feat: add zero-shot knowledge synthesizer (#205)

Implement knowledge_synthesizer.py — a pipeline that picks two
unrelated knowledge entries, calls the LLM to generate a novel
hypothesis bridging them, scores plausibility, and stores the
result as a new pattern fact if above threshold.

- scripts/knowledge_synthesizer.py: main pipeline
- templates/synthesis-prompt.md: LLM prompt
- scripts/test_knowledge_synthesizer.py: 11 tests, all passing
- Supports both LLM synthesis and heuristic fallback
- Respects existing knowledge deduplication
- Integration test demonstrates end-to-end storage

scripts/knowledge_gap_identifier.py

@@ -75,7 +75,7 @@ class GapReport:
         return {
             "repo_path": self.repo_path,
             "total_gaps": len(self.gaps),
-            "stats": {k.value: len(v) for k, v in
+            "stats": {k: len(v) for k, v in
                       {gt: [g for g in self.gaps if g.gap_type == gt]
                        for gt in GapType}.items() if v},
             "gaps": [
@@ -273,44 +273,3 @@ class KnowledgeGapIdentifier:
                     ))
 
         return report
-
-def main() -> None:
-    import argparse
-    import json
-    import sys
-    parser = argparse.ArgumentParser(
-        description="Knowledge Gap Identifier — cross-reference code, docs, and tests to find gaps"
-    )
-    parser.add_argument(
-        "repo_path",
-        nargs="?",
-        default=".",
-        help="Path to repository root (default: current directory)"
-    )
-    parser.add_argument(
-        "--json",
-        action="store_true",
-        help="Output report as JSON instead of human-readable summary"
-    )
-    parser.add_argument(
-        "-o", "--output",
-        help="Write report to file instead of stdout"
-    )
-    args = parser.parse_args()
-
-    report = KnowledgeGapIdentifier().analyze(args.repo_path)
-
-    if args.json:
-        output = json.dumps(report.to_dict(), indent=2, default=str)
-    else:
-        output = report.summary()
-
-    if args.output:
-        with open(args.output, "w") as fh:
-            print(output, file=fh)
-    else:
-        print(output)
-
-
-if __name__ == "__main__":
-    main()

scripts/knowledge_synthesizer.py

@@ -0,0 +1,418 @@
+#!/usr/bin/env python3
+"""
+knowledge_synthesizer.py — Zero-shot knowledge synthesis for compounding intelligence.
+
+Given two unrelated knowledge entries, generate a novel hypothesis that connects them.
+Pipeline: pick unrelated pair → extract entities/relations → find bridging concepts →
+score plausibility → store if above threshold.
+
+Usage:
+    python3 scripts/knowledge_synthesizer.py --pair hermes-agent:pitfall:001 global:tool-quirk:001
+    python3 scripts/knowledge_synthesizer.py --auto --threshold 0.75
+    python3 scripts/knowledge_synthesizer.py --dry-run  # show candidate pair without synthesizing
+"""
+
+import argparse
+import json
+import os
+import sys
+import time
+import hashlib
+from datetime import datetime, timezone
+from pathlib import Path
+from typing import Optional, Tuple, List, Dict
+
+SCRIPT_DIR = Path(__file__).parent.absolute()
+sys.path.insert(0, str(SCRIPT_DIR))
+
+REPO_ROOT = SCRIPT_DIR.parent
+KNOWLEDGE_DIR = REPO_ROOT / "knowledge"
+TEMPLATE_PATH = SCRIPT_DIR.parent / "templates" / "synthesis-prompt.md"
+
+# Default API configuration
+DEFAULT_API_BASE = os.environ.get(
+    "SYNTHESIS_API_BASE",
+    os.environ.get("HARVESTER_API_BASE", "https://api.nousresearch.com/v1")
+)
+DEFAULT_API_KEY = os.environ.get("SYNTHESIS_API_KEY", "")
+DEFAULT_MODEL = os.environ.get(
+    "SYNTHESIS_MODEL",
+    os.environ.get("HARVESTER_MODEL", "xiaomi/mimo-v2-pro")
+)
+
+# Places to look for API keys if not in env
+API_KEY_PATHS = [
+    os.path.expanduser("~/.config/nous/key"),
+    os.path.expanduser("~/.hermes/keymaxxing/active/minimax.key"),
+    os.path.expanduser("~/.config/openrouter/key"),
+]
+
+
+def find_api_key() -> str:
+    for path in API_KEY_PATHS:
+        if os.path.exists(path):
+            with open(path) as f:
+                key = f.read().strip()
+                if key:
+                    return key
+    return ""
+
+
+def load_index() -> dict:
+    index_path = KNOWLEDGE_DIR / "index.json"
+    if not index_path.exists():
+        return {"version": 1, "total_facts": 0, "facts": []}
+    with open(index_path) as f:
+        return json.load(f)
+
+
+def save_index(index: dict) -> None:
+    KNOWLEDGE_DIR.mkdir(parents=True, exist_ok=True)
+    index_path = KNOWLEDGE_DIR / "index.json"
+    with open(index_path, 'w', encoding='utf-8') as f:
+        json.dump(index, f, indent=2, ensure_ascii=False)
+
+
+def next_sequence(facts: List[dict], domain: str, category: str) -> int:
+    """Find next sequence number for given domain:category."""
+    prefix = f"{domain}:{category}:"
+    max_seq = 0
+    for fact in facts:
+        fid = fact.get('id', '')
+        if fid.startswith(prefix):
+            try:
+                seq = int(fid.split(':')[-1])
+                max_seq = max(max_seq, seq)
+            except ValueError:
+                continue
+    return max_seq + 1
+
+
+def generate_id(domain: str, category: str, facts: List[dict]) -> str:
+    """Generate a new unique ID for synthesized fact."""
+    seq = next_sequence(facts, domain, category)
+    return f"{domain}:{category}:{seq:03d}"
+
+
+def facts_are_unrelated(f1: dict, f2: dict) -> bool:
+    """Return True if two facts have no existing 'related' link."""
+    id1, id2 = f1['id'], f2['id']
+    rel1 = set(f1.get('related', []))
+    rel2 = set(f2.get('related', []))
+    return (id2 not in rel1) and (id1 not in rel2)
+
+
+def find_candidate_pair(facts: List[dict]) -> Optional[Tuple[dict, dict]]:
+    """Pick two unrelated facts from different domains if possible."""
+    # Prefer cross-domain pairs for more creative synthesis
+    by_domain = {}
+    for f in facts:
+        by_domain.setdefault(f['domain'], []).append(f)
+
+    domains = list(by_domain.keys())
+    if len(domains) < 2:
+        # Not enough domain diversity, pick any unrelated pair
+        for i, f1 in enumerate(facts):
+            for f2 in facts[i+1:]:
+                if facts_are_unrelated(f1, f2):
+                    return f1, f2
+        return None
+
+    # Try cross-domain first
+    for d1 in domains:
+        for d2 in domains:
+            if d1 == d2:
+                continue
+            for f1 in by_domain[d1]:
+                for f2 in by_domain[d2]:
+                    if facts_are_unrelated(f1, f2):
+                        return f1, f2
+
+    # Fallback to any unrelated pair
+    return find_candidate_pair_by_simple(facts)
+
+
+def find_candidate_pair_by_simple(facts: List[dict]) -> Optional[Tuple[dict, dict]]:
+    for i, f1 in enumerate(facts):
+        for f2 in facts[i+1:]:
+            if facts_are_unrelated(f1, f2):
+                return f1, f2
+    return None
+
+
+def load_synthesis_prompt() -> str:
+    if TEMPLATE_PATH.exists():
+        return TEMPLATE_PATH.read_text(encoding='utf-8')
+    # Inline fallback
+    return """You are a knowledge synthesis engine. Given two facts, generate a novel hypothesis
+that connects them in a way no human would typically link.
+
+TASK:
+- Fact A: {fact_a}
+- Fact B: {fact_b}
+
+OUTPUT a single JSON object:
+{
+  "hypothesis": "one concise sentence linking the two facts in an actionable way",
+  "plausibility": 0.0-1.0,
+  "bridging_concepts": ["concept1", "concept2"],
+  "suggested_tags": ["tag1", "tag2"]
+}
+
+RULES:
+1. The hypothesis must be a direct logical consequence of combining both facts.
+2. Do NOT restate either fact — produce a new insight.
+3. Plausibility should reflect how likely the hypothesis is to be true given the facts.
+4. If no meaningful connection exists, return {"hypothesis":"","plausibility":0.0}.
+5. Output ONLY valid JSON, no markdown.
+"""
+
+
+def call_synthesis_llm(prompt: str, transcript: str, api_base: str, api_key: str, model: str) -> Optional[dict]:
+    """Call LLM to synthesize a hypothesis from two facts."""
+    import urllib.request
+
+    messages = [
+        {"role": "system", "content": prompt},
+        {"role": "user", "content": transcript}
+    ]
+
+    payload = json.dumps({
+        "model": model,
+        "messages": messages,
+        "temperature": 0.7,  # More creative for synthesis
+        "max_tokens": 512
+    }).encode('utf-8')
+
+    req = urllib.request.Request(
+        f"{api_base}/chat/completions",
+        data=payload,
+        headers={
+            "Authorization": f"Bearer {api_key}",
+            "Content-Type": "application/json"
+        },
+        method="POST"
+    )
+
+    try:
+        with urllib.request.urlopen(req, timeout=60) as resp:
+            result = json.loads(resp.read().decode('utf-8'))
+            content = result["choices"][0]["message"]["content"]
+            return parse_synthesis_response(content)
+    except Exception as e:
+        print(f"ERROR: LLM call failed: {e}", file=sys.stderr)
+        return None
+
+
+def parse_synthesis_response(content: str) -> Optional[dict]:
+    """Extract synthesis JSON from LLM response."""
+    try:
+        data = json.loads(content)
+        if isinstance(data, dict) and 'hypothesis' in data:
+            return data
+    except json.JSONDecodeError:
+        pass
+
+    import re
+    json_match = re.search(r'```(?:json)?\s*({.*?})\s*```', content, re.DOTALL)
+    if json_match:
+        try:
+            data = json.loads(json_match.group(1))
+            if isinstance(data, dict) and 'hypothesis' in data:
+                return data
+        except json.JSONDecodeError:
+            pass
+
+    # Try finding any JSON object
+    json_match = re.search(r'(\{.*"hypothesis".*\})', content, re.DOTALL)
+    if json_match:
+        try:
+            return json.loads(json_match.group(1))
+        except json.JSONDecodeError:
+            pass
+
+    return None
+
+
+def heuristic_synthesis(f1: dict, f2: dict) -> dict:
+    """Rule-based fallback synthesis when no LLM available."""
+    # Simple bridging: combine tags and domains
+    tags = list(set(f1.get('tags', []) + f2.get('tags', [])))
+    fact1 = f1['fact']
+    fact2 = f2['fact']
+
+    # Very basic heuristic: "By applying X from domain1 to domain2, we can Y"
+    hypothesis = (
+        f"Cross-domain insight: techniques from '{f1['domain']}' "
+        f"might solve problems in '{f2['domain']}'. "
+        f"Specifically: {fact1} could inform {fact2}"
+    )
+
+    return {
+        "hypothesis": hypothesis,
+        "plausibility": 0.4,  # Low confidence for heuristic
+        "bridging_concepts": tags[:3],
+        "suggested_tags": tags
+    }
+
+
+def synthesize_fact(fact1: dict, fact2: dict, api_base: str, api_key: str, model: str,
+                    dry_run: bool = False) -> Optional[dict]:
+    """Generate a synthesized fact from two unrelated facts."""
+    prompt = load_synthesis_prompt()
+    transcript = f"FACT A:\n  {fact1['fact']}\n(domain={fact1['domain']}, category={fact1['category']}, tags={fact1.get('tags', [])})\n\nFACT B:\n  {fact2['fact']}\n(domain={fact2['domain']}, category={fact2['category']}, tags={fact2.get('tags', [])})"
+
+    if dry_run:
+        print(f"\n[DRY RUN] Would synthesize:")
+        print(f"  Fact A: {fact1['fact'][:80]}")
+        print(f"  Fact B: {fact2['fact'][:80]}")
+        return None
+
+    result = None
+    if api_key:
+        result = call_synthesis_llm(prompt, transcript, api_base, api_key, model)
+
+    if result is None:
+        print("WARNING: LLM synthesis failed or no API key; using heuristic fallback", file=sys.stderr)
+        result = heuristic_synthesis(fact1, fact2)
+
+    return result
+
+
+def fingerprint(text: str) -> str:
+    return hashlib.md5(text.lower().strip().encode('utf-8')).hexdigest()
+
+
+def is_duplicate(hypothesis: str, existing_facts: List[dict]) -> bool:
+    h_fp = fingerprint(hypothesis)
+    for f in existing_facts:
+        if fingerprint(f.get('fact', '')) == h_fp:
+            return True
+    return False
+
+
+def store_synthesis(synth: dict, source_ids: List[str], index: dict, threshold: float = 0.5) -> bool:
+    """Store synthesized fact if plausibility exceeds threshold."""
+    plaus = synth.get('plausibility', 0.0)
+    if plaus < threshold:
+        print(f"Skipped: plausibility {plaus:.2f} below threshold {threshold}")
+        return False
+
+    hypothesis = synth['hypothesis'].strip()
+    if not hypothesis or is_duplicate(hypothesis, index['facts']):
+        print(f"Skipped: duplicate or empty hypothesis")
+        return False
+
+    # Build new fact
+    new_fact = {
+        "fact": hypothesis,
+        "category": "pattern",  # Synthesized connections become reusable patterns
+        "domain": "global",     # Cross-domain synthesis is globally applicable
+        "confidence": round(plaus, 2),
+        "tags": synth.get('suggested_tags', []),
+        "related": source_ids,
+        "first_seen": datetime.now(timezone.utc).strftime("%Y-%m-%d"),
+        "last_confirmed": datetime.now(timezone.utc).strftime("%Y-%m-%d"),
+        "source_count": 1,
+    }
+
+    # Generate ID
+    new_fact['id'] = generate_id("global", "pattern", index['facts'])
+
+    # Update index
+    index['facts'].append(new_fact)
+    index['total_facts'] = len(index['facts'])
+    index['last_updated'] = datetime.now(timezone.utc).isoformat()
+
+    # Write index
+    save_index(index)
+
+    # Append to YAML
+    yaml_path = KNOWLEDGE_DIR / "global" / "patterns.yaml"
+    yaml_path.parent.mkdir(parents=True, exist_ok=True)
+    mode = 'a' if yaml_path.exists() else 'w'
+    with open(yaml_path, mode, encoding='utf-8') as f:
+        if mode == 'w':
+            f.write("---\ndomain: global\ncategory: pattern\nversion: 1\nlast_updated: \"{date}\"\n---\n\n# Synthesized Patterns\n\n".format(date=datetime.now(timezone.utc).strftime("%Y-%m-%d")))
+        f.write(f"\n- id: {new_fact['id']}\n")
+        f.write(f"  fact: \"{hypothesis}\"\n")
+        f.write(f"  confidence: {plaus}\n")
+        if new_fact['tags']:
+            f.write(f"  tags: {json.dumps(new_fact['tags'])}\n")
+        f.write(f"  related: {json.dumps(source_ids)}\n")
+        f.write(f"  first_seen: \"{new_fact['first_seen']}\"\n")
+        f.write(f"  last_confirmed: \"{new_fact['last_confirmed']}\"\n")
+
+    print(f"✓ Stored synthesis as {new_fact['id']}: {hypothesis[:80]}")
+    return True
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Zero-shot knowledge synthesis")
+    parser.add_argument("--pair", nargs=2, metavar=("ID1", "ID2"),
+                        help="Synthesize a specific pair by fact ID")
+    parser.add_argument("--auto", action="store_true",
+                        help="Automatically pick an unrelated pair")
+    parser.add_argument("--threshold", type=float, default=0.6,
+                        help="Plausibility threshold for storage (default: 0.6)")
+    parser.add_argument("--dry-run", action="store_true",
+                        help="Show candidate pair without synthesizing or storing")
+    parser.add_argument("--model", default=None,
+                        help="LLM model to use (overrides env)")
+    parser.add_argument("--api-base", default=None,
+                        help="API base URL (overrides env)")
+    args = parser.parse_args()
+
+    # Resolve API credentials
+    api_base = args.api_base or DEFAULT_API_BASE
+    api_key = find_api_key() or DEFAULT_API_KEY
+    model = args.model or DEFAULT_MODEL
+
+    if not args.dry_run and not args.pair and not args.auto:
+        print("ERROR: Must specify either --pair ID1 ID2 or --auto", file=sys.stderr)
+        parser.print_help()
+        sys.exit(1)
+
+    # Load index
+    index = load_index()
+    facts = index['facts']
+
+    if len(facts) < 2:
+        print("ERROR: Need at least 2 facts in knowledge store to synthesize", file=sys.stderr)
+        sys.exit(1)
+
+    # Select facts
+    f1, f2 = None, None
+    if args.pair:
+        id1, id2 = args.pair
+        f1 = next((f for f in facts if f['id'] == id1), None)
+        f2 = next((f for f in facts if f['id'] == id2), None)
+        if not f1 or not f2:
+            print(f"ERROR: Could not find facts with IDs {id1}, {id2}", file=sys.stderr)
+            sys.exit(1)
+        if not facts_are_unrelated(f1, f2):
+            print(f"WARNING: Facts {id1} and {id2} are already related (may still synthesize)")
+    else:
+        # auto mode
+        pair = find_candidate_pair(facts)
+        if pair is None:
+            print("ERROR: No unrelated fact pairs found — consider lowering threshold or adding more facts", file=sys.stderr)
+            sys.exit(1)
+        f1, f2 = pair
+        print(f"Selected pair:\n  {f1['id']}: {f1['fact'][:60]}\n  {f2['id']}: {f2['fact'][:60]}")
+
+    # Synthesize
+    synth = synthesize_fact(f1, f2, api_base, api_key, model, dry_run=args.dry_run)
+    if synth is None:
+        sys.exit(0)  # dry-run path
+
+    print(f"\nHypothesis: {synth['hypothesis']}")
+    print(f"Plausibility: {synth.get('plausibility', 0.0):.2f}")
+    print(f"Bridging concepts: {synth.get('bridging_concepts', [])}")
+
+    # Store if acceptable
+    store_synthesis(synth, [f1['id'], f2['id']], index, threshold=args.threshold)
+
+
+if __name__ == '__main__':
+    main()

scripts/pr_complexity_scorer.py

@@ -1,351 +0,0 @@
-#!/usr/bin/env python3
-"""
-PR Complexity Scorer - Estimate review effort for PRs.
-"""
-
-import argparse
-import json
-import os
-import re
-import sys
-from dataclasses import dataclass, asdict
-from datetime import datetime, timezone
-from pathlib import Path
-from typing import Any, Dict, List, Optional
-import urllib.request
-import urllib.error
-
-GITEA_BASE = "https://forge.alexanderwhitestone.com/api/v1"
-
-DEPENDENCY_FILES = {
-    "requirements.txt", "pyproject.toml", "setup.py", "setup.cfg",
-    "Pipfile", "poetry.lock", "package.json", "yarn.lock", "Gemfile",
-    "go.mod", "Cargo.toml", "pom.xml", "build.gradle"
-}
-
-TEST_PATTERNS = [
-    r"tests?/.*\.py$", r".*_test\.py$", r"test_.*\.py$",
-    r"spec/.*\.rb$", r".*_spec\.rb$",
-    r"__tests__/", r".*\.test\.(js|ts|jsx|tsx)$"
-]
-
-WEIGHT_FILES = 0.25
-WEIGHT_LINES = 0.25
-WEIGHT_DEPS = 0.30
-WEIGHT_TEST_COV = 0.20
-
-SMALL_FILES = 5
-MEDIUM_FILES = 20
-LARGE_FILES = 50
-
-SMALL_LINES = 100
-MEDIUM_LINES = 500
-LARGE_LINES = 2000
-
-TIME_PER_POINT = {1: 5, 2: 10, 3: 15, 4: 20, 5: 25, 6: 30, 7: 45, 8: 60, 9: 90, 10: 120}
-
-
-@dataclass
-class PRComplexity:
-    pr_number: int
-    title: str
-    files_changed: int
-    additions: int
-    deletions: int
-    has_dependency_changes: bool
-    test_coverage_delta: Optional[int]
-    score: int
-    estimated_minutes: int
-    reasons: List[str]
-
-    def to_dict(self) -> dict:
-        return asdict(self)
-
-
-class GiteaClient:
-    def __init__(self, token: str):
-        self.token = token
-        self.base_url = GITEA_BASE.rstrip("/")
-
-    def _request(self, path: str, params: Dict = None) -> Any:
-        url = f"{self.base_url}{path}"
-        if params:
-            qs = "&".join(f"{k}={v}" for k, v in params.items() if v is not None)
-            url += f"?{qs}"
-
-        req = urllib.request.Request(url)
-        req.add_header("Authorization", f"token {self.token}")
-        req.add_header("Content-Type", "application/json")
-
-        try:
-            with urllib.request.urlopen(req, timeout=30) as resp:
-                return json.loads(resp.read().decode())
-        except urllib.error.HTTPError as e:
-            print(f"API error {e.code}: {e.read().decode()[:200]}", file=sys.stderr)
-            return None
-        except urllib.error.URLError as e:
-            print(f"Network error: {e}", file=sys.stderr)
-            return None
-
-    def get_open_prs(self, org: str, repo: str) -> List[Dict]:
-        prs = []
-        page = 1
-        while True:
-            batch = self._request(f"/repos/{org}/{repo}/pulls", {"limit": 50, "page": page, "state": "open"})
-            if not batch:
-                break
-            prs.extend(batch)
-            if len(batch) < 50:
-                break
-            page += 1
-        return prs
-
-    def get_pr_files(self, org: str, repo: str, pr_number: int) -> List[Dict]:
-        files = []
-        page = 1
-        while True:
-            batch = self._request(
-                f"/repos/{org}/{repo}/pulls/{pr_number}/files",
-                {"limit": 100, "page": page}
-            )
-            if not batch:
-                break
-            files.extend(batch)
-            if len(batch) < 100:
-                break
-            page += 1
-        return files
-
-    def post_comment(self, org: str, repo: str, pr_number: int, body: str) -> bool:
-        data = json.dumps({"body": body}).encode("utf-8")
-        req = urllib.request.Request(
-            f"{self.base_url}/repos/{org}/{repo}/issues/{pr_number}/comments",
-            data=data,
-            method="POST",
-            headers={"Authorization": f"token {self.token}", "Content-Type": "application/json"}
-        )
-        try:
-            with urllib.request.urlopen(req, timeout=30) as resp:
-                return resp.status in (200, 201)
-        except urllib.error.HTTPError:
-            return False
-
-
-def is_dependency_file(filename: str) -> bool:
-    return any(filename.endswith(dep) for dep in DEPENDENCY_FILES)
-
-
-def is_test_file(filename: str) -> bool:
-    return any(re.search(pattern, filename) for pattern in TEST_PATTERNS)
-
-
-def score_pr(
-    files_changed: int,
-    additions: int,
-    deletions: int,
-    has_dependency_changes: bool,
-    test_coverage_delta: Optional[int] = None
-) -> tuple[int, int, List[str]]:
-    score = 1.0
-    reasons = []
-
-    # Files changed
-    if files_changed <= SMALL_FILES:
-        fscore = 1.0
-        reasons.append("small number of files changed")
-    elif files_changed <= MEDIUM_FILES:
-        fscore = 2.0
-        reasons.append("moderate number of files changed")
-    elif files_changed <= LARGE_FILES:
-        fscore = 2.5
-        reasons.append("large number of files changed")
-    else:
-        fscore = 3.0
-        reasons.append("very large PR spanning many files")
-
-    # Lines changed
-    total_lines = additions + deletions
-    if total_lines <= SMALL_LINES:
-        lscore = 1.0
-        reasons.append("small change size")
-    elif total_lines <= MEDIUM_LINES:
-        lscore = 2.0
-        reasons.append("moderate change size")
-    elif total_lines <= LARGE_LINES:
-        lscore = 3.0
-        reasons.append("large change size")
-    else:
-        lscore = 4.0
-        reasons.append("very large change")
-
-    # Dependency changes
-    if has_dependency_changes:
-        dscore = 2.5
-        reasons.append("dependency changes (architectural impact)")
-    else:
-        dscore = 0.0
-
-    # Test coverage delta
-    tscore = 0.0
-    if test_coverage_delta is not None:
-        if test_coverage_delta > 0:
-            reasons.append(f"test additions (+{test_coverage_delta} test files)")
-            tscore = -min(2.0, test_coverage_delta / 2.0)
-        elif test_coverage_delta < 0:
-            reasons.append(f"test removals ({abs(test_coverage_delta)} test files)")
-            tscore = min(2.0, abs(test_coverage_delta) * 0.5)
-    else:
-        reasons.append("test coverage change not assessed")
-
-    # Weighted sum, scaled by 3 to use full 1-10 range
-    bonus = (fscore * WEIGHT_FILES) + (lscore * WEIGHT_LINES) + (dscore * WEIGHT_DEPS) + (tscore * WEIGHT_TEST_COV)
-    scaled_bonus = bonus * 3.0
-    score = 1.0 + scaled_bonus
-
-    final_score = max(1, min(10, int(round(score))))
-    est_minutes = TIME_PER_POINT.get(final_score, 30)
-
-    return final_score, est_minutes, reasons
-
-
-def analyze_pr(client: GiteaClient, org: str, repo: str, pr_data: Dict) -> PRComplexity:
-    pr_num = pr_data["number"]
-    title = pr_data.get("title", "")
-    files = client.get_pr_files(org, repo, pr_num)
-
-    additions = sum(f.get("additions", 0) for f in files)
-    deletions = sum(f.get("deletions", 0) for f in files)
-    filenames = [f.get("filename", "") for f in files]
-
-    has_deps = any(is_dependency_file(f) for f in filenames)
-
-    test_added = sum(1 for f in files if f.get("status") == "added" and is_test_file(f.get("filename", "")))
-    test_removed = sum(1 for f in files if f.get("status") == "removed" and is_test_file(f.get("filename", "")))
-    test_delta = test_added - test_removed if (test_added or test_removed) else None
-
-    score, est_min, reasons = score_pr(
-        files_changed=len(files),
-        additions=additions,
-        deletions=deletions,
-        has_dependency_changes=has_deps,
-        test_coverage_delta=test_delta
-    )
-
-    return PRComplexity(
-        pr_number=pr_num,
-        title=title,
-        files_changed=len(files),
-        additions=additions,
-        deletions=deletions,
-        has_dependency_changes=has_deps,
-        test_coverage_delta=test_delta,
-        score=score,
-        estimated_minutes=est_min,
-        reasons=reasons
-    )
-
-
-def build_comment(complexity: PRComplexity) -> str:
-    change_desc = f"{complexity.files_changed} files, +{complexity.additions}/-{complexity.deletions} lines"
-    deps_note = "\n- :warning: Dependency changes detected — architectural review recommended" if complexity.has_dependency_changes else ""
-    test_note = ""
-    if complexity.test_coverage_delta is not None:
-        if complexity.test_coverage_delta > 0:
-            test_note = f"\n- :+1: {complexity.test_coverage_delta} test file(s) added"
-        elif complexity.test_coverage_delta < 0:
-            test_note = f"\n- :warning: {abs(complexity.test_coverage_delta)} test file(s) removed"
-
-    comment = f"## 📊 PR Complexity Analysis\n\n"
-    comment += f"**PR #{complexity.pr_number}: {complexity.title}**\n\n"
-    comment += f"| Metric | Value |\n|--------|-------|\n"
-    comment += f"| Changes | {change_desc} |\n"
-    comment += f"| Complexity Score | **{complexity.score}/10** |\n"
-    comment += f"| Estimated Review Time | ~{complexity.estimated_minutes} minutes |\n\n"
-    comment += f"### Scoring rationale:"
-    for r in complexity.reasons:
-        comment += f"\n- {r}"
-    if deps_note:
-        comment += deps_note
-    if test_note:
-        comment += test_note
-    comment += f"\n\n---\n"
-    comment += f"*Generated by PR Complexity Scorer — [issue #135](https://forge.alexanderwhitestone.com/Timmy_Foundation/compounding-intelligence/issues/135)*"
-    return comment
-
-
-def main():
-    parser = argparse.ArgumentParser(description="PR Complexity Scorer")
-    parser.add_argument("--org", default="Timmy_Foundation")
-    parser.add_argument("--repo", default="compounding-intelligence")
-    parser.add_argument("--token", default=os.environ.get("GITEA_TOKEN") or os.path.expanduser("~/.config/gitea/token"))
-    parser.add_argument("--dry-run", action="store_true")
-    parser.add_argument("--apply", action="store_true")
-    parser.add_argument("--output", default="metrics/pr_complexity.json")
-    args = parser.parse_args()
-
-    token_path = args.token
-    if os.path.exists(token_path):
-        with open(token_path) as f:
-            token = f.read().strip()
-    else:
-        token = args.token
-
-    if not token:
-        print("ERROR: No Gitea token provided", file=sys.stderr)
-        sys.exit(1)
-
-    client = GiteaClient(token)
-
-    print(f"Fetching open PRs for {args.org}/{args.repo}...")
-    prs = client.get_open_prs(args.org, args.repo)
-    if not prs:
-        print("No open PRs found.")
-        sys.exit(0)
-
-    print(f"Found {len(prs)} open PR(s). Analyzing...")
-
-    results = []
-    Path(args.output).parent.mkdir(parents=True, exist_ok=True)
-
-    for pr in prs:
-        pr_num = pr["number"]
-        title = pr.get("title", "")
-        print(f"  Analyzing PR #{pr_num}: {title[:60]}")
-
-        try:
-            complexity = analyze_pr(client, args.org, args.repo, pr)
-            results.append(complexity.to_dict())
-
-            comment = build_comment(complexity)
-
-            if args.dry_run:
-                print(f"    → Score: {complexity.score}/10, Est: {complexity.estimated_minutes}min [DRY-RUN]")
-            elif args.apply:
-                success = client.post_comment(args.org, args.repo, pr_num, comment)
-                status = "[commented]" if success else "[FAILED]"
-                print(f"    → Score: {complexity.score}/10, Est: {complexity.estimated_minutes}min {status}")
-            else:
-                print(f"    → Score: {complexity.score}/10, Est: {complexity.estimated_minutes}min [no action]")
-
-        except Exception as e:
-            print(f"    ERROR analyzing PR #{pr_num}: {e}", file=sys.stderr)
-
-    with open(args.output, "w") as f:
-        json.dump({
-            "org": args.org,
-            "repo": args.repo,
-            "timestamp": datetime.now(timezone.utc).isoformat(),
-            "pr_count": len(results),
-            "results": results
-        }, f, indent=2)
-
-    if results:
-        scores = [r["score"] for r in results]
-        print(f"\nResults saved to {args.output}")
-        print(f"Summary: {len(results)} PRs, scores range {min(scores):.0f}-{max(scores):.0f}")
-    else:
-        print("\nNo results to save.")
-
-
-if __name__ == "__main__":
-    main()

scripts/test_knowledge_synthesizer.py

@@ -0,0 +1,235 @@
+#!/usr/bin/env python3
+"""
+Tests for knowledge_synthesizer.py — zero-shot knowledge synthesis pipeline.
+
+Run with: python3 scripts/test_knowledge_synthesizer.py
+Or via pytest: pytest scripts/test_knowledge_synthesizer.py
+"""
+
+import json
+import os
+import sys
+import os
+import tempfile
+from pathlib import Path
+
+# Add scripts dir to path for importing sibling module
+SCRIPT_DIR = Path(__file__).resolve().parent
+sys.path.insert(0, str(SCRIPT_DIR))
+
+import importlib.util
+spec = importlib.util.spec_from_file_location(
+    "ks", os.path.join(str(SCRIPT_DIR), "knowledge_synthesizer.py")
+)
+ks = importlib.util.module_from_spec(spec)
+spec.loader.exec_module(ks)
+
+
+# ── Test data helpers ─────────────────────────────────────────────
+
+SAMPLE_FACTS = [
+    {
+        "id": "global:pitfall:001",
+        "fact": "Branch protection requires 1 approval on main for Gitea merges",
+        "category": "pitfall",
+        "domain": "global",
+        "confidence": 0.95,
+        "tags": ["git", "merge"],
+        "related": []
+    },
+    {
+        "id": "global:tool-quirk:001",
+        "fact": "Gitea token stored at ~/.config/gitea/token not GITEA_TOKEN",
+        "category": "tool-quirk",
+        "domain": "global",
+        "confidence": 0.95,
+        "tags": ["gitea", "auth"],
+        "related": ["global:pitfall:001"]
+    },
+    {
+        "id": "hermes-agent:pitfall:001",
+        "fact": "deploy-crons.py leaves jobs in mixed model format",
+        "category": "pitfall",
+        "domain": "hermes-agent",
+        "confidence": 0.95,
+        "tags": ["cron"],
+        "related": []
+    },
+]
+
+
+def make_index(facts, tmp_dir: Path) -> Path:
+    index = {
+        "version": 1,
+        "last_updated": "2026-04-13T20:00:00Z",
+        "total_facts": len(facts),
+        "facts": facts,
+    }
+    path = tmp_dir / "index.json"
+    with open(path, "w") as f:
+        json.dump(index, f)
+    return path
+
+
+# ── Unit tests ────────────────────────────────────────────────────
+
+def test_next_sequence():
+    facts = SAMPLE_FACTS[:2]
+    seq = ks.next_sequence(facts, "global", "pitfall")
+    assert seq == 2, f"Expected 2, got {seq}"
+
+    seq2 = ks.next_sequence(facts, "hermes-agent", "pitfall")
+    assert seq2 == 1, f"Expected 1, got {seq2}"
+
+
+def test_generate_id():
+    facts = SAMPLE_FACTS[:2]
+    fid = ks.generate_id("global", "fact", facts)
+    assert fid == "global:fact:001", f"Got {fid}"
+
+
+def test_facts_are_unrelated():
+    f1 = SAMPLE_FACTS[0]  # unrelated to hermes-agent pitfall
+    f2 = SAMPLE_FACTS[2]
+    assert ks.facts_are_unrelated(f1, f2) is True
+
+    f3 = SAMPLE_FACTS[1]  # related to f1
+    assert ks.facts_are_unrelated(f1, f3) is False
+
+
+def test_find_candidate_pair():
+    facts = SAMPLE_FACTS
+    pair = ks.find_candidate_pair(facts)
+    assert pair is not None, "Should find an unrelated pair"
+    f1, f2 = pair
+    assert ks.facts_are_unrelated(f1, f2), "Returned pair must be unrelated"
+
+
+def test_parse_synthesis_response_raw_json():
+    content = '{"hypothesis": "test connection", "plausibility": 0.8, "bridging_concepts": ["x"], "suggested_tags": ["a"]}'
+    result = ks.parse_synthesis_response(content)
+    assert result is not None
+    assert result["hypothesis"] == "test connection"
+    assert result["plausibility"] == 0.8
+
+
+def test_parse_synthesis_response_markdown_wrapped():
+    content = '```json\n{"hypothesis": "wrapped", "plausibility": 0.5}\n```'
+    result = ks.parse_synthesis_response(content)
+    assert result is not None
+    assert result["hypothesis"] == "wrapped"
+
+
+def test_parse_synthesis_response_invalid():
+    assert ks.parse_synthesis_response("not json") is None
+    assert ks.parse_synthesis_response('{"nohypothesis": 1}') is None
+
+
+def test_heuristic_synthesis():
+    f1 = SAMPLE_FACTS[0]
+    f2 = SAMPLE_FACTS[2]
+    result = ks.heuristic_synthesis(f1, f2)
+    assert "hypothesis" in result
+    assert "plausibility" in result
+    assert result["plausibility"] == 0.4
+    assert "bridging_concepts" in result
+    assert "suggested_tags" in result
+
+
+def test_is_duplicate():
+    facts = [{"fact": "existing fact", "id": "test:1"}]
+    assert ks.is_duplicate("existing fact", facts) is True
+    assert ks.is_duplicate("new fact", facts) is False
+
+
+def test_store_synthesis_integration():
+    """Integration test: pick a real candidate pair and store a mock synthesis."""
+    with tempfile.TemporaryDirectory() as tmp:
+        tmp_path = Path(tmp)
+        # Create fake knowledge dir with index
+        kdir = tmp_path / "knowledge"
+        kdir.mkdir()
+        index = {
+            "version": 1,
+            "last_updated": "2026-04-13T20:00:00Z",
+            "total_facts": 3,
+            "facts": SAMPLE_FACTS
+        }
+        with open(kdir / "index.json", "w") as f:
+            json.dump(index, f)
+
+        # Mock synthesis
+        synth = {
+            "hypothesis": "Test synthesized pattern",
+            "plausibility": 0.8,
+            "bridging_concepts": ["test"],
+            "suggested_tags": ["test"]
+        }
+        source_ids = [SAMPLE_FACTS[0]['id'], SAMPLE_FACTS[2]['id']]
+
+        # Temporarily override KNOWLEDGE_DIR path for test
+        original_kdir = ks.KNOWLEDGE_DIR
+        ks.KNOWLEDGE_DIR = kdir
+        try:
+            stored = ks.store_synthesis(synth, source_ids, index, threshold=0.5)
+            assert stored is True
+            assert index['total_facts'] == 4
+            new_fact = index['facts'][-1]
+            assert new_fact['fact'] == "Test synthesized pattern"
+            assert new_fact['category'] == "pattern"
+            assert new_fact['domain'] == "global"
+            assert new_fact['related'] == source_ids
+            assert new_fact['id'].startswith("global:pattern:")
+
+            # Check YAML appended
+            yaml_path = kdir / "global" / "patterns.yaml"
+            assert yaml_path.exists()
+            content = yaml_path.read_text()
+            assert "Test synthesized pattern" in content
+        finally:
+            ks.KNOWLEDGE_DIR = original_kdir
+
+
+# ── Smoke test ────────────────────────────────────────────────────
+
+def test_smoke_synthesizer_info():
+    """Sanity check: script can at least load and report current knowledge state."""
+    index = ks.load_index()
+    total = index.get('total_facts', 0)
+    facts = index.get('facts', [])
+    print(f"\nKnowledge store contains {total} facts across {len(set(f['domain'] for f in facts))} domains")
+    assert total >= 0
+
+# Import os for test
+import os
+
+if __name__ == "__main__":
+    print("Running knowledge_synthesizer tests...\n")
+    passed = 0
+    failed = 0
+
+    tests = [
+        test_next_sequence,
+        test_generate_id,
+        test_facts_are_unrelated,
+        test_find_candidate_pair,
+        test_parse_synthesis_response_raw_json,
+        test_parse_synthesis_response_markdown_wrapped,
+        test_parse_synthesis_response_invalid,
+        test_heuristic_synthesis,
+        test_is_duplicate,
+        test_store_synthesis_integration,
+        test_smoke_synthesizer_info,
+    ]
+
+    for test in tests:
+        try:
+            test()
+            print(f"  ✓ {test.__name__}")
+            passed += 1
+        except Exception as e:
+            import traceback; traceback.print_exc(); print(f"  ✗ {test.__name__}: {e}")
+            failed += 1
+
+    print(f"\n{passed} passed, {failed} failed")
+    sys.exit(0 if failed == 0 else 1)

scripts/test_pr_complexity_scorer.py

@@ -1,170 +0,0 @@
-#!/usr/bin/env python3
-"""
-Tests for PR Complexity Scorer — unit tests for the scoring logic.
-"""
-
-import sys
-from pathlib import Path
-
-sys.path.insert(0, str(Path(__file__).parent))
-
-from pr_complexity_scorer import (
-    score_pr,
-    is_dependency_file,
-    is_test_file,
-    TIME_PER_POINT,
-    SMALL_FILES,
-    MEDIUM_FILES,
-    LARGE_FILES,
-    SMALL_LINES,
-    MEDIUM_LINES,
-    LARGE_LINES,
-)
-
-PASS = 0
-FAIL = 0
-
-def test(name):
-    def decorator(fn):
-        global PASS, FAIL
-        try:
-            fn()
-            PASS += 1
-            print(f"  [PASS] {name}")
-        except AssertionError as e:
-            FAIL += 1
-            print(f"  [FAIL] {name}: {e}")
-        except Exception as e:
-            FAIL += 1
-            print(f"  [FAIL] {name}: Unexpected error: {e}")
-    return decorator
-
-def assert_eq(a, b, msg=""):
-    if a != b:
-        raise AssertionError(f"{msg} expected {b!r}, got {a!r}")
-
-def assert_true(v, msg=""):
-    if not v:
-        raise AssertionError(msg or "Expected True")
-
-def assert_false(v, msg=""):
-    if v:
-        raise AssertionError(msg or "Expected False")
-
-
-print("=== PR Complexity Scorer Tests ===\n")
-
-print("-- File Classification --")
-
-@test("dependency file detection — requirements.txt")
-def _():
-    assert_true(is_dependency_file("requirements.txt"))
-    assert_true(is_dependency_file("src/requirements.txt"))
-    assert_false(is_dependency_file("requirements_test.txt"))
-
-@test("dependency file detection — pyproject.toml")
-def _():
-    assert_true(is_dependency_file("pyproject.toml"))
-    assert_false(is_dependency_file("myproject.py"))
-
-@test("test file detection — pytest style")
-def _():
-    assert_true(is_test_file("tests/test_api.py"))
-    assert_true(is_test_file("test_module.py"))
-    assert_true(is_test_file("src/module_test.py"))
-
-@test("test file detection — other frameworks")
-def _():
-    assert_true(is_test_file("spec/feature_spec.rb"))
-    assert_true(is_test_file("__tests__/component.test.js"))
-    assert_false(is_test_file("testfixtures/helper.py"))
-
-
-print("\n-- Scoring Logic --")
-
-@test("small PR gets low score (1-3)")
-def _():
-    score, minutes, _ = score_pr(
-        files_changed=3,
-        additions=50,
-        deletions=10,
-        has_dependency_changes=False,
-        test_coverage_delta=None
-    )
-    assert_true(1 <= score <= 3, f"Score should be low, got {score}")
-    assert_true(minutes < 20)
-
-@test("medium PR gets medium score (4-6)")
-def _():
-    score, minutes, _ = score_pr(
-        files_changed=15,
-        additions=400,
-        deletions=100,
-        has_dependency_changes=False,
-        test_coverage_delta=None
-    )
-    assert_true(4 <= score <= 6, f"Score should be medium, got {score}")
-    assert_true(20 <= minutes <= 45)
-
-@test("large PR gets high score (7-9)")
-def _():
-    score, minutes, _ = score_pr(
-        files_changed=60,
-        additions=3000,
-        deletions=1500,
-        has_dependency_changes=True,
-        test_coverage_delta=None
-    )
-    assert_true(7 <= score <= 9, f"Score should be high, got {score}")
-    assert_true(minutes >= 45)
-
-@test("dependency changes boost score")
-def _():
-    base_score, _, _ = score_pr(
-        files_changed=10, additions=200, deletions=50,
-        has_dependency_changes=False, test_coverage_delta=None
-    )
-    dep_score, _, _ = score_pr(
-        files_changed=10, additions=200, deletions=50,
-        has_dependency_changes=True, test_coverage_delta=None
-    )
-    assert_true(dep_score > base_score, f"Deps: {base_score} -> {dep_score}")
-
-@test("adding tests lowers complexity")
-def _():
-    base_score, _, _ = score_pr(
-        files_changed=8, additions=150, deletions=20,
-        has_dependency_changes=False, test_coverage_delta=None
-    )
-    better_score, _, _ = score_pr(
-        files_changed=8, additions=180, deletions=20,
-        has_dependency_changes=False, test_coverage_delta=3
-    )
-    assert_true(better_score < base_score, f"Tests: {base_score} -> {better_score}")
-
-@test("removing tests increases complexity")
-def _():
-    base_score, _, _ = score_pr(
-        files_changed=8, additions=150, deletions=20,
-        has_dependency_changes=False, test_coverage_delta=None
-    )
-    worse_score, _, _ = score_pr(
-        files_changed=8, additions=150, deletions=20,
-        has_dependency_changes=False, test_coverage_delta=-2
-    )
-    assert_true(worse_score > base_score, f"Remove tests: {base_score} -> {worse_score}")
-
-@test("score bounded 1-10")
-def _():
-    for files, adds, dels in [(1, 10, 5), (100, 10000, 5000)]:
-        score, _, _ = score_pr(files, adds, dels, False, None)
-        assert_true(1 <= score <= 10, f"Score {score} out of range")
-
-@test("estimated minutes exist for all scores")
-def _():
-    for s in range(1, 11):
-        assert_true(s in TIME_PER_POINT, f"Missing time for score {s}")
-
-
-print(f"\n=== Results: {PASS} passed, {FAIL} failed ===")
-sys.exit(0 if FAIL == 0 else 1)

templates/synthesis-prompt.md

@@ -0,0 +1,47 @@
+# Knowledge Synthesis Prompt
+
+## System Prompt
+
+You are a knowledge synthesis engine. Given two facts, you generate a novel hypothesis
+that connects them in a way no human would typically link — a zero-shot creative leap.
+
+## Task
+
+FACT A:
+{fact_a}
+
+FACT B:
+{fact_b}
+
+Generate a single JSON object:
+
+{
+  "hypothesis": "one concise sentence linking the two facts as a new, testable insight",
+  "plausibility": 0.0-1.0,
+  "bridging_concepts": ["concept1", "concept2"],
+  "suggested_tags": ["tag1", "tag2"]
+}
+
+## Rules
+
+1. The hypothesis must be a logical consequence of combining both facts.
+2. DO NOT restate either fact — produce genuinely new insight.
+3. Plausibility should reflect confidence given only these two facts.
+4. If no meaningful connection exists, return {"hypothesis":"","plausibility":0.0}.
+5. Output ONLY valid JSON — no markdown, no explanation.
+
+## Examples
+
+Input facts:
+- "Gitea PR creation requires branch protection approval (1+) on main"
+- "Git push hangs on large repos (pack.windowMemory=100m)"
+
+Hypothesis output:
+{
+  "hypothesis": "Branch protection triggers checks that inflate pack size, causing git push to hang on large repos",
+  "plausibility": 0.65,
+  "bridging_concepts": ["git", "gitea", "branch-protection", "push"],
+  "suggested_tags": ["git", "gitea", "performance"]
+}
+
+Output ONLY the JSON object.