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/import_graph.py

@@ -1,271 +0,0 @@
-#!/usr/bin/env python3
-"""
-Import Graph Visualizer — Issue #133
-
-Parses Python files in a codebase and generates a module-level import
-dependency graph in DOT format. Detects circular imports.
-
-Usage:
-  python3 scripts/import_graph.py /path/to/hermes-agent
-  python3 scripts/import_graph.py /path/to/hermes-agent --output deps.dot
-  python3 scripts/import_graph.py /path/to/hermes-agent --render-png
-"""
-
-import argparse
-import ast
-import sys
-from pathlib import Path
-from collections import defaultdict
-from typing import Dict, Set, List, Optional
-
-
-def python_files(root: Path) -> List[Path]:
-    """Yield all .py files under root, excluding common noise dirs."""
-    exlude_dirs = {'.git', '__pycache__', '.venv', 'venv', 'node_modules', 'dist', 'build', '.tox'}
-    for path in root.rglob('*.py'):
-        if any(part in exlude_dirs for part in path.parts):
-            continue
-        yield path
-
-
-def module_name(filepath: Path, root: Path) -> str:
-    """Convert a .py file path to its dotted module name relative to root."""
-    rel = filepath.relative_to(root)
-    parts = list(rel.parts)
-    if parts[-1] == '__init__.py':
-        parts = parts[:-1]  # package __init__ → the package itself
-    elif parts[-1].endswith('.py'):
-        parts[-1] = parts[-1][:-3]  # strip .py
-    # Remove any __pycache__ segments
-    parts = [p for p in parts if p != '__pycache__']
-    return '.'.join(parts)
-
-
-def compute_package_base(filepath: Path) -> Path:
-    """Return the directory containing the top-level __init__.py for this file's package.
-    For a file at a/b/c/d.py, return a/b/c if c is a package, else a/b, else a."""
-    parent = filepath.parent
-    while parent != parent.parent:  # while we can go up
-        if (parent / '__init__.py').exists():
-            parent = parent.parent
-        else:
-            break
-    return parent
-
-
-def resolve_import(from_node: ast.ImportFrom, current_file: Path, root: Path) -> Optional[str]:
-    """Resolve a single ImportFrom target to an absolute dotted module name.
-    Returns None if the import is external (stdlib/third-party) or unresolvable."""
-    level = from_node.level  # 0 = absolute, >0 = relative
-    imported = from_node.module  # may be None for `from . import X`
-
-    # External (stdlib/third-party) if level==0 and not a local package
-    # We detect local packages by checking if the module path could exist under root
-
-    if level == 0 and imported:
-        # Absolute import — check if it points to something inside the scanned root
-        candidate = root / imported.replace('.', '/')
-        if candidate.exists() or (candidate / '__init__.py').exists():
-            return imported
-        # Could be a submodule of something we're scanning
-        # e.g. from hermes.tools import foo and we're scanning hermes/
-        return imported
-
-    # Relative import
-    # Compute the package base of the current file
-    package_base = compute_package_base(current_file)
-    rel_to_base = current_file.parent.relative_to(package_base) if package_base != current_file.parent else Path()
-
-    if level == 1:  # from . import X  or  from .X import Y
-        target_package = current_file.parent
-    else:  # level >= 2: from ..X import Y etc.
-        up = level - 1
-        target_package = current_file.parent
-        for _ in range(up):
-            if target_package != target_package.parent:
-                target_package = target_package.parent
-            else:
-                return None  # went past root
-
-    if imported:
-        target_module = imported.replace('.', '/')
-        full_path = target_package / target_module
-        # Convert back to dotted relative to root
-        if full_path.exists() or (full_path.with_suffix('.py')).exists() or (full_path / '__init__.py').exists():
-            try:
-                rel = full_path.relative_to(root)
-                parts = list(rel.parts)
-                if (full_path / '__init__.py').exists():
-                    pass  # keep all parts
-                elif full_path.is_file() and full_path.name.endswith('.py'):
-                    parts[-1] = parts[-1][:-3]
-                return '.'.join(parts)
-            except ValueError:
-                pass
-        return None
-    else:
-        # from . import X — target_package is the package itself
-        try:
-            rel = target_package.relative_to(root)
-            return '.'.join(rel.parts)
-        except ValueError:
-            return None
-
-
-def scan_imports(root: Path) -> Dict[str, Set[str]]:
-    """Scan all Python files under root and return {module: {imported_modules}}."""
-    graph = defaultdict(set)
-    all_modules = set()
-
-    # First pass: collect all module names
-    for filepath in python_files(root):
-        mod = module_name(filepath, root)
-        all_modules.add(mod)
-
-    # Second pass: resolve imports
-    for filepath in python_files(root):
-        src_mod = module_name(filepath, root)
-        try:
-            content = filepath.read_text(errors='ignore')
-            tree = ast.parse(content, filename=str(filepath))
-        except Exception:
-            continue
-
-        for node in ast.walk(tree):
-            if isinstance(node, ast.Import):
-                for alias in node.names:
-                    name = alias.name.split('.')[0]  # top-level package only
-                    # If name matches a local module, add edge
-                    if any(m.startswith(name) for m in all_modules):
-                        graph[src_mod].add(name)
-            elif isinstance(node, ast.ImportFrom):
-                # level 0 = absolute, level >0 = relative
-                resolved = resolve_import(node, filepath, root)
-                if resolved:
-                    # For `from X.Y import Z`, the dependency is on X.Y
-                    graph[src_mod].add(resolved)
-                else:
-                    # Unresolvable — likely external (stdlib/third-party)
-                    pass
-
-    return dict(graph)
-
-
-def detect_cycles(graph: Dict[str, Set[str]]) -> List[List[str]]:
-    """Detect all cycles in the directed graph using DFS."""
-    cycles = []
-    visited = set()
-    rec_stack = set()
-    path = []
-
-    def dfs(node: str):
-        visited.add(node)
-        rec_stack.add(node)
-        path.append(node)
-
-        for neighbor in sorted(graph.get(node, [])):
-            if neighbor not in visited:
-                result = dfs(neighbor)
-                if result:
-                    return result
-            elif neighbor in rec_stack:
-                # cycle: from path start of neighbor to now
-                start = path.index(neighbor)
-                return path[start:] + [neighbor]
-
-        path.pop()
-        rec_stack.remove(node)
-        return None
-
-    for node in sorted(graph):
-        if node not in visited:
-            cycle = dfs(node)
-            if cycle:
-                cycles.append(cycle)
-
-    return cycles
-
-
-def to_dot(graph: Dict[str, Set[str]], cycles: List[List[str]] = None) -> str:
-    """Generate DOT format output."""
-    cycle_nodes = set()
-    if cycles:
-        for cycle in cycles:
-            cycle_nodes.update(cycle)
-
-    lines = ['digraph import_graph {']
-    lines.append('  rankdir=LR;')
-    lines.append('  node [shape=box, style=filled, fontname="Helvetica"];')
-    lines.append('  edge [arrowhead=vee];')
-    lines.append('')
-
-    for src in sorted(graph):
-        fill = '#2d1b69' if src in cycle_nodes else '#16213e'
-        lines.append(f'  "{src}" [fillcolor="{fill}"];')
-
-    for src, deps in sorted(graph.items()):
-        for dst in sorted(deps):
-            color = '#e4572e' if dst in cycle_nodes else '#4a4a6a'
-            lines.append(f'  "{src}" -> "{dst}" [color="{color}"];')
-
-    lines.append('}')
-    return '\n'.join(lines)
-
-
-def main():
-    parser = argparse.ArgumentParser(description='Generate Python import graph for a codebase')
-    parser.add_argument('path', help='Path to Python project (e.g. hermes-agent directory)')
-    parser.add_argument('--output', '-o', help='Write DOT to file instead of stdout')
-    parser.add_argument('--cycles-only', action='store_true', help='Only report cycles, exit 1 if any')
-    parser.add_argument('--render-png', action='store_true', help='Render PNG via graphviz (requires dot)')
-    parser.add_argument('--render-svg', action='store_true', help='Render SVG via graphviz')
-    args = parser.parse_args()
-
-    root = Path(args.path).resolve()
-    if not root.is_dir():
-        print(f"Error: {root} is not a directory", file=sys.stderr)
-        sys.exit(1)
-
-    print(f"Scanning {root}...", file=sys.stderr)
-    graph = scan_imports(root)
-    cycles = detect_cycles(graph)
-
-    if args.cycles_only:
-        if cycles:
-            print("CIRCULAR DEPENDENCIES:", file=sys.stderr)
-            for cycle in cycles:
-                print(f"  {' → '.join(cycle)}", file=sys.stderr)
-            sys.exit(1)
-        else:
-            print("No circular dependencies found.", file=sys.stderr)
-            sys.exit(0)
-
-    # Prepare output
-    output = to_dot(graph, cycles)
-
-    if args.output:
-        Path(args.output).write_text(output)
-        print(f"DOT written to {args.output}", file=sys.stderr)
-
-        # Optional rendering
-        if args.render_png or args.render_svg:
-            import subprocess
-            out_path = Path(args.output)
-            if args.render_png:
-                png_out = out_path.with_suffix('.png')
-                subprocess.run(['dot', '-Tpng', str(out_path), '-o', str(png_out)], check=True)
-                print(f"PNG rendered to {png_out}", file=sys.stderr)
-            if args.render_svg:
-                svg_out = out_path.with_suffix('.svg')
-                subprocess.run(['dot', '-Tsvg', str(out_path), '-o', str(svg_out)], check=True)
-                print(f"SVG rendered to {svg_out}", file=sys.stderr)
-    else:
-        print(output)
-
-    # Summary
-    print(f"\nSummary: {len(graph)} modules, {sum(len(d) for d in graph.values())} import edges, {len(cycles)} cycles",
-          file=sys.stderr)
-
-
-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/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)

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.

tests/test_import_graph.py

@@ -1,53 +0,0 @@
-"""Smoke test for import_graph — verifies it works on a real Python codebase.
-
-We run import_graph.py against the compounding-intelligence repo itself
-and validate that DOT output is well-formed and includes expected modules.
-"""
-
-import subprocess
-import sys
-from pathlib import Path
-
-REPO_ROOT = Path(__file__).resolve().parents[1]  # tests/ → repo root
-
-
-def test_import_graph_creates_dot():
-    """import_graph.py produces valid DOT output for this repo."""
-    script = REPO_ROOT / 'scripts' / 'import_graph.py'
-    result = subprocess.run(
-        [sys.executable, str(script), str(REPO_ROOT), '--output', '/dev/null'],
-        capture_output=True, text=True, timeout=30
-    )
-    assert result.returncode == 0, f"script failed: {result.stderr}"
-    # Should have printed a summary
-    assert ' modules,' in result.stderr or 'Summary:' in result.stderr
-
-
-def test_import_graph_excludes_site_packages():
-    """import_graph.py does not crash on unparseable files or external deps."""
-    script = REPO_ROOT / 'scripts' / 'import_graph.py'
-    # Run on a tiny fixture if available, else just ensure it exits cleanly
-    result = subprocess.run(
-        [sys.executable, str(script), str(REPO_ROOT / 'scripts')],
-        capture_output=True, text=True, timeout=30
-    )
-    assert result.returncode == 0
-
-
-def test_import_graph_cycles_only_flag():
-    """--cycles-only exits 0 when no cycles, 1 when cycles exist."""
-    script = REPO_ROOT / 'scripts' / 'import_graph.py'
-    result = subprocess.run(
-        [sys.executable, str(script), str(REPO_ROOT / 'scripts'), '--cycles-only'],
-        capture_output=True, text=True, timeout=30
-    )
-    # The scripts/ dir should have no cycles — exit 0
-    assert result.returncode in (0, 1), "unexpected return code"
-
-
-if __name__ == '__main__':
-    # Run inline
-    test_import_graph_creates_dot()
-    test_import_graph_excludes_site_packages()
-    test_import_graph_cycles_only_flag()
-    print("All import_graph smoke tests passed.")