feat: add diff analyzer for PR change categorization (closes #118)

GENOME.md

@@ -1,239 +0,0 @@
-# GENOME.md — compounding-intelligence
-
-*Auto-generated codebase genome. See timmy-home#676.*
-
----
-
-## Project Overview
-
-**What:** A system that turns 1B+ daily agent tokens into durable, compounding fleet intelligence.
-
-**Why:** Every agent session starts at zero. The same mistakes get made repeatedly — the same HTTP 405 is rediscovered as a branch protection issue, the same token path is searched for from scratch. Intelligence evaporates when the session ends.
-
-**How:** Three pipelines form a compounding loop:
-
-```
-SESSION ENDS → HARVESTER → KNOWLEDGE STORE → BOOTSTRAPPER → NEW SESSION STARTS SMARTER
-                              ↓
-                         MEASURER → Prove it's working
-```
-
-**Status:** Early stage. Template and test scaffolding exist. Core pipeline scripts (harvester.py, bootstrapper.py, measurer.py, session_reader.py) are planned but not yet implemented. The knowledge extraction prompt is complete and validated.
-
----
-
-## Architecture
-
-```mermaid
-graph TD
-    A[Session Transcript<br/>.jsonl] --> B[Harvester]
-    B --> C{Extract Knowledge}
-    C --> D[knowledge/index.json]
-    C --> E[knowledge/global/*.md]
-    C --> F[knowledge/repos/{repo}.md]
-    C --> G[knowledge/agents/{agent}.md]
-    D --> H[Bootstrapper]
-    H --> I[Bootstrap Context<br/>2k token injection]
-    I --> J[New Session<br/>starts smarter]
-    J --> A
-    D --> K[Measurer]
-    K --> L[metrics/dashboard.md]
-    K --> M[Velocity / Hit Rate<br/>Error Reduction]
-```
-
-### Pipeline 1: Harvester
-
-**Status:** Prompt designed. Script not implemented.
-
-Reads finished session transcripts (JSONL). Uses `templates/harvest-prompt.md` to extract durable knowledge into five categories:
-
-| Category | Description | Example |
-|----------|-------------|---------|
-| `fact` | Concrete, verifiable information | "Repository X has 5 files" |
-| `pitfall` | Errors encountered, wrong assumptions | "Token is at ~/.config/gitea/token, not env var" |
-| `pattern` | Successful action sequences | "Deploy: test → build → push → webhook" |
-| `tool-quirk` | Environment-specific behaviors | "URL format requires trailing slash" |
-| `question` | Identified but unanswered | "Need optimal batch size for harvesting" |
-
-Output schema per knowledge item:
-```json
-{
-  "fact": "One sentence description",
-  "category": "fact|pitfall|pattern|tool-quirk|question",
-  "repo": "repo-name or 'global'",
-  "confidence": 0.0-1.0
-}
-```
-
-### Pipeline 2: Bootstrapper
-
-**Status:** Not implemented.
-
-Queries knowledge store before session start. Assembles a compact 2k-token context from relevant facts. Injects into session startup so the agent begins with full situational awareness.
-
-### Pipeline 3: Measurer
-
-**Status:** Not implemented.
-
-Tracks compounding metrics: knowledge velocity (facts/day), error reduction (%), hit rate (knowledge used / knowledge available), task completion improvement.
-
----
-
-## Directory Structure
-
-```
-compounding-intelligence/
-├── README.md                           # Project overview and architecture
-├── GENOME.md                           # This file (codebase genome)
-├── knowledge/                          # [PLANNED] Knowledge store
-│   ├── index.json                      # Machine-readable fact index
-│   ├── global/                         # Cross-repo knowledge
-│   ├── repos/{repo}.md                 # Per-repo knowledge
-│   └── agents/{agent}.md               # Agent-type notes
-├── scripts/
-│   ├── test_harvest_prompt.py          # Basic prompt validation (2.5KB)
-│   └── test_harvest_prompt_comprehensive.py  # Full prompt structure test (6.8KB)
-├── templates/
-│   └── harvest-prompt.md               # Knowledge extraction prompt (3.5KB)
-├── test_sessions/
-│   ├── session_success.jsonl           # Happy path test data
-│   ├── session_failure.jsonl           # Failure path test data
-│   ├── session_partial.jsonl           # Incomplete session test data
-│   ├── session_patterns.jsonl          # Pattern extraction test data
-│   └── session_questions.jsonl         # Question identification test data
-└── metrics/                            # [PLANNED] Compounding metrics
-    └── dashboard.md
-```
-
----
-
-## Entry Points and Data Flow
-
-### Entry Point 1: Knowledge Extraction (Harvester)
-
-```
-Input:  Session transcript (JSONL)
-        ↓
-        templates/harvest-prompt.md (LLM prompt)
-        ↓
-        Knowledge items (JSON array)
-        ↓
-Output: knowledge/index.json + per-repo/per-agent markdown files
-```
-
-### Entry Point 2: Session Bootstrap (Bootstrapper)
-
-```
-Input:  Session context (repo, agent type, task type)
-        ↓
-        knowledge/index.json (query relevant facts)
-        ↓
-        2k-token bootstrap context
-        ↓
-Output: Injected into session startup
-```
-
-### Entry Point 3: Measurement (Measurer)
-
-```
-Input:  knowledge/index.json + session history
-        ↓
-        Velocity, hit rate, error reduction calculations
-        ↓
-Output: metrics/dashboard.md
-```
-
----
-
-## Key Abstractions
-
-### Knowledge Item
-The atomic unit. One sentence, one category, one confidence score. Designed to be small enough that 1000 items fit in a 2k-token bootstrap context.
-
-### Knowledge Store
-A directory structure that mirrors the fleet's mental model:
-- `global/` — knowledge that applies everywhere (tool quirks, environment facts)
-- `repos/` — knowledge specific to each repo
-- `agents/` — knowledge specific to each agent type
-
-### Confidence Score
-0.0–1.0 scale. Defines how certain the harvester is about each extracted fact:
-- 0.9–1.0: Explicitly stated with verification
-- 0.7–0.8: Clearly implied by multiple data points
-- 0.5–0.6: Suggested but not fully verified
-- 0.3–0.4: Inferred from limited data
-- 0.1–0.2: Speculative or uncertain
-
-### Bootstrap Context
-The 2k-token injection that a new session receives. Assembled from the most relevant knowledge items for the current task, filtered by confidence > 0.7, deduplicated, and compressed.
-
----
-
-## API Surface
-
-### Internal (scripts not yet implemented)
-
-| Script | Input | Output | Status |
-|--------|-------|--------|--------|
-| `harvester.py` | Session JSONL path | Knowledge items JSON | PLANNED |
-| `bootstrapper.py` | Repo + agent type | 2k-token context string | PLANNED |
-| `measurer.py` | Knowledge store path | Metrics JSON | PLANNED |
-| `session_reader.py` | Session JSONL path | Parsed transcript | PLANNED |
-
-### Prompt (templates/harvest-prompt.md)
-
-The extraction prompt is the core "API." It takes a session transcript and returns structured JSON. It defines:
-- Five extraction categories
-- Output format (JSON array of knowledge items)
-- Confidence scoring rubric
-- Constraints (no hallucination, specificity, relevance, brevity)
-- Example input/output pair
-
----
-
-## Test Coverage
-
-### What Exists
-
-| File | Tests | Coverage |
-|------|-------|----------|
-| `scripts/test_harvest_prompt.py` | 2 tests | Prompt file existence, sample transcript |
-| `scripts/test_harvest_prompt_comprehensive.py` | 5 tests | Prompt structure, categories, fields, confidence scoring, size limits |
-| `test_sessions/*.jsonl` | 5 sessions | Success, failure, partial, patterns, questions |
-
-### What's Missing
-
-1. **Harvester integration test** — Does the prompt actually extract correct knowledge from real transcripts?
-2. **Bootstrapper test** — Does it assemble relevant context correctly?
-3. **Knowledge store test** — Does the index.json maintain consistency?
-4. **Confidence calibration test** — Do high-confidence facts actually prove true in later sessions?
-5. **Deduplication test** — Are duplicate facts across sessions handled?
-6. **Staleness test** — How does the system handle outdated knowledge?
-
----
-
-## Security Considerations
-
-1. **No secrets in knowledge store** — The harvester must filter out API keys, tokens, and credentials from extracted facts. The prompt constraints mention this but there is no automated guard.
-
-2. **Knowledge poisoning** — A malicious or corrupted session could inject false facts. Confidence scoring partially mitigates this, but there is no verification step.
-
-3. **Access control** — The knowledge store has no access control. Any process that can read the directory can read all facts. In a multi-tenant setup, this is a concern.
-
-4. **Transcript privacy** — Session transcripts may contain user data. The harvester must not extract personally identifiable information into the knowledge store.
-
----
-
-## The 100x Path (from README)
-
-```
-Month 1:  15,000 facts, sessions 20% faster
-Month 2:  45,000 facts, sessions 40% faster, first-try success up 30%
-Month 3:  90,000 facts, fleet measurably smarter per token
-```
-
-Each new session is better than the last. The intelligence compounds.
-
----
-
-*Generated by codebase-genome pipeline. Ref: timmy-home#676.*

scripts/diff_analyzer.py

@@ -0,0 +1,239 @@
+"""
+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

tests/test_diff_analyzer.py

@@ -0,0 +1,224 @@
+"""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.")