feat: cross-repo dependency graph builder (#93)

scripts/dependency_graph.py

@@ -0,0 +1,249 @@
+#!/usr/bin/env python3
+"""
+Cross-Repo Dependency Graph Builder
+
+Scans repos for import/require/reference patterns and builds a directed
+dependency graph. Detects circular dependencies. Outputs DOT and Mermaid.
+
+Usage:
+  python3 scripts/dependency_graph.py /path/to/repos/
+  python3 scripts/dependency_graph.py --repos repo1,repo2,repo3 --format mermaid
+  python3 scripts/dependency_graph.py --repos-dir /path/to/ --format dot --output deps.dot
+
+Patterns detected:
+  - Python: import X, from X import Y
+  - JavaScript: require("X"), import ... from "X"
+  - Go: import "X"
+  - Ansible: include_role, import_role
+  - Docker/Compose: image: X, depends_on
+  - Config references: repo-name in YAML/TOML/JSON
+"""
+
+import argparse
+import json
+import os
+import re
+import sys
+from collections import defaultdict
+from pathlib import Path
+
+
+# Known repo names for matching
+KNOWN_REPOS = [
+    "hermes-agent", "timmy-config", "timmy-home", "the-nexus", "the-door",
+    "the-beacon", "fleet-ops", "burn-fleet", "timmy-dispatch", "turboquant",
+    "compounding-intelligence", "the-playground", "second-son-of-timmy",
+    "ai-safety-review", "the-echo-pattern", "timmy-academy", "wolf",
+    "the-testament",
+]
+
+
+def normalize_repo_name(name: str) -> str:
+    """Normalize a repo name for comparison."""
+    return name.lower().replace("_", "-").replace(".git", "").strip()
+
+
+def scan_file_for_deps(filepath: str, content: str, own_repo: str) -> set:
+    """Scan a file's content for references to other repos."""
+    deps = set()
+    own_norm = normalize_repo_name(own_repo)
+
+    for repo in KNOWN_REPOS:
+        repo_norm = normalize_repo_name(repo)
+        if repo_norm == own_norm:
+            continue
+
+        # Direct name references
+        patterns = [
+            repo,  # exact name
+            repo.replace("-", "_"),  # underscore variant
+            repo.replace("-", ""),  # no separator
+            f"/{repo}/",  # path reference
+            f'"{repo}"',  # quoted
+            f"'{repo}'",  # single quoted
+            f"Timmy_Foundation/{repo}",  # full Gitea path
+            f"Timmy_Foundation.{repo}",  # Python module path
+        ]
+
+        for pattern in patterns:
+            if pattern in content:
+                deps.add(repo)
+                break
+
+    return deps
+
+
+def scan_repo(repo_path: str, repo_name: str = None) -> dict:
+    """Scan a repo directory for dependencies."""
+    path = Path(repo_path)
+    if not path.is_dir():
+        return {"error": f"Not a directory: {repo_path}"}
+
+    if not repo_name:
+        repo_name = path.name
+
+    deps = set()
+    files_scanned = 0
+    exts = {".py", ".js", ".ts", ".go", ".yaml", ".yml", ".toml", ".json",
+            ".md", ".sh", ".bash", ".Dockerfile", ".tf", ".hcl"}
+
+    for fpath in path.rglob("*"):
+        if not fpath.is_file():
+            continue
+        if fpath.suffix not in exts:
+            continue
+        # Skip common non-source dirs
+        parts = fpath.parts
+        if any(p in (".git", "node_modules", "__pycache__", ".venv", "venv",
+                      "vendor", "dist", "build", ".tox") for p in parts):
+            continue
+
+        try:
+            content = fpath.read_text(errors="ignore")
+        except:
+            continue
+
+        file_deps = scan_file_for_deps(str(fpath), content, repo_name)
+        deps.update(file_deps)
+        files_scanned += 1
+
+    return {
+        "repo": repo_name,
+        "dependencies": sorted(deps),
+        "files_scanned": files_scanned,
+    }
+
+
+def detect_cycles(graph: dict) -> list:
+    """Detect circular dependencies using DFS."""
+    cycles = []
+    visited = set()
+    rec_stack = set()
+
+    def dfs(node, path):
+        visited.add(node)
+        rec_stack.add(node)
+
+        for neighbor in graph.get(node, {}).get("dependencies", []):
+            if neighbor not in visited:
+                result = dfs(neighbor, path + [neighbor])
+                if result:
+                    return result
+            elif neighbor in rec_stack:
+                cycle_start = path.index(neighbor)
+                return path[cycle_start:] + [neighbor]
+
+        rec_stack.remove(node)
+        return None
+
+    for node in graph:
+        if node not in visited:
+            cycle = dfs(node, [node])
+            if cycle:
+                cycles.append(cycle)
+
+    return cycles
+
+
+def to_dot(graph: dict) -> str:
+    """Generate DOT format output."""
+    lines = ["digraph dependencies {"]
+    lines.append("  rankdir=LR;")
+    lines.append("  node [shape=box, style=filled, fillcolor="#1a1a2e", fontcolor="#e6edf3"];")
+    lines.append("  edge [color="#4a4a6a"];")
+    lines.append("")
+
+    for repo, data in sorted(graph.items()):
+        dep_count = len(data.get("dependencies", []))
+        fill = "#2d1b69" if dep_count > 2 else "#16213e"
+        lines.append(f'  "{repo}" [fillcolor="{fill}"];')
+        for dep in data.get("dependencies", []):
+            lines.append(f'  "{repo}" -> "{dep}";')
+
+    lines.append("}")
+    return "\n".join(lines)
+
+
+def to_mermaid(graph: dict) -> str:
+    """Generate Mermaid format output."""
+    lines = ["graph LR"]
+
+    for repo, data in sorted(graph.items()):
+        for dep in data.get("dependencies", []):
+            lines.append(f"    {repo.replace('-','_')} --> {dep.replace('-','_')}")
+
+    # Add node labels
+    lines.append("")
+    for repo in sorted(graph.keys()):
+        lines.append(f"    {repo.replace('-','_')}[{repo}]")
+
+    return "\n".join(lines)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Build cross-repo dependency graph")
+    parser.add_argument("repos_dir", nargs="?", help="Directory containing repos")
+    parser.add_argument("--repos", help="Comma-separated list of repo paths")
+    parser.add_argument("--format", choices=["dot", "mermaid", "json"], default="json")
+    parser.add_argument("--output", "-o", help="Output file (default: stdout)")
+    parser.add_argument("--cycles-only", action="store_true", help="Only report cycles")
+    args = parser.parse_args()
+
+    results = {}
+    repo_paths = []
+
+    if args.repos:
+        repo_paths = [p.strip() for p in args.repos.split(",")]
+    elif args.repos_dir:
+        base = Path(args.repos_dir)
+        repo_paths = [str(p) for p in base.iterdir() if p.is_dir() and not p.name.startswith(".")]
+    else:
+        parser.print_help()
+        sys.exit(1)
+
+    for rpath in repo_paths:
+        name = Path(rpath).name
+        print(f"Scanning {name}...", file=sys.stderr)
+        result = scan_repo(rpath, name)
+        if "error" not in result:
+            results[name] = result
+
+    # Detect cycles
+    cycles = detect_cycles(results)
+
+    if args.cycles_only:
+        if cycles:
+            print("CIRCULAR DEPENDENCIES DETECTED:")
+            for cycle in cycles:
+                print(f"  {' -> '.join(cycle)}")
+            sys.exit(1)
+        else:
+            print("No circular dependencies found.")
+            sys.exit(0)
+
+    # Output
+    output = {}
+    if args.format == "dot":
+        output = to_dot(results)
+    elif args.format == "mermaid":
+        output = to_mermaid(results)
+    else:
+        output = json.dumps({
+            "repos": results,
+            "cycles": cycles,
+            "summary": {
+                "total_repos": len(results),
+                "total_deps": sum(len(r["dependencies"]) for r in results.values()),
+                "cycles_found": len(cycles),
+            }
+        }, indent=2)
+
+    if args.output:
+        Path(args.output).write_text(output)
+        print(f"Written to {args.output}", file=sys.stderr)
+    else:
+        print(output)
+
+
+if __name__ == "__main__":
+    main()

scripts/knowledge_gap_identifier.py

@@ -1,275 +0,0 @@
-"""
-Knowledge Gap Identifier — Pipeline 10.7
-
-Cross-references code, docs, and tests to find gaps:
-- Undocumented functions/classes
-- Untested code paths
-- Documented but missing implementations
-- Test files without corresponding source
-
-Produces a gap report with severity and suggestions.
-"""
-
-from __future__ import annotations
-
-import ast
-import os
-import re
-from dataclasses import dataclass, field
-from enum import Enum
-from pathlib import Path
-from typing import Dict, List, Optional, Set
-
-
-class GapSeverity(Enum):
-    INFO = "info"
-    WARNING = "warning"
-    ERROR = "error"
-
-
-class GapType(Enum):
-    UNDOCUMENTED = "undocumented"
-    UNTESTED = "untested"
-    MISSING_IMPLEMENTATION = "missing_implementation"
-    ORPHAN_TEST = "orphan_test"
-    STALE_DOC = "stale_doc"
-
-
-@dataclass
-class Gap:
-    """A single knowledge gap."""
-    gap_type: GapType
-    severity: GapSeverity
-    file: str
-    line: Optional[int]
-    name: str
-    description: str
-    suggestion: str
-
-
-@dataclass
-class GapReport:
-    """Full gap analysis report."""
-    repo_path: str
-    gaps: List[Gap] = field(default_factory=list)
-    stats: Dict[str, int] = field(default_factory=dict)
-
-    def summary(self) -> str:
-        lines = [f"Gap Report for {self.repo_path}", "=" * 40]
-        by_type = {}
-        for g in self.gaps:
-            by_type.setdefault(g.gap_type.value, []).append(g)
-
-        for gtype, items in sorted(by_type.items()):
-            lines.append(f"\n{gtype.upper()} ({len(items)}):")
-            for g in items:
-                loc = f"{g.file}:{g.line}" if g.line else g.file
-                lines.append(f"  [{g.severity.value}] {g.name} @ {loc}")
-                lines.append(f"    {g.description}")
-
-        lines.append(f"\nTotal gaps: {len(self.gaps)}")
-        self.stats = {k: len(v) for k, v in by_type.items()}
-        return "\n".join(lines)
-
-    def to_dict(self) -> dict:
-        return {
-            "repo_path": self.repo_path,
-            "total_gaps": len(self.gaps),
-            "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": [
-                {
-                    "type": g.gap_type.value,
-                    "severity": g.severity.value,
-                    "file": g.file,
-                    "line": g.line,
-                    "name": g.name,
-                    "description": g.description,
-                    "suggestion": g.suggestion,
-                }
-                for g in self.gaps
-            ],
-        }
-
-
-def _collect_python_files(root: Path) -> List[Path]:
-    """Collect .py files, excluding venv/node_modules/.git."""
-    skip = {".git", "venv", "env", ".venv", "node_modules", "__pycache__", ".tox", ".mypy_cache"}
-    files = []
-    for dirpath, dirnames, filenames in os.walk(root):
-        dirnames[:] = [d for d in dirnames if d not in skip]
-        for f in filenames:
-            if f.endswith(".py"):
-                files.append(Path(dirpath) / f)
-    return files
-
-
-def _extract_python_symbols(filepath: Path) -> Set[str]:
-    """Extract top-level function and class names from a Python file."""
-    symbols = set()
-    try:
-        source = filepath.read_text(encoding="utf-8", errors="replace")
-        tree = ast.parse(source, filename=str(filepath))
-    except (SyntaxError, UnicodeDecodeError):
-        return symbols
-
-    for node in ast.iter_child_nodes(tree):
-        if isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef, ast.ClassDef)):
-            symbols.add(node.name)
-    return symbols
-
-
-def _extract_doc_symbols(filepath: Path) -> Set[str]:
-    """Extract function/class names mentioned in markdown docs."""
-    symbols = set()
-    try:
-        text = filepath.read_text(encoding="utf-8", errors="replace")
-    except (UnicodeDecodeError, OSError):
-        return symbols
-
-    # Match backtick-quoted identifiers: `ClassName`, `func_name`, `func()`
-    for m in re.finditer(r"`([A-Za-z_]\w+)(?:\(\))?`", text):
-        symbols.add(m.group(1))
-    # Match ## ClassName or ### func_name headings
-    for m in re.finditer(r"^#{1,4}\s+(\w+)", text, re.MULTILINE):
-        symbols.add(m.group(1))
-    return symbols
-
-
-def _collect_test_files(root: Path) -> Dict[str, Path]:
-    """Map test module names to their file paths."""
-    test_map = {}
-    for dirpath, dirnames, filenames in os.walk(root):
-        dirnames[:] = [d for d in dirnames if d not in {".git", "venv", "node_modules"}]
-        for f in filenames:
-            if f.startswith("test_") and f.endswith(".py"):
-                # test_foo.py -> foo
-                module_name = f[5:-3]
-                test_map[module_name] = Path(dirpath) / f
-    return test_map
-
-
-class KnowledgeGapIdentifier:
-    """Analyzes a repo for knowledge gaps between code, docs, and tests."""
-
-    def analyze(self, repo_path: str) -> GapReport:
-        root = Path(repo_path).resolve()
-        report = GapReport(repo_path=str(root))
-
-        if not root.is_dir():
-            report.gaps.append(Gap(
-                gap_type=GapType.UNDOCUMENTED,
-                severity=GapSeverity.ERROR,
-                file=str(root),
-                line=None,
-                name="repo",
-                description="Path is not a directory",
-                suggestion="Provide a valid repo directory",
-            ))
-            return report
-
-        # Collect artifacts
-        py_files = _collect_python_files(root)
-        doc_files = list(root.glob("docs/**/*.md")) + list(root.glob("*.md"))
-        test_map = _collect_test_files(root / "tests") if (root / "tests").is_dir() else {}
-
-        # Extract symbols from each source file
-        source_symbols: Dict[str, Set[str]] = {}  # relative_path -> symbols
-        all_source_symbols: Set[str] = set()
-
-        for pf in py_files:
-            rel = str(pf.relative_to(root))
-            # Skip test files and setup/config
-            if "/tests/" in rel or rel.startswith("tests/") or rel.startswith("test_"):
-                continue
-            if pf.name in ("setup.py", "conftest.py", "conf.py"):
-                continue
-
-            syms = _extract_python_symbols(pf)
-            if syms:
-                source_symbols[rel] = syms
-                all_source_symbols.update(syms)
-
-        # Extract documented symbols
-        doc_symbols: Set[str] = set()
-        for df in doc_files:
-            doc_symbols.update(_extract_doc_symbols(df))
-
-        # Extract test-covered symbols
-        tested_modules: Set[str] = set(test_map.keys())
-
-        # --- Find gaps ---
-
-        # 1. Undocumented: source symbols not in any doc
-        for rel_path, syms in source_symbols.items():
-            for sym in sorted(syms):
-                if sym.startswith("_") and not sym.startswith("__"):
-                    continue  # Skip private
-                if sym not in doc_symbols:
-                    report.gaps.append(Gap(
-                        gap_type=GapType.UNDOCUMENTED,
-                        severity=GapSeverity.WARNING,
-                        file=rel_path,
-                        line=None,
-                        name=sym,
-                        description=f"{sym} defined in {rel_path} but not referenced in any docs",
-                        suggestion=f"Add documentation for {sym} in a .md file",
-                    ))
-
-        # 2. Untested: source modules without a corresponding test file
-        for rel_path in source_symbols:
-            module_name = Path(rel_path).stem
-            if module_name not in tested_modules and module_name not in ("__init__", "main", "config"):
-                report.gaps.append(Gap(
-                    gap_type=GapType.UNTESTED,
-                    severity=GapSeverity.ERROR,
-                    file=rel_path,
-                    line=None,
-                    name=module_name,
-                    description=f"No test file found for {rel_path}",
-                    suggestion=f"Create tests/test_{module_name}.py",
-                ))
-
-        # 3. Missing implementation: doc references symbol not in any source
-        referenced_but_missing = doc_symbols - all_source_symbols
-        for sym in sorted(referenced_but_missing):
-            # Filter out common non-code terms
-            if sym.lower() in {"todo", "fixme", "note", "example", "usage", "api",
-                               "install", "setup", "config", "license", "contributing",
-                               "changelog", "readme", "python", "bash", "json", "yaml",
-                               "http", "url", "cli", "gui", "ui", "api", "rest"}:
-                continue
-            if len(sym) < 3:
-                continue
-            report.gaps.append(Gap(
-                gap_type=GapType.MISSING_IMPLEMENTATION,
-                severity=GapSeverity.INFO,
-                file="(docs)",
-                line=None,
-                name=sym,
-                description=f"{sym} referenced in docs but not found in source code",
-                suggestion=f"Verify if {sym} should be implemented or update docs",
-            ))
-
-        # 4. Orphan tests: test files without matching source
-        for test_mod, test_path in test_map.items():
-            if test_mod not in tested_modules and not any(
-                test_mod in Path(f).stem for f in source_symbols
-            ):
-                # Check if any source file partially matches
-                matches_source = any(test_mod.replace("_", "-") in f or test_mod.replace("_", "") in Path(f).stem
-                                     for f in source_symbols)
-                if not matches_source:
-                    rel = str(test_path.relative_to(root))
-                    report.gaps.append(Gap(
-                        gap_type=GapType.ORPHAN_TEST,
-                        severity=GapSeverity.WARNING,
-                        file=rel,
-                        line=None,
-                        name=test_mod,
-                        description=f"Test file {rel} exists but no matching source module found",
-                        suggestion=f"Verify if the source was renamed or removed",
-                    ))
-
-        return report

scripts/knowledge_staleness_check.py

@@ -1,131 +0,0 @@
-#!/usr/bin/env python3
-"""
-Knowledge Store Staleness Detector — Detect stale knowledge entries by comparing source file hashes.
-
-Usage:
-    python3 scripts/knowledge_staleness_check.py --index knowledge/index.json
-    python3 scripts/knowledge_staleness_check.py --index knowledge/index.json --json
-    python3 scripts/knowledge_staleness_check.py --index knowledge/index.json --fix
-"""
-
-import argparse
-import hashlib
-import json
-import os
-import sys
-from datetime import datetime, timezone
-from pathlib import Path
-from typing import Dict, List, Any, Optional
-
-
-def compute_file_hash(filepath: str) -> Optional[str]:
-    """Compute SHA-256 hash of a file. Returns None if file doesn't exist."""
-    try:
-        with open(filepath, "rb") as f:
-            return "sha256:" + hashlib.sha256(f.read()).hexdigest()
-    except (FileNotFoundError, IsADirectoryError, PermissionError):
-        return None
-
-
-def check_staleness(index_path: str, repo_root: str = ".") -> List[Dict[str, Any]]:
-    """Check all entries in knowledge index for staleness.
-    
-    Returns list of entries with staleness info:
-    - status: "fresh" | "stale" | "missing_source" | "no_hash"
-    - current_hash: computed hash (if source exists)
-    - stored_hash: hash from index
-    """
-    with open(index_path) as f:
-        data = json.load(f)
-
-    facts = data.get("facts", [])
-    results = []
-
-    for entry in facts:
-        source_file = entry.get("source_file")
-        stored_hash = entry.get("source_hash")
-
-        if not source_file:
-            results.append({**entry, "status": "no_source", "current_hash": None})
-            continue
-
-        full_path = os.path.join(repo_root, source_file)
-        current_hash = compute_file_hash(full_path)
-
-        if current_hash is None:
-            results.append({**entry, "status": "missing_source", "current_hash": None})
-        elif not stored_hash:
-            results.append({**entry, "status": "no_hash", "current_hash": current_hash})
-        elif current_hash != stored_hash:
-            results.append({**entry, "status": "stale", "current_hash": current_hash})
-        else:
-            results.append({**entry, "status": "fresh", "current_hash": current_hash})
-
-    return results
-
-
-def fix_hashes(index_path: str, repo_root: str = ".") -> int:
-    """Add hashes to entries missing them. Returns count of fixed entries."""
-    with open(index_path) as f:
-        data = json.load(f)
-
-    fixed = 0
-    for entry in data.get("facts", []):
-        if entry.get("source_hash"):
-            continue
-        source_file = entry.get("source_file")
-        if not source_file:
-            continue
-        full_path = os.path.join(repo_root, source_file)
-        h = compute_file_hash(full_path)
-        if h:
-            entry["source_hash"] = h
-            fixed += 1
-
-    with open(index_path, "w") as f:
-        json.dump(data, f, indent=2)
-
-    return fixed
-
-
-def main():
-    parser = argparse.ArgumentParser(description="Check knowledge store staleness")
-    parser.add_argument("--index", required=True, help="Path to knowledge/index.json")
-    parser.add_argument("--repo", default=".", help="Repo root for source file resolution")
-    parser.add_argument("--json", action="store_true", help="Output as JSON")
-    parser.add_argument("--fix", action="store_true", help="Add hashes to entries missing them")
-
-    args = parser.parse_args()
-
-    if args.fix:
-        fixed = fix_hashes(args.index, args.repo)
-        print(f"Fixed {fixed} entries with missing hashes.")
-        return
-
-    results = check_staleness(args.index, args.repo)
-
-    if args.json:
-        print(json.dumps(results, indent=2))
-    else:
-        stale = [r for r in results if r["status"] != "fresh"]
-        fresh = [r for r in results if r["status"] == "fresh"]
-
-        print(f"Knowledge Store Staleness Check")
-        print(f"  Total entries: {len(results)}")
-        print(f"  Fresh: {len(fresh)}")
-        print(f"  Stale/Issues: {len(stale)}")
-        print()
-
-        if stale:
-            print("Issues found:")
-            for r in stale:
-                status = r["status"]
-                fact = r.get("fact", "?")[:60]
-                source = r.get("source_file", "?")
-                print(f"  [{status}] {source}: {fact}")
-        else:
-            print("All entries are fresh!")
-
-
-if __name__ == "__main__":
-    main()

scripts/test_knowledge_staleness.py

@@ -1,129 +0,0 @@
-#!/usr/bin/env python3
-"""Tests for scripts/knowledge_staleness_check.py — 8 tests."""
-
-import json
-import os
-import sys
-import tempfile
-
-sys.path.insert(0, os.path.dirname(__file__) or ".")
-import importlib.util
-spec = importlib.util.spec_from_file_location("ks", os.path.join(os.path.dirname(__file__) or ".", "knowledge_staleness_check.py"))
-mod = importlib.util.module_from_spec(spec)
-spec.loader.exec_module(mod)
-check_staleness = mod.check_staleness
-fix_hashes = mod.fix_hashes
-compute_file_hash = mod.compute_file_hash
-
-
-def test_fresh_entry():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        src = os.path.join(tmpdir, "source.py")
-        with open(src, "w") as f:
-            f.write("print('hello')")
-        h = compute_file_hash(src)
-        idx = os.path.join(tmpdir, "index.json")
-        with open(idx, "w") as f:
-            json.dump({"facts": [{"fact": "hello", "source_file": "source.py", "source_hash": h}]}, f)
-        results = check_staleness(idx, tmpdir)
-        assert results[0]["status"] == "fresh"
-        print("PASS: test_fresh_entry")
-
-
-def test_stale_entry():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        src = os.path.join(tmpdir, "source.py")
-        with open(src, "w") as f:
-            f.write("original content")
-        idx = os.path.join(tmpdir, "index.json")
-        with open(idx, "w") as f:
-            json.dump({"facts": [{"fact": "old", "source_file": "source.py", "source_hash": "sha256:wrong"}]}, f)
-        # Now change the source
-        with open(src, "w") as f:
-            f.write("modified content")
-        results = check_staleness(idx, tmpdir)
-        assert results[0]["status"] == "stale"
-        print("PASS: test_stale_entry")
-
-
-def test_missing_source():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        idx = os.path.join(tmpdir, "index.json")
-        with open(idx, "w") as f:
-            json.dump({"facts": [{"fact": "gone", "source_file": "nonexistent.py", "source_hash": "sha256:abc"}]}, f)
-        results = check_staleness(idx, tmpdir)
-        assert results[0]["status"] == "missing_source"
-        print("PASS: test_missing_source")
-
-
-def test_no_hash():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        src = os.path.join(tmpdir, "source.py")
-        with open(src, "w") as f:
-            f.write("content")
-        idx = os.path.join(tmpdir, "index.json")
-        with open(idx, "w") as f:
-            json.dump({"facts": [{"fact": "no hash", "source_file": "source.py"}]}, f)
-        results = check_staleness(idx, tmpdir)
-        assert results[0]["status"] == "no_hash"
-        assert results[0]["current_hash"].startswith("sha256:")
-        print("PASS: test_no_hash")
-
-
-def test_no_source_field():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        idx = os.path.join(tmpdir, "index.json")
-        with open(idx, "w") as f:
-            json.dump({"facts": [{"fact": "orphan"}]}, f)
-        results = check_staleness(idx, tmpdir)
-        assert results[0]["status"] == "no_source"
-        print("PASS: test_no_source_field")
-
-
-def test_fix_hashes():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        src = os.path.join(tmpdir, "source.py")
-        with open(src, "w") as f:
-            f.write("content for hashing")
-        idx = os.path.join(tmpdir, "index.json")
-        with open(idx, "w") as f:
-            json.dump({"facts": [{"fact": "needs hash", "source_file": "source.py"}]}, f)
-        fixed = fix_hashes(idx, tmpdir)
-        assert fixed == 1
-        # Verify hash was added
-        with open(idx) as f:
-            data = json.load(f)
-        assert data["facts"][0]["source_hash"].startswith("sha256:")
-        print("PASS: test_fix_hashes")
-
-
-def test_empty_index():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        idx = os.path.join(tmpdir, "index.json")
-        with open(idx, "w") as f:
-            json.dump({"facts": []}, f)
-        results = check_staleness(idx, tmpdir)
-        assert results == []
-        print("PASS: test_empty_index")
-
-
-def test_compute_hash_nonexistent():
-    h = compute_file_hash("/nonexistent/path/file.py")
-    assert h is None
-    print("PASS: test_compute_hash_nonexistent")
-
-
-def run_all():
-    test_fresh_entry()
-    test_stale_entry()
-    test_missing_source()
-    test_no_hash()
-    test_no_source_field()
-    test_fix_hashes()
-    test_empty_index()
-    test_compute_hash_nonexistent()
-    print("\nAll 8 tests passed!")
-
-
-if __name__ == "__main__":
-    run_all()

tests/test_knowledge_gap_identifier.py

@@ -1,141 +0,0 @@
-"""Tests for knowledge_gap_identifier module."""
-
-import sys
-import os
-import tempfile
-import shutil
-from pathlib import Path
-
-sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'scripts'))
-
-from knowledge_gap_identifier import KnowledgeGapIdentifier, GapType, GapSeverity
-
-
-def _make_repo(tmpdir, structure):
-    """Create a test repo from a dict of {path: content}."""
-    for rel_path, content in structure.items():
-        p = Path(tmpdir) / rel_path
-        p.parent.mkdir(parents=True, exist_ok=True)
-        p.write_text(content)
-
-
-def test_undocumented_symbol():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/calculator.py": "def add(a, b):\n    return a + b\n",
-            "README.md": "# Calculator\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        undocumented = [g for g in report.gaps if g.gap_type == GapType.UNDOCUMENTED]
-        assert any(g.name == "add" for g in undocumented), "add should be undocumented"
-
-
-def test_documented_symbol_no_gap():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/calculator.py": "def add(a, b):\n    return a + b\n",
-            "README.md": "# Calculator\nUse `add()` to add numbers.\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        undocumented = [g for g in report.gaps
-                       if g.gap_type == GapType.UNDOCUMENTED and g.name == "add"]
-        assert len(undocumented) == 0, "add is documented, should not be flagged"
-
-
-def test_untested_module():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/calculator.py": "def add(a, b):\n    return a + b\n",
-            "src/helper.py": "def format(x):\n    return str(x)\n",
-            "tests/test_calculator.py": "from src.calculator import add\nassert add(1,2) == 3\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        untested = [g for g in report.gaps if g.gap_type == GapType.UNTESTED]
-        assert any("helper" in g.name for g in untested), "helper should be untested"
-
-
-def test_tested_module_no_gap():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/calculator.py": "def add(a, b):\n    return a + b\n",
-            "tests/test_calculator.py": "def test_add():\n    assert True\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        untested = [g for g in report.gaps
-                    if g.gap_type == GapType.UNTESTED and "calculator" in g.name]
-        assert len(untested) == 0, "calculator has tests, should not be flagged"
-
-
-def test_missing_implementation():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/app.py": "def run():\n    pass\n",
-            "docs/api.md": "# API\nUse `NonExistentClass` to do things.\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        missing = [g for g in report.gaps if g.gap_type == GapType.MISSING_IMPLEMENTATION]
-        assert any(g.name == "NonExistentClass" for g in missing)
-
-
-def test_private_symbols_skipped():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/app.py": "def _internal():\n    pass\ndef public():\n    pass\n",
-            "README.md": "# App\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        undocumented_names = [g.name for g in report.gaps if g.gap_type == GapType.UNDOCUMENTED]
-        assert "_internal" not in undocumented_names, "Private symbols should be skipped"
-        assert "public" in undocumented_names
-
-
-def test_empty_repo():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        assert len(report.gaps) == 0
-
-
-def test_invalid_path():
-    report = KnowledgeGapIdentifier().analyze("/nonexistent/path/xyz")
-    assert len(report.gaps) == 1
-    assert report.gaps[0].severity == GapSeverity.ERROR
-
-
-def test_report_summary():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/app.py": "class MyService:\n    def handle(self):\n        pass\n",
-            "README.md": "# App\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        summary = report.summary()
-        assert "UNDOCUMENTED" in summary
-        assert "MyService" in summary
-
-
-def test_report_to_dict():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        _make_repo(tmpdir, {
-            "src/app.py": "def hello():\n    pass\n",
-            "README.md": "# App\n",
-        })
-        report = KnowledgeGapIdentifier().analyze(tmpdir)
-        d = report.to_dict()
-        assert "total_gaps" in d
-        assert "gaps" in d
-        assert isinstance(d["gaps"], list)
-        assert d["total_gaps"] > 0
-
-
-if __name__ == "__main__":
-    test_undocumented_symbol()
-    test_documented_symbol_no_gap()
-    test_untested_module()
-    test_tested_module_no_gap()
-    test_missing_implementation()
-    test_private_symbols_skipped()
-    test_empty_repo()
-    test_invalid_path()
-    test_report_summary()
-    test_report_to_dict()
-    print("All 10 tests passed.")