feat: knowledge store staleness detector (#92)

scripts/diff_analyzer.py

@@ -1,239 +0,0 @@
-"""
-Diff Analyzer — Pipeline 6.1
-
-Reads PR diffs and categorizes changes: new code, deleted code, modified code, moved code.
-Produces a change summary with line counts per category.
-
-Usage:
-    from diff_analyzer import DiffAnalyzer
-    analyzer = DiffAnalyzer()
-    summary = analyzer.analyze(diff_text)
-"""
-
-from __future__ import annotations
-
-import re
-from dataclasses import dataclass, field
-from enum import Enum
-from typing import List, Optional
-
-
-class ChangeCategory(Enum):
-    """Categories of code changes in a diff hunk."""
-    ADDED = "added"
-    DELETED = "deleted"
-    MODIFIED = "modified"
-    MOVED = "moved"
-    CONTEXT = "context"
-
-
-@dataclass
-class Hunk:
-    """A single diff hunk with metadata."""
-    header: str
-    old_start: int
-    old_count: int
-    new_start: int
-    new_count: int
-    lines: List[str] = field(default_factory=list)
-    category: ChangeCategory = ChangeCategory.CONTEXT
-    old_lines: int = 0
-    new_lines: int = 0
-
-
-@dataclass
-class FileChange:
-    """Changes within a single file."""
-    path: str
-    old_path: Optional[str] = None  # For renames
-    is_new: bool = False
-    is_deleted: bool = False
-    is_renamed: bool = False
-    hunks: List[Hunk] = field(default_factory=list)
-    added_lines: int = 0
-    deleted_lines: int = 0
-    context_lines: int = 0
-
-
-@dataclass
-class ChangeSummary:
-    """Summary of all changes in a diff."""
-    files_changed: int = 0
-    files_added: int = 0
-    files_deleted: int = 0
-    files_renamed: int = 0
-    files_modified: int = 0
-    total_added: int = 0
-    total_deleted: int = 0
-    total_context: int = 0
-    hunks_added: int = 0
-    hunks_deleted: int = 0
-    hunks_modified: int = 0
-    hunks_moved: int = 0
-    file_changes: List[FileChange] = field(default_factory=list)
-
-    def to_dict(self) -> dict:
-        """Serialize to dict for JSON output."""
-        return {
-            "files_changed": self.files_changed,
-            "files_added": self.files_added,
-            "files_deleted": self.files_deleted,
-            "files_renamed": self.files_renamed,
-            "files_modified": self.files_modified,
-            "total_added": self.total_added,
-            "total_deleted": self.total_deleted,
-            "total_context": self.total_context,
-            "hunks_added": self.hunks_added,
-            "hunks_deleted": self.hunks_deleted,
-            "hunks_modified": self.hunks_modified,
-            "hunks_moved": self.hunks_moved,
-            "files": [
-                {
-                    "path": fc.path,
-                    "old_path": fc.old_path,
-                    "is_new": fc.is_new,
-                    "is_deleted": fc.is_deleted,
-                    "is_renamed": fc.is_renamed,
-                    "added": fc.added_lines,
-                    "deleted": fc.deleted_lines,
-                    "context": fc.context_lines,
-                }
-                for fc in self.file_changes
-            ],
-        }
-
-
-# Regex for unified diff headers
-_HUNK_RE = re.compile(
-    r"^@@\s+-(\d+)(?:,(\d+))?\s+\+(\d+)(?:,(\d+))?\s+@@(.*)$"
-)
-_FILE_HEADER_RE = re.compile(r"^diff --git a/(.*) b/(.*)$")
-_RENAME_RE = re.compile(r"^rename from (.+)$|^rename to (.+)$")
-
-
-class DiffAnalyzer:
-    """Parses unified diffs and categorizes changes."""
-
-    def analyze(self, diff_text: str) -> ChangeSummary:
-        """Analyze a unified diff string and return a ChangeSummary."""
-        summary = ChangeSummary()
-        lines = diff_text.splitlines(keepends=False)
-
-        current_file: Optional[FileChange] = None
-        current_hunk: Optional[Hunk] = None
-        old_path: Optional[str] = None
-        new_path: Optional[str] = None
-
-        for line in lines:
-            # File header
-            m = _FILE_HEADER_RE.match(line)
-            if m:
-                # Save previous file
-                if current_file:
-                    self._classify_file(current_file)
-                    summary.file_changes.append(current_file)
-
-                old_path = m.group(1)
-                new_path = m.group(2)
-                current_file = FileChange(path=new_path, old_path=old_path)
-                current_hunk = None
-                continue
-
-            if current_file is None:
-                continue
-
-            # Detect new/deleted file markers
-            if line.startswith("new file mode"):
-                current_file.is_new = True
-                continue
-            if line.startswith("deleted file mode"):
-                current_file.is_deleted = True
-                continue
-
-            # Detect renames
-            rm = _RENAME_RE.match(line)
-            if rm:
-                current_file.is_renamed = True
-                continue
-
-            # Hunk header
-            hm = _HUNK_RE.match(line)
-            if hm:
-                if current_hunk:
-                    self._classify_hunk(current_hunk)
-                    current_file.hunks.append(current_hunk)
-
-                current_hunk = Hunk(
-                    header=line,
-                    old_start=int(hm.group(1)),
-                    old_count=int(hm.group(2) or 1),
-                    new_start=int(hm.group(3)),
-                    new_count=int(hm.group(4) or 1),
-                )
-                continue
-
-            if current_hunk is None:
-                continue
-
-            # Hunk content
-            current_hunk.lines.append(line)
-
-            if line.startswith("+"):
-                current_hunk.new_lines += 1
-                current_file.added_lines += 1
-            elif line.startswith("-"):
-                current_hunk.old_lines += 1
-                current_file.deleted_lines += 1
-            elif line.startswith(" "):
-                current_file.context_lines += 1
-
-        # Finalize last hunk and file
-        if current_hunk:
-            self._classify_hunk(current_hunk)
-            if current_file:
-                current_file.hunks.append(current_hunk)
-        if current_file:
-            self._classify_file(current_file)
-            summary.file_changes.append(current_file)
-
-        # Aggregate
-        summary.files_changed = len(summary.file_changes)
-        for fc in summary.file_changes:
-            summary.total_added += fc.added_lines
-            summary.total_deleted += fc.deleted_lines
-            summary.total_context += fc.context_lines
-            if fc.is_new:
-                summary.files_added += 1
-            elif fc.is_deleted:
-                summary.files_deleted += 1
-            elif fc.is_renamed:
-                summary.files_renamed += 1
-            else:
-                summary.files_modified += 1
-
-            for h in fc.hunks:
-                if h.category == ChangeCategory.ADDED:
-                    summary.hunks_added += 1
-                elif h.category == ChangeCategory.DELETED:
-                    summary.hunks_deleted += 1
-                elif h.category == ChangeCategory.MODIFIED:
-                    summary.hunks_modified += 1
-                elif h.category == ChangeCategory.MOVED:
-                    summary.hunks_moved += 1
-
-        return summary
-
-    def _classify_hunk(self, hunk: Hunk) -> None:
-        """Classify a hunk based on its add/delete ratio."""
-        if hunk.new_lines > 0 and hunk.old_lines == 0:
-            hunk.category = ChangeCategory.ADDED
-        elif hunk.old_lines > 0 and hunk.new_lines == 0:
-            hunk.category = ChangeCategory.DELETED
-        elif hunk.new_lines > 0 and hunk.old_lines > 0:
-            hunk.category = ChangeCategory.MODIFIED
-        else:
-            hunk.category = ChangeCategory.CONTEXT
-
-    def _classify_file(self, fc: FileChange) -> None:
-        """Final file classification (renames already detected via headers)."""
-        pass

scripts/knowledge_staleness_check.py

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

tests/test_diff_analyzer.py

@@ -1,224 +0,0 @@
-"""Tests for diff_analyzer module."""
-
-import sys
-import os
-sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'scripts'))
-
-from diff_analyzer import DiffAnalyzer, ChangeCategory
-
-
-def test_parse_simple_addition():
-    diff = """diff --git a/foo.py b/foo.py
-new file mode 100644
---- /dev/null
-+++ b/foo.py
-@@ -0,0 +1,3 @@
-+def hello():
-+    return "world"
-+# end
-"""
-    analyzer = DiffAnalyzer()
-    summary = analyzer.analyze(diff)
-
-    assert summary.files_changed == 1
-    assert summary.files_added == 1
-    assert summary.files_modified == 0
-    assert summary.total_added == 3
-    assert summary.total_deleted == 0
-    assert summary.hunks_added == 1
-    assert len(summary.file_changes) == 1
-    assert summary.file_changes[0].is_new is True
-    assert summary.file_changes[0].path == "foo.py"
-
-
-def test_parse_simple_deletion():
-    diff = """diff --git a/old.py b/old.py
-deleted file mode 100644
---- a/old.py
-+++ /dev/null
-@@ -1,2 +0,0 @@
--x = 1
--y = 2
-"""
-    analyzer = DiffAnalyzer()
-    summary = analyzer.analyze(diff)
-
-    assert summary.files_changed == 1
-    assert summary.files_deleted == 1
-    assert summary.total_deleted == 2
-    assert summary.total_added == 0
-    assert summary.hunks_deleted == 1
-    assert summary.file_changes[0].is_deleted is True
-
-
-def test_parse_modification():
-    diff = """diff --git a/bar.py b/bar.py
---- a/bar.py
-+++ b/bar.py
-@@ -10,3 +10,4 @@ def foo():
-     existing()
--    old_call()
-+    new_call()
-+    extra_step()
-     return
-"""
-    analyzer = DiffAnalyzer()
-    summary = analyzer.analyze(diff)
-
-    assert summary.files_changed == 1
-    assert summary.files_modified == 1
-    assert summary.total_added == 2   # +new_call(), +extra_step()
-    assert summary.total_deleted == 1  # -old_call()
-    assert summary.total_context == 2  # 2 context lines
-    assert summary.hunks_modified == 1
-
-
-def test_parse_multiple_files():
-    diff = """diff --git a/a.py b/a.py
---- a/a.py
-+++ b/a.py
-@@ -1,1 +1,2 @@
- existing
-+added
-diff --git a/b.py b/b.py
-new file mode 100644
---- /dev/null
-+++ b/b.py
-@@ -0,0 +1,1 @@
-+new file
-diff --git a/c.py b/c.py
-deleted file mode 100644
---- a/c.py
-+++ /dev/null
-@@ -1,1 +0,0 @@
--gone
-"""
-    analyzer = DiffAnalyzer()
-    summary = analyzer.analyze(diff)
-
-    assert summary.files_changed == 3
-    assert summary.files_added == 1
-    assert summary.files_deleted == 1
-    assert summary.files_modified == 1
-    assert summary.total_added == 2
-    assert summary.total_deleted == 1
-
-
-def test_parse_rename():
-    diff = """diff --git a/old_name.py b/new_name.py
-rename from old_name.py
-rename to new_name.py
---- a/old_name.py
-+++ b/new_name.py
-@@ -1,1 +1,1 @@
--old_func()
-+new_func()
-"""
-    analyzer = DiffAnalyzer()
-    summary = analyzer.analyze(diff)
-
-    assert summary.files_changed == 1
-    assert summary.files_renamed == 1
-    assert summary.file_changes[0].is_renamed is True
-    assert summary.file_changes[0].old_path == "old_name.py"
-    assert summary.file_changes[0].path == "new_name.py"
-
-
-def test_parse_mixed_hunks():
-    """A file with one add hunk and one delete hunk."""
-    diff = """diff --git a/mixed.py b/mixed.py
---- a/mixed.py
-+++ b/mixed.py
-@@ -5,0 +6,2 @@
-+new_line_1
-+new_line_2
-@@ -20,2 +22,0 @@
--removed_1
--removed_2
-"""
-    analyzer = DiffAnalyzer()
-    summary = analyzer.analyze(diff)
-
-    assert summary.files_changed == 1
-    assert summary.hunks_added == 1
-    assert summary.hunks_deleted == 1
-    assert summary.total_added == 2
-    assert summary.total_deleted == 2
-
-
-def test_empty_diff():
-    analyzer = DiffAnalyzer()
-    summary = analyzer.analyze("")
-
-    assert summary.files_changed == 0
-    assert summary.total_added == 0
-    assert summary.total_deleted == 0
-
-
-def test_to_dict():
-    diff = """diff --git a/test.py b/test.py
-new file mode 100644
---- /dev/null
-+++ b/test.py
-@@ -0,0 +1,2 @@
-+line1
-+line2
-"""
-    analyzer = DiffAnalyzer()
-    summary = analyzer.analyze(diff)
-    d = summary.to_dict()
-
-    assert d["files_changed"] == 1
-    assert d["files_added"] == 1
-    assert d["total_added"] == 2
-    assert d["total_deleted"] == 0
-    assert len(d["files"]) == 1
-    assert d["files"][0]["path"] == "test.py"
-    assert d["files"][0]["is_new"] is True
-
-
-def test_context_only_hunk():
-    """A hunk with only context lines (rare but possible)."""
-    diff = """diff --git a/noop.py b/noop.py
---- a/noop.py
-+++ b/noop.py
-@@ -5,3 +5,3 @@
- context1
- context2
- context3
-"""
-    analyzer = DiffAnalyzer()
-    summary = analyzer.analyze(diff)
-
-    assert summary.total_context == 3
-    assert summary.total_added == 0
-    assert summary.total_deleted == 0
-
-
-def test_binary_files_skipped():
-    """Binary file diffs have no content lines — just headers."""
-    diff = """diff --git a/image.png b/image.png
---- a/image.png
-+++ b/image.png
-Binary files a/image.png and b/image.png differ
-"""
-    analyzer = DiffAnalyzer()
-    summary = analyzer.analyze(diff)
-
-    assert summary.files_changed == 1
-    assert summary.total_added == 0
-    assert summary.total_deleted == 0
-
-
-if __name__ == "__main__":
-    test_parse_simple_addition()
-    test_parse_simple_deletion()
-    test_parse_modification()
-    test_parse_multiple_files()
-    test_parse_rename()
-    test_parse_mixed_hunks()
-    test_empty_diff()
-    test_to_dict()
-    test_context_only_hunk()
-    test_binary_files_skipped()
-    print("All 10 tests passed.")