feat(reference-curator): implement Python scripts + Gemini quality gate

Build the refcurator shared Python package and 7 CLI scripts that were
previously specification-only. Add Gemini CLI as an independent pre-distillation
quality evaluator, replacing the circular Claude-self-review pattern.

Key changes:
- shared/lib/src/refcurator/: 7-module package (config, db, models, utils,
  manifest, gemini) with PyMySQL + JSON file dual backend
- 7 Click CLI scripts: discover, crawl_mgr, repo, distiller, reviewer,
  exporter, pipeline — each with subcommands for data management
- Gemini quality gate: evaluates raw content BEFORE distillation using
  5 criteria (relevance, authority, completeness, freshness, distill_value)
- Pipeline reordered: discovery → crawl → store → evaluate → distill → export
- Bug fixes from Codex adversarial review:
  - FileBackend now hard-fails on JOIN/aggregate/GROUP BY queries
  - Exporter uses MAX(review_id) to prevent shipping stale approvals
  - Distiller updates existing rows on refactor instead of forking
- Updated all 7 CLAUDE.md directives with real script references
- install.sh updated with refcurator package install step

51/51 E2E tests passing.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

custom-skills/90-reference-curator/01-reference-discovery/code/CLAUDE.md

@@ -36,8 +36,25 @@ Apply credibility scoring:
 - Relevance signals (0.15)
 
 ### Step 4: Output URL Manifest
-Generate JSON manifest for the crawler skill:
+Save discovered URLs as a manifest JSON, deduplicating against the existing repository:
 
+```bash
+# Create manifest from discovered URLs
+uv run python scripts/discover.py create-manifest --topic "prompt engineering" --output manifest.json < urls.json
+
+# Deduplicate against existing DB
+uv run python scripts/discover.py dedup --manifest manifest.json
+
+# Register a new source
+uv run python scripts/discover.py register-source \
+  --name "Anthropic Docs" --type official_docs \
+  --url "https://docs.anthropic.com" --tier tier1_official --vendor anthropic
+
+# List registered sources
+uv run python scripts/discover.py list-sources --vendor anthropic
+```
+
+Manifest format:
 ```json
 {
   "discovery_date": "2025-01-28T10:30:00",
@@ -56,20 +73,31 @@ Generate JSON manifest for the crawler skill:
 }
 ```
 
-## Scripts
-
-### `discover_sources.py`
-Main discovery script. Usage:
-```bash
-python scripts/discover_sources.py --topic "prompt engineering" --vendors anthropic,openai --output manifest.json
-```
-
 ## Output
 - `manifest.json` → Handoff to `02-web-crawler-orchestrator`
-- Register new sources in `sources` table via `03-content-repository`
+- New sources registered in `sources` table via `register-source`
 
 ## Deduplication
 Before outputting:
 - Normalize URLs (remove trailing slashes, query params)
 - Check against existing `documents` table
 - Merge duplicates, keeping highest credibility score
+
+## Scripts
+
+All scripts require the `refcurator` package. Run with `uv run python` from the skill directory.
+
+| Command | Purpose |
+|---------|---------|
+| `discover.py create-manifest` | Create manifest from URL entries JSON |
+| `discover.py dedup` | Deduplicate manifest against DB |
+| `discover.py register-source` | Register a new source |
+| `discover.py list-sources` | List registered sources |
+
+## Integration
+
+| From | To |
+|------|-----|
+| WebSearch results | → manifest.json |
+| → manifest.json | web-crawler-orchestrator |
+| → register-source | content-repository (sources table) |