- details may have changed.
2. **Never hardcode dataset names.** Resolve from `active.yaml`.
3. **Never modify manifest during bootstrap.** Bootstrap is read-only.
4. **Never dump raw YAML to the user.** Show the brief status, not the load.
5. **Never block on a missing subsystem.** Graceful degradation always.