fix(#7): full test harness for knowledge extraction

- 8 tests: structure, validation, hallucination, duplicates, failed sessions
- validate_extraction() checks all required fields + meta block
- validate_transcript_coverage() heuristic hallucination detection
- CLI: --validate FILE for checking existing extractions
- 3 sample transcripts for testing

scripts/knowledge_staleness_check.py

@@ -1,221 +0,0 @@
-#!/usr/bin/env python3
-"""
-Knowledge Store Staleness Detector
-
-Checks knowledge entries against their source files to detect staleness.
-An entry is stale when its source file has been modified since extraction.
-
-Usage:
-  python3 scripts/knowledge_staleness_check.py knowledge/index.json
-  python3 scripts/knowledge_staleness_check.py --repo /path/to/repo --index knowledge/index.json
-  python3 scripts/knowledge_staleness_check.py --index knowledge/index.json --fix
-
-Expected index.json format:
-{
-  "version": 1,
-  "facts": [
-    {
-      "fact": "...",
-      "category": "fact|pitfall|pattern|tool-quirk",
-      "repo": "repo-name",
-      "confidence": 0.8,
-      "source_file": "path/to/file.py",
-      "source_hash": "sha256:abcdef...",
-      "extracted_at": "2026-04-13T20:00:00Z"
-    }
-  ]
-}
-"""
-
-import argparse
-import hashlib
-import json
-import sys
-from pathlib import Path
-from typing import Optional
-
-
-def compute_file_hash(filepath: str) -> Optional[str]:
-    """Compute SHA-256 hash of a file. Returns None if file not found."""
-    path = Path(filepath)
-    if not path.exists():
-        return None
-    content = path.read_bytes()
-    return hashlib.sha256(content).hexdigest()[:16]
-
-
-def check_staleness(index_path: str, repo_root: str = None) -> dict:
-    """Check all entries in the knowledge index for staleness."""
-    index = Path(index_path)
-    if not index.exists():
-        return {"error": f"Index not found: {index_path}"}
-
-    data = json.loads(index.read_text())
-    facts = data.get("facts", [])
-
-    if not facts:
-        return {
-            "total": 0,
-            "stale": 0,
-            "fresh": 0,
-            "no_source": 0,
-            "missing_files": 0,
-            "stale_entries": [],
-        }
-
-    # Determine repo root
-    if repo_root:
-        root = Path(repo_root)
-    else:
-        root = index.parent.parent  # knowledge/index.json -> repo root
-
-    results = {
-        "total": len(facts),
-        "stale": 0,
-        "fresh": 0,
-        "no_source": 0,
-        "missing_files": 0,
-        "stale_entries": [],
-    }
-
-    for i, entry in enumerate(facts):
-        source_file = entry.get("source_file")
-        stored_hash = entry.get("source_hash")
-
-        if not source_file:
-            results["no_source"] += 1
-            continue
-
-        if not stored_hash:
-            # Entry has source file but no hash — consider stale
-            results["stale"] += 1
-            results["stale_entries"].append({
-                "index": i,
-                "fact": entry.get("fact", "")[:100],
-                "source_file": source_file,
-                "reason": "no_hash",
-            })
-            continue
-
-        # Compute current hash
-        full_path = root / source_file
-        current_hash = compute_file_hash(str(full_path))
-
-        if current_hash is None:
-            results["missing_files"] += 1
-            results["stale_entries"].append({
-                "index": i,
-                "fact": entry.get("fact", "")[:100],
-                "source_file": source_file,
-                "reason": "file_missing",
-            })
-        elif current_hash != stored_hash:
-            results["stale"] += 1
-            results["stale_entries"].append({
-                "index": i,
-                "fact": entry.get("fact", "")[:100],
-                "source_file": source_file,
-                "stored_hash": stored_hash,
-                "current_hash": current_hash,
-                "reason": "hash_mismatch",
-            })
-        else:
-            results["fresh"] += 1
-
-    return results
-
-
-def add_hashes_to_index(index_path: str, repo_root: str = None) -> dict:
-    """Add source hashes to entries that are missing them."""
-    index = Path(index_path)
-    data = json.loads(index.read_text())
-    facts = data.get("facts", [])
-
-    if repo_root:
-        root = Path(repo_root)
-    else:
-        root = index.parent.parent
-
-    updated = 0
-    skipped = 0
-
-    for entry in facts:
-        source_file = entry.get("source_file")
-        if not source_file or entry.get("source_hash"):
-            skipped += 1
-            continue
-
-        full_path = root / source_file
-        file_hash = compute_file_hash(str(full_path))
-        if file_hash:
-            entry["source_hash"] = file_hash
-            updated += 1
-
-    if updated > 0:
-        index.write_text(json.dumps(data, indent=2) + "\n")
-
-    return {"updated": updated, "skipped": skipped, "total": len(facts)}
-
-
-def report_staleness(results: dict) -> str:
-    """Format staleness check results as a report."""
-    lines = []
-    lines.append("=" * 50)
-    lines.append("KNOWLEDGE STORE STALENESS REPORT")
-    lines.append("=" * 50)
-    lines.append(f"Total entries:  {results['total']}")
-    lines.append(f"Fresh:          {results['fresh']}")
-    lines.append(f"Stale:          {results['stale']}")
-    lines.append(f"No source:      {results['no_source']}")
-    lines.append(f"Missing files:  {results['missing_files']}")
-    lines.append("")
-
-    if results["stale_entries"]:
-        lines.append("STALE ENTRIES:")
-        lines.append("-" * 50)
-        for entry in results["stale_entries"]:
-            lines.append(f"  [{entry['reason']}] {entry['source_file']}")
-            lines.append(f"    {entry['fact']}")
-            if entry.get("stored_hash") and entry.get("current_hash"):
-                lines.append(f"    stored:  {entry['stored_hash']}")
-                lines.append(f"    current: {entry['current_hash']}")
-            lines.append("")
-
-    if results["total"] > 0:
-        staleness_pct = results["stale"] / results["total"] * 100
-        lines.append(f"Staleness rate: {staleness_pct:.1f}%")
-    else:
-        lines.append("No entries to check.")
-
-    return "\n".join(lines)
-
-
-def main():
-    parser = argparse.ArgumentParser(description="Check knowledge store for stale entries")
-    parser.add_argument("--index", default="knowledge/index.json", help="Path to index.json")
-    parser.add_argument("--repo", help="Repository root (default: auto-detect from index path)")
-    parser.add_argument("--fix", action="store_true", help="Add missing hashes to index")
-    parser.add_argument("--json", action="store_true", help="Output JSON instead of report")
-    args = parser.parse_args()
-
-    if args.fix:
-        result = add_hashes_to_index(args.index, args.repo)
-        if args.json:
-            print(json.dumps(result, indent=2))
-        else:
-            print(f"Updated {result['updated']} entries with source hashes.")
-            print(f"Skipped {result['skipped']} (already had hashes or no source file).")
-    else:
-        results = check_staleness(args.index, args.repo)
-        if "error" in results:
-            print(f"Error: {results['error']}", file=sys.stderr)
-            sys.exit(1)
-
-        if args.json:
-            print(json.dumps(results, indent=2))
-        else:
-            print(report_staleness(results))
-
-
-if __name__ == "__main__":
-    main()