From 9f7931a1f9591ffde050c9e80976306c802d2183 Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Thu, 9 Apr 2026 22:56:00 +0800
Subject: [PATCH 01/15] docs: add /understand-knowledge design spec for
 personal knowledge base plugin

New skill that takes markdown knowledge bases (Obsidian, Logseq, Dendron, Foam,
Karpathy-style, Zettelkasten, plain) and produces interactive knowledge graphs
with typed nodes/edges, auto-format detection, and dashboard visualization.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../2026-04-09-understand-knowledge-design.md | 335 ++++++++++++++++++
 1 file changed, 335 insertions(+)
 create mode 100644 docs/superpowers/specs/2026-04-09-understand-knowledge-design.md

diff --git a/docs/superpowers/specs/2026-04-09-understand-knowledge-design.md b/docs/superpowers/specs/2026-04-09-understand-knowledge-design.md
new file mode 100644
index 0000000..2c63252
--- /dev/null
+++ b/docs/superpowers/specs/2026-04-09-understand-knowledge-design.md
@@ -0,0 +1,335 @@
+# /understand-knowledge — Personal Knowledge Base Plugin Design
+
+## Overview
+
+A new `/understand-knowledge` skill within the existing Understand Anything plugin that takes any folder of markdown notes and produces an interactive knowledge graph visualized in the existing dashboard.
+
+Inspired by Andrej Karpathy's LLM Wiki pattern — where an LLM compiles and maintains a structured wiki from raw sources — this plugin goes further by adding typed relationship discovery and interactive graph visualization that tools like Obsidian and Logseq cannot provide.
+
+### Goals
+
+- Accept any markdown-based knowledge base (Obsidian vault, Logseq graph, Dendron workspace, Foam, Karpathy-style LLM wiki, Zettelkasten, or plain markdown)
+- Auto-detect the format and adapt parsing accordingly
+- Use LLM analysis to discover implicit relationships beyond explicit links
+- Produce a knowledge graph with typed nodes and edges
+- Visualize in the existing dashboard with knowledge-specific layout, sidebar, and reading mode
+
+### Non-Goals
+
+- Real-time sync with the knowledge base tool (Obsidian, Logseq, etc.)
+- Replacing the user's existing PKM tool — this is a visualization/analysis layer on top
+- Supporting non-markdown formats (PDFs, bookmarks) in v1
+
+---
+
+## Schema Extensions
+
+### New Node Types (5)
+
+Added to the existing `NodeType` union (currently 16 types):
+
+```typescript
+export type NodeType =
+  // existing (16)
+  | "file" | "function" | "class" | "module" | "concept"
+  | "config" | "document" | "service" | "table" | "endpoint"
+  | "pipeline" | "schema" | "resource"
+  | "domain" | "flow" | "step"
+  // knowledge (5 new → 21 total)
+  | "article" | "entity" | "topic" | "claim" | "source";
+```
+
+| Type | What it represents | Example |
+|------|-------------------|---------|
+| `article` | A wiki/note page — the primary content unit | "LLM Knowledge Bases.md" |
+| `entity` | A named thing: person, tool, paper, org, project | "Andrej Karpathy", "Obsidian" |
+| `topic` | A thematic cluster grouping related articles | "Personal Knowledge Management" |
+| `claim` | A specific assertion, insight, or takeaway | "RAG loses context at chunk boundaries" |
+| `source` | Raw/reference material that articles are compiled from | A paper URL, a raw PDF reference |
+
+### New Edge Types (6)
+
+Added to the existing `EdgeType` union (currently 29 types):
+
+```typescript
+export type EdgeType =
+  // existing (29)
+  | ...
+  // knowledge (6 new → 35 total)
+  | "cites" | "contradicts" | "builds_on"
+  | "exemplifies" | "categorized_under" | "authored_by";
+```
+
+| Type | Direction | Meaning |
+|------|-----------|---------|
+| `cites` | article → source | References or draws from |
+| `contradicts` | claim → claim | Conflicts or disagrees with |
+| `builds_on` | article → article | Extends, refines, or deepens |
+| `exemplifies` | entity → concept/topic | Is a concrete example of |
+| `categorized_under` | article/entity → topic | Belongs to this theme |
+| `authored_by` | article → entity | Written or created by |
+
+### New Metadata Interface
+
+```typescript
+export interface KnowledgeMeta {
+  format?: "obsidian" | "logseq" | "dendron" | "foam" | "karpathy" | "zettelkasten" | "plain";
+  wikilinks?: string[];
+  backlinks?: string[];
+  frontmatter?: Record<string, unknown>;
+  sourceUrl?: string;
+  confidence?: number; // 0-1, for LLM-inferred relationships
+}
+```
+
+Added as an optional field on `GraphNode`:
+
+```typescript
+export interface GraphNode {
+  // ...existing fields
+  knowledgeMeta?: KnowledgeMeta;
+}
+```
+
+### Graph-Level Kind Flag
+
+```typescript
+export interface KnowledgeGraph {
+  version: string;
+  kind: "codebase" | "knowledge"; // NEW
+  project: ProjectMeta;
+  nodes: GraphNode[];
+  edges: GraphEdge[];
+  layers: Layer[];
+  tour: TourStep[];
+}
+```
+
+The `kind` field tells the dashboard which layout, sidebar, and visual styling to use. For backward compatibility, graphs without a `kind` field default to `"codebase"`.
+
+---
+
+## Format Detection & Format Guides
+
+### Auto-Detection Logic
+
+Scans the target directory for signature files/patterns. Priority order (first match wins):
+
+| Priority | Signal | Detected Format |
+|----------|--------|----------------|
+| 1 | `.obsidian/` directory | Obsidian |
+| 2 | `logseq/` + `pages/` directories | Logseq |
+| 3 | `.dendron.yml` or `*.schema.yml` | Dendron |
+| 4 | `.foam/` or `.vscode/foam.json` | Foam |
+| 5 | `raw/` + `wiki/` + `index.md` | Karpathy |
+| 6 | `[[wikilinks]]` + unique ID prefixes in filenames | Zettelkasten |
+| 7 | Fallback | Plain markdown |
+
+### Format Guides
+
+Located at `skills/understand-knowledge/formats/`. Each guide tells the LLM agents how to parse that format:
+
+```
+skills/understand-knowledge/
+  SKILL.md
+  formats/
+    obsidian.md        — [[wikilinks]], [[note|alias]], [[note#heading]],
+                         #tags, YAML frontmatter, .obsidian/ config,
+                         dataview annotations, canvas files
+    logseq.md          — block-based outliner, ((block-refs)),
+                         journals/YYYY_MM_DD.md, pages/,
+                         property:: value syntax, TODO/DONE states
+    dendron.md         — dot-delimited hierarchy (a.b.c.md),
+                         .schema.yml for structure validation,
+                         cross-vault links, refactoring rules
+    foam.md            — [[wikilinks]] + link reference definitions
+                         at file bottom, .foam/config, placeholder links
+    karpathy.md        — raw/ → wiki/ pipeline, index.md master map,
+                         log.md append-only record, _meta/ state,
+                         LLM-maintained cross-references
+    zettelkasten.md    — atomic notes, unique ID prefixes (timestamps),
+                         typed semantic links, one idea per note
+    plain.md           — standard [markdown](links), folder hierarchy,
+                         heading structure, no special conventions
+```
+
+Each format guide covers:
+- How to parse links (wikilinks vs standard vs block refs)
+- Where metadata lives (frontmatter vs inline properties vs block properties)
+- What the folder structure means (journals/ = daily notes, pages/ = permanent notes)
+- What conventions to respect vs what to infer
+
+### Format Guide Authoring Process
+
+Format guides must be research-backed. During implementation, the agent building each format guide must:
+1. Read the official documentation for that format (Obsidian Help, Logseq docs, Dendron wiki, Foam docs, etc.)
+2. Study real-world examples of that format's structure
+3. Write the guide based on verified behavior, not assumptions
+
+---
+
+## Agent Pipeline
+
+```
+knowledge-scanner → format-detector → article-analyzer → relationship-builder → graph-reviewer
+```
+
+### Agent Definitions
+
+| Agent | Input | Output | Model |
+|-------|-------|--------|-------|
+| `knowledge-scanner` | Target directory path | File manifest: all `.md` files with paths, sizes, first 20 lines preview | `inherit` |
+| `format-detector` | File manifest + directory structure | Detected format + format-specific parsing hints | `inherit` |
+| `article-analyzer` | Individual `.md` file + format guide | Per-file nodes (article, entities, claims) + explicit edges (wikilinks, tags) | `inherit` |
+| `relationship-builder` | All per-file results | Cross-file implicit edges (builds_on, contradicts, categorized_under) + topic clustering + layers | `inherit` |
+| `graph-reviewer` | Assembled graph | Validated graph — deduped entities, consistent edge weights, orphan detection | `inherit` |
+
+### Key Differences from Codebase Pipeline
+
+- **No tree-sitter** — markdown parsing is simpler, mostly regex + LLM interpretation
+- **format-detector** replaces framework detection — picks the right format guide
+- **article-analyzer** replaces file-analyzer — extracts knowledge concepts instead of code structure
+- **relationship-builder** is the heavy LLM step — discovers implicit connections across files that explicit links miss
+- **graph-reviewer** stays similar — validates the assembled graph for consistency
+
+### Intermediate Files
+
+Same pattern as codebase analysis:
+
+```
+.understand-anything/intermediate/
+  knowledge-manifest.json      — scanner output
+  format-detection.json        — detected format + hints
+  article-*.json               — per-file analysis
+  relationships.json           — cross-file edges
+  knowledge-graph.json         — final assembled graph
+```
+
+Intermediate files are cleaned up after graph assembly (same as codebase flow).
+
+### Incremental Mode (`--ingest`)
+
+When the user runs `/understand-knowledge --ingest path/to/new-source.md`:
+
+1. **knowledge-scanner** — runs on just the new file(s)
+2. **format-detector** — skipped (format already known from initial scan)
+3. **article-analyzer** — processes only new/changed files
+4. **relationship-builder** — runs on new nodes against the existing graph, finds connections to what's already there
+5. **graph-reviewer** — validates the merged result
+
+Existing nodes are preserved; only new nodes/edges are added or updated.
+
+---
+
+## Dashboard Changes
+
+All changes are scoped to graphs with `"kind": "knowledge"`.
+
+### Vertical Flow Layout
+
+- Default to top-down vertical layout (like existing domain/business flow view)
+- Topics at top → articles in middle → entities/claims/sources at bottom
+- Reads like a knowledge hierarchy: broad themes flow down into specifics
+- User can still switch to horizontal or force-directed layout via controls
+
+### Knowledge Sidebar
+
+Replaces NodeInfo when a knowledge graph is loaded:
+
+| Selection | Sidebar Shows |
+|-----------|---------------|
+| Nothing selected | ProjectOverview: format detected, total articles/entities/topics/claims/sources |
+| Article node | Title, summary, tags, frontmatter metadata, backlinks list (clickable), outgoing links, related topics |
+| Entity node | Name, type (person/tool/paper/org), articles that mention it, relationships to other entities |
+| Topic node | Description, child articles, child entities, cross-topic connections |
+| Claim node | Assertion text, supporting articles, contradicting claims (if any), confidence score |
+| Source node | Original URL/path, articles that cite it, ingestion date |
+
+### Reading Mode
+
+- Clicking an article node triggers a reading panel that slides up from the bottom (same pattern as current code viewer overlay)
+- Shows the full compiled markdown rendered as HTML
+- Includes a mini backlinks sidebar within the panel
+- Clicking a `[[wikilink]]` or entity reference in the reading panel navigates the graph to that node
+
+### Node Visual Styling
+
+| Node Type | Shape | Color Accent |
+|-----------|-------|-------------|
+| `article` | Rounded rectangle | Warm amber |
+| `entity` | Circle | Soft blue |
+| `topic` | Large rounded rectangle | Muted gold |
+| `claim` | Diamond | Green/red depending on contradictions |
+| `source` | Small square | Gray |
+
+### Edge Visual Styling
+
+| Edge Type | Style |
+|-----------|-------|
+| `cites` | Dashed line |
+| `contradicts` | Red line |
+| `builds_on` | Solid with arrow |
+| `categorized_under` | Thin gray |
+| `authored_by` | Dotted blue |
+| `exemplifies` | Dotted green |
+
+---
+
+## Skill Interface
+
+### Usage
+
+```bash
+# Full scan — first time or rescan
+/understand-knowledge
+
+# Point at a specific directory
+/understand-knowledge path/to/my-notes
+
+# Incremental ingest — add new sources to existing graph
+/understand-knowledge --ingest path/to/new-note.md
+/understand-knowledge --ingest path/to/new-folder/
+```
+
+### Behavior
+
+1. Auto-detects format (Obsidian, Logseq, Karpathy, etc.)
+2. Announces: "Detected Obsidian vault with 342 notes. Scanning..."
+3. Runs the agent pipeline (scanner → detector → analyzer → relationship-builder → reviewer)
+4. Writes `knowledge-graph.json` to `.understand-anything/` with `"kind": "knowledge"`
+5. Auto-triggers `/understand-dashboard` after completion
+
+### File Structure
+
+```
+skills/understand-knowledge/
+  SKILL.md                     — skill entry point, orchestration logic
+  formats/
+    obsidian.md
+    logseq.md
+    dendron.md
+    foam.md
+    karpathy.md
+    zettelkasten.md
+    plain.md
+```
+
+### Coexistence with `/understand`
+
+- `/understand` produces `"kind": "codebase"` graphs
+- `/understand-knowledge` produces `"kind": "knowledge"` graphs
+- Both write to `.understand-anything/knowledge-graph.json`
+- Running one replaces the other
+- To scope knowledge analysis to a subdirectory (e.g., `docs/` within a code repo), use `/understand-knowledge path/to/docs`
+
+---
+
+## What This Enables That Nothing Else Does
+
+| Existing Tools | Limitation | Our Advantage |
+|---------------|-----------|---------------|
+| Obsidian graph view | Untyped edges — all links look the same | Typed edges: cites, contradicts, builds_on |
+| Logseq graph | Only shows explicit links | LLM discovers implicit relationships |
+| All PKM tools | Single-format only | Cross-format support with auto-detection |
+| Karpathy LLM Wiki | Flat text wiki, no visualization | Interactive graph dashboard with guided tours |
+| None | No knowledge graph tours | Tour mode walks through a knowledge base step by step |

From 7c999602bf0916e595fadcffceff98eb88ad65cf Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Thu, 9 Apr 2026 23:06:32 +0800
Subject: [PATCH 02/15] docs: add /understand-knowledge implementation plan (14
 tasks)

Detailed step-by-step plan covering core type extensions, schema validation,
dashboard changes (CSS, store, sidebar, reading panel, edge styling, layout),
agent definitions, format guides, and skill definition.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../plans/2026-04-09-understand-knowledge.md  | 1740 +++++++++++++++++
 1 file changed, 1740 insertions(+)
 create mode 100644 docs/superpowers/plans/2026-04-09-understand-knowledge.md

diff --git a/docs/superpowers/plans/2026-04-09-understand-knowledge.md b/docs/superpowers/plans/2026-04-09-understand-knowledge.md
new file mode 100644
index 0000000..4c0635f
--- /dev/null
+++ b/docs/superpowers/plans/2026-04-09-understand-knowledge.md
@@ -0,0 +1,1740 @@
+# /understand-knowledge Implementation Plan
+
+> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.
+
+**Goal:** Add a `/understand-knowledge` skill that takes any folder of markdown notes (Obsidian, Logseq, Dendron, Foam, Karpathy-style, Zettelkasten, or plain) and produces an interactive knowledge graph with typed nodes, edges, and dashboard visualization.
+
+**Architecture:** Extends the existing schema with 5 knowledge node types and 6 knowledge edge types. A new 5-agent pipeline (knowledge-scanner → format-detector → article-analyzer → relationship-builder → graph-reviewer) processes markdown files. The dashboard renders knowledge graphs with vertical layout, a knowledge-specific sidebar, and a reading mode panel — all driven by a new `kind` field on the root graph object.
+
+**Tech Stack:** TypeScript, Zod (schema validation), React + ReactFlow (dashboard), dagre (layout), TailwindCSS v4, Vitest (testing)
+
+**Spec:** `docs/superpowers/specs/2026-04-09-understand-knowledge-design.md`
+
+---
+
+## File Structure
+
+### Core package changes
+- Modify: `understand-anything-plugin/packages/core/src/types.ts` — add 5 node types, 6 edge types, `KnowledgeMeta` interface, `kind` field
+- Modify: `understand-anything-plugin/packages/core/src/schema.ts` — add new types to Zod schemas, add aliases
+- Modify: `understand-anything-plugin/packages/core/src/types.test.ts` — add tests for new types
+- Test: `understand-anything-plugin/packages/core/src/__tests__/knowledge-schema.test.ts` — validation tests for knowledge-specific schema
+
+### Dashboard changes
+- Modify: `understand-anything-plugin/packages/dashboard/src/store.ts` — add knowledge node types, edge categories, `ViewMode`, node categories
+- Modify: `understand-anything-plugin/packages/dashboard/src/components/CustomNode.tsx` — add colors for 5 new node types
+- Modify: `understand-anything-plugin/packages/dashboard/src/components/NodeInfo.tsx` — add badge colors and edge labels for new types, add knowledge sidebar sections
+- Modify: `understand-anything-plugin/packages/dashboard/src/components/ProjectOverview.tsx` — add knowledge-specific stats
+- Modify: `understand-anything-plugin/packages/dashboard/src/index.css` — add CSS variables for 5 new node colors
+- Modify: `understand-anything-plugin/packages/dashboard/src/App.tsx` — detect `kind` field, set view mode
+- Create: `understand-anything-plugin/packages/dashboard/src/components/KnowledgeInfo.tsx` — knowledge-specific sidebar
+- Create: `understand-anything-plugin/packages/dashboard/src/components/ReadingPanel.tsx` — full article reading overlay
+
+### Skill & agent definitions
+- Create: `understand-anything-plugin/skills/understand-knowledge/SKILL.md` — skill entry point
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/obsidian.md`
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/logseq.md`
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/dendron.md`
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/foam.md`
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/karpathy.md`
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/zettelkasten.md`
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/plain.md`
+- Create: `understand-anything-plugin/agents/knowledge-scanner.md`
+- Create: `understand-anything-plugin/agents/format-detector.md`
+- Create: `understand-anything-plugin/agents/article-analyzer.md`
+- Create: `understand-anything-plugin/agents/relationship-builder.md`
+
+Existing `graph-reviewer.md` agent is reused for the final validation step.
+
+---
+
+## Task 1: Extend Core Types
+
+**Files:**
+- Modify: `understand-anything-plugin/packages/core/src/types.ts`
+
+- [ ] **Step 1: Add knowledge node types to NodeType union**
+
+In `understand-anything-plugin/packages/core/src/types.ts`, add the 5 knowledge types after the domain types:
+
+```typescript
+// Node types (21 total: 5 code + 8 non-code + 3 domain + 5 knowledge)
+export type NodeType =
+  | "file" | "function" | "class" | "module" | "concept"
+  | "config" | "document" | "service" | "table" | "endpoint"
+  | "pipeline" | "schema" | "resource"
+  | "domain" | "flow" | "step"
+  | "article" | "entity" | "topic" | "claim" | "source";
+```
+
+- [ ] **Step 2: Add knowledge edge types to EdgeType union**
+
+```typescript
+// Edge types (35 total in 8 categories)
+export type EdgeType =
+  | "imports" | "exports" | "contains" | "inherits" | "implements"
+  | "calls" | "subscribes" | "publishes" | "middleware"
+  | "reads_from" | "writes_to" | "transforms" | "validates"
+  | "depends_on" | "tested_by" | "configures"
+  | "related" | "similar_to"
+  | "deploys" | "serves" | "provisions" | "triggers"
+  | "migrates" | "documents" | "routes" | "defines_schema"
+  | "contains_flow" | "flow_step" | "cross_domain"
+  | "cites" | "contradicts" | "builds_on" | "exemplifies" | "categorized_under" | "authored_by";
+```
+
+- [ ] **Step 3: Add KnowledgeMeta interface**
+
+Add after the `DomainMeta` interface:
+
+```typescript
+// Optional knowledge metadata for article/entity/topic/claim/source nodes
+export interface KnowledgeMeta {
+  format?: "obsidian" | "logseq" | "dendron" | "foam" | "karpathy" | "zettelkasten" | "plain";
+  wikilinks?: string[];
+  backlinks?: string[];
+  frontmatter?: Record<string, unknown>;
+  sourceUrl?: string;
+  confidence?: number; // 0-1, for LLM-inferred relationships
+}
+```
+
+- [ ] **Step 4: Add knowledgeMeta to GraphNode**
+
+```typescript
+export interface GraphNode {
+  id: string;
+  type: NodeType;
+  name: string;
+  filePath?: string;
+  lineRange?: [number, number];
+  summary: string;
+  tags: string[];
+  complexity: "simple" | "moderate" | "complex";
+  languageNotes?: string;
+  domainMeta?: DomainMeta;
+  knowledgeMeta?: KnowledgeMeta;
+}
+```
+
+- [ ] **Step 5: Add kind field to KnowledgeGraph**
+
+```typescript
+export interface KnowledgeGraph {
+  version: string;
+  kind?: "codebase" | "knowledge"; // undefined defaults to "codebase" for backward compat
+  project: ProjectMeta;
+  nodes: GraphNode[];
+  edges: GraphEdge[];
+  layers: Layer[];
+  tour: TourStep[];
+}
+```
+
+- [ ] **Step 6: Build core and verify no type errors**
+
+Run: `pnpm --filter @understand-anything/core build`
+Expected: Clean build, no errors
+
+- [ ] **Step 7: Commit**
+
+```bash
+git add understand-anything-plugin/packages/core/src/types.ts
+git commit -m "feat(core): add knowledge node types, edge types, KnowledgeMeta, and graph kind field"
+```
+
+---
+
+## Task 2: Extend Schema Validation
+
+**Files:**
+- Modify: `understand-anything-plugin/packages/core/src/schema.ts`
+- Create: `understand-anything-plugin/packages/core/src/__tests__/knowledge-schema.test.ts`
+
+- [ ] **Step 1: Add knowledge edge types to EdgeTypeSchema**
+
+In `understand-anything-plugin/packages/core/src/schema.ts`, update the `EdgeTypeSchema` z.enum to include the 6 new types:
+
+```typescript
+export const EdgeTypeSchema = z.enum([
+  "imports", "exports", "contains", "inherits", "implements",
+  "calls", "subscribes", "publishes", "middleware",
+  "reads_from", "writes_to", "transforms", "validates",
+  "depends_on", "tested_by", "configures",
+  "related", "similar_to",
+  "deploys", "serves", "provisions", "triggers",
+  "migrates", "documents", "routes", "defines_schema",
+  "contains_flow", "flow_step", "cross_domain",
+  // Knowledge
+  "cites", "contradicts", "builds_on", "exemplifies", "categorized_under", "authored_by",
+]);
+```
+
+- [ ] **Step 2: Add knowledge node type aliases**
+
+Add to `NODE_TYPE_ALIASES`:
+
+```typescript
+  // Knowledge aliases
+  note: "article",
+  page: "article",
+  wiki_page: "article",
+  person: "entity",
+  tool: "entity",
+  paper: "entity",
+  organization: "entity",
+  org: "entity",
+  category: "topic",
+  theme: "topic",
+  tag_topic: "topic",
+  assertion: "claim",
+  insight: "claim",
+  takeaway: "claim",
+  reference: "source",
+  raw: "source",
+  citation: "source",
+```
+
+- [ ] **Step 3: Add knowledge edge type aliases**
+
+Add to `EDGE_TYPE_ALIASES`:
+
+```typescript
+  // Knowledge aliases
+  references: "cites",
+  cited_by: "cites",
+  sourced_from: "cites",
+  conflicts_with: "contradicts",
+  disagrees_with: "contradicts",
+  extends: "builds_on",  // Note: "extends" was already mapped to "inherits" — knowledge context will use builds_on via the relationship-builder agent prompt, so keep "extends" → "inherits" for code
+  refines: "builds_on",
+  deepens: "builds_on",
+  example_of: "exemplifies",
+  instance_of: "exemplifies",
+  belongs_to: "categorized_under",
+  tagged_with: "categorized_under",
+  part_of: "categorized_under",
+  written_by: "authored_by",
+  created_by: "authored_by",
+```
+
+- [ ] **Step 4: Write the failing test for knowledge graph validation**
+
+Create `understand-anything-plugin/packages/core/src/__tests__/knowledge-schema.test.ts`:
+
+```typescript
+import { describe, it, expect } from "vitest";
+import { validateGraph } from "../schema";
+import type { KnowledgeGraph } from "../types";
+
+describe("knowledge graph schema validation", () => {
+  const minimalKnowledgeGraph: KnowledgeGraph = {
+    version: "1.0",
+    kind: "knowledge",
+    project: {
+      name: "Test KB",
+      languages: [],
+      frameworks: [],
+      description: "A test knowledge base",
+      analyzedAt: new Date().toISOString(),
+      gitCommitHash: "abc123",
+    },
+    nodes: [
+      {
+        id: "article:test-note",
+        type: "article",
+        name: "Test Note",
+        summary: "A test article node",
+        tags: ["test"],
+        complexity: "simple",
+      },
+      {
+        id: "entity:karpathy",
+        type: "entity",
+        name: "Andrej Karpathy",
+        summary: "AI researcher",
+        tags: ["person", "ai"],
+        complexity: "simple",
+      },
+      {
+        id: "topic:pkm",
+        type: "topic",
+        name: "Personal Knowledge Management",
+        summary: "Tools and methods for managing personal knowledge",
+        tags: ["knowledge", "productivity"],
+        complexity: "moderate",
+      },
+    ],
+    edges: [
+      {
+        source: "article:test-note",
+        target: "entity:karpathy",
+        type: "authored_by",
+        direction: "forward",
+        weight: 0.8,
+      },
+      {
+        source: "article:test-note",
+        target: "topic:pkm",
+        type: "categorized_under",
+        direction: "forward",
+        weight: 0.7,
+      },
+    ],
+    layers: [
+      {
+        id: "layer:pkm",
+        name: "PKM",
+        description: "Personal Knowledge Management topic cluster",
+        nodeIds: ["article:test-note", "topic:pkm"],
+      },
+    ],
+    tour: [],
+  };
+
+  it("validates a minimal knowledge graph", () => {
+    const result = validateGraph(minimalKnowledgeGraph);
+    const fatals = result.issues.filter((i) => i.level === "fatal");
+    expect(fatals).toHaveLength(0);
+  });
+
+  it("accepts all knowledge node types", () => {
+    const graph = {
+      ...minimalKnowledgeGraph,
+      nodes: [
+        ...minimalKnowledgeGraph.nodes,
+        { id: "claim:rag-bad", type: "claim", name: "RAG loses context", summary: "An assertion", tags: ["claim"], complexity: "simple" },
+        { id: "source:paper1", type: "source", name: "Attention paper", summary: "A source", tags: ["paper"], complexity: "simple" },
+      ],
+    };
+    const result = validateGraph(graph);
+    const fatals = result.issues.filter((i) => i.level === "fatal");
+    expect(fatals).toHaveLength(0);
+  });
+
+  it("accepts all knowledge edge types", () => {
+    const graph = {
+      ...minimalKnowledgeGraph,
+      nodes: [
+        ...minimalKnowledgeGraph.nodes,
+        { id: "claim:c1", type: "claim", name: "Claim 1", summary: "c1", tags: [], complexity: "simple" },
+        { id: "claim:c2", type: "claim", name: "Claim 2", summary: "c2", tags: [], complexity: "simple" },
+        { id: "source:s1", type: "source", name: "Source 1", summary: "s1", tags: [], complexity: "simple" },
+        { id: "article:a2", type: "article", name: "Article 2", summary: "a2", tags: [], complexity: "simple" },
+      ],
+      edges: [
+        ...minimalKnowledgeGraph.edges,
+        { source: "article:test-note", target: "source:s1", type: "cites", direction: "forward", weight: 0.7 },
+        { source: "claim:c1", target: "claim:c2", type: "contradicts", direction: "forward", weight: 0.6 },
+        { source: "article:a2", target: "article:test-note", type: "builds_on", direction: "forward", weight: 0.7 },
+        { source: "entity:karpathy", target: "topic:pkm", type: "exemplifies", direction: "forward", weight: 0.5 },
+      ],
+    };
+    const result = validateGraph(graph);
+    const fatals = result.issues.filter((i) => i.level === "fatal");
+    expect(fatals).toHaveLength(0);
+  });
+
+  it("resolves knowledge node type aliases", () => {
+    const graph = {
+      ...minimalKnowledgeGraph,
+      nodes: [
+        { id: "note:n1", type: "note", name: "A Note", summary: "note alias", tags: [], complexity: "simple" },
+        { id: "person:p1", type: "person", name: "A Person", summary: "person alias", tags: [], complexity: "simple" },
+      ],
+      edges: [],
+      layers: [],
+    };
+    const result = validateGraph(graph);
+    const noteNode = result.graph.nodes.find((n) => n.id === "note:n1");
+    const personNode = result.graph.nodes.find((n) => n.id === "person:p1");
+    expect(noteNode?.type).toBe("article");
+    expect(personNode?.type).toBe("entity");
+  });
+
+  it("resolves knowledge edge type aliases", () => {
+    const graph = {
+      ...minimalKnowledgeGraph,
+      edges: [
+        { source: "article:test-note", target: "entity:karpathy", type: "written_by", direction: "forward", weight: 0.8 },
+      ],
+    };
+    const result = validateGraph(graph);
+    const edge = result.graph.edges.find((e) => e.source === "article:test-note" && e.target === "entity:karpathy");
+    expect(edge?.type).toBe("authored_by");
+  });
+});
+```
+
+- [ ] **Step 5: Run tests to verify they fail**
+
+Run: `pnpm --filter @understand-anything/core test -- --run src/__tests__/knowledge-schema.test.ts`
+Expected: Tests fail because EdgeTypeSchema doesn't include knowledge types yet (if schema.ts wasn't updated), or pass if Steps 1-3 were done correctly.
+
+- [ ] **Step 6: Run all core tests to verify nothing is broken**
+
+Run: `pnpm --filter @understand-anything/core test -- --run`
+Expected: All existing tests pass, new knowledge tests pass
+
+- [ ] **Step 7: Commit**
+
+```bash
+git add understand-anything-plugin/packages/core/src/schema.ts understand-anything-plugin/packages/core/src/__tests__/knowledge-schema.test.ts
+git commit -m "feat(core): add knowledge types to schema validation with aliases and tests"
+```
+
+---
+
+## Task 3: Dashboard — CSS Variables & Node Colors
+
+**Files:**
+- Modify: `understand-anything-plugin/packages/dashboard/src/index.css`
+
+- [ ] **Step 1: Add CSS variables for 5 knowledge node types**
+
+In `understand-anything-plugin/packages/dashboard/src/index.css`, add after the existing `--color-node-resource` line:
+
+```css
+  /* Knowledge node colors */
+  --color-node-article: #d4a574;   /* warm amber */
+  --color-node-entity: #7ba4c9;    /* soft blue */
+  --color-node-topic: #c9b06c;     /* muted gold */
+  --color-node-claim: #6fb07a;     /* soft green */
+  --color-node-source: #8a8a8a;    /* gray */
+```
+
+- [ ] **Step 2: Add Tailwind text-color utilities for knowledge nodes**
+
+Verify TailwindCSS v4 picks up the CSS variables automatically. If the existing pattern uses `text-node-*` classes defined elsewhere, add matching entries. Check if there's a Tailwind config or if the CSS variables are consumed directly.
+
+Look at how existing `text-node-file` etc. are defined — if they're in the CSS file as utility classes, add:
+
+```css
+  .text-node-article { color: var(--color-node-article); }
+  .text-node-entity { color: var(--color-node-entity); }
+  .text-node-topic { color: var(--color-node-topic); }
+  .text-node-claim { color: var(--color-node-claim); }
+  .text-node-source { color: var(--color-node-source); }
+```
+
+And corresponding `border-node-*` and `bg-node-*` variants if the pattern requires them.
+
+- [ ] **Step 3: Commit**
+
+```bash
+git add understand-anything-plugin/packages/dashboard/src/index.css
+git commit -m "feat(dashboard): add CSS variables and utility classes for knowledge node types"
+```
+
+---
+
+## Task 4: Dashboard — Store & Type Maps
+
+**Files:**
+- Modify: `understand-anything-plugin/packages/dashboard/src/store.ts`
+
+- [ ] **Step 1: Add knowledge types to NodeType union**
+
+Update the local `NodeType` in store.ts:
+
+```typescript
+export type NodeType = "file" | "function" | "class" | "module" | "concept" | "config" | "document" | "service" | "table" | "endpoint" | "pipeline" | "schema" | "resource" | "domain" | "flow" | "step" | "article" | "entity" | "topic" | "claim" | "source";
+```
+
+- [ ] **Step 2: Add knowledge edge category**
+
+Update `EdgeCategory` and `EDGE_CATEGORY_MAP`:
+
+```typescript
+export type EdgeCategory = "structural" | "behavioral" | "data-flow" | "dependencies" | "semantic" | "infrastructure" | "domain" | "knowledge";
+
+export const EDGE_CATEGORY_MAP: Record<EdgeCategory, string[]> = {
+  structural: ["imports", "exports", "contains", "inherits", "implements"],
+  behavioral: ["calls", "subscribes", "publishes", "middleware"],
+  "data-flow": ["reads_from", "writes_to", "transforms", "validates"],
+  dependencies: ["depends_on", "tested_by", "configures"],
+  semantic: ["related", "similar_to"],
+  infrastructure: ["deploys", "serves", "provisions", "triggers"],
+  domain: ["contains_flow", "flow_step", "cross_domain"],
+  knowledge: ["cites", "contradicts", "builds_on", "exemplifies", "categorized_under", "authored_by"],
+};
+```
+
+- [ ] **Step 3: Add knowledge to ALL_NODE_TYPES and ALL_EDGE_CATEGORIES**
+
+```typescript
+export const ALL_NODE_TYPES: NodeType[] = ["file", "function", "class", "module", "concept", "config", "document", "service", "table", "endpoint", "pipeline", "schema", "resource", "domain", "flow", "step", "article", "entity", "topic", "claim", "source"];
+
+export const ALL_EDGE_CATEGORIES: EdgeCategory[] = ["structural", "behavioral", "data-flow", "dependencies", "semantic", "infrastructure", "domain", "knowledge"];
+```
+
+- [ ] **Step 4: Add "knowledge" to ViewMode and NodeCategory**
+
+```typescript
+export type ViewMode = "structural" | "domain" | "knowledge";
+
+export type NodeCategory = "code" | "config" | "docs" | "infra" | "data" | "domain" | "knowledge";
+```
+
+Update the `NODE_CATEGORY_MAP` (find where it maps node types to categories) to include:
+
+```typescript
+  article: "knowledge",
+  entity: "knowledge",
+  topic: "knowledge",
+  claim: "knowledge",
+  source: "knowledge",
+```
+
+- [ ] **Step 5: Add knowledge node type filter default**
+
+In the store's initial state `nodeTypeFilters`, add:
+
+```typescript
+nodeTypeFilters: { code: true, config: true, docs: true, infra: true, data: true, domain: true, knowledge: true },
+```
+
+- [ ] **Step 6: Build dashboard and verify no errors**
+
+Run: `pnpm --filter @understand-anything/dashboard build`
+Expected: Clean build
+
+- [ ] **Step 7: Commit**
+
+```bash
+git add understand-anything-plugin/packages/dashboard/src/store.ts
+git commit -m "feat(dashboard): add knowledge types to store, edge categories, and view mode"
+```
+
+---
+
+## Task 5: Dashboard — CustomNode & NodeInfo Type Maps
+
+**Files:**
+- Modify: `understand-anything-plugin/packages/dashboard/src/components/CustomNode.tsx`
+- Modify: `understand-anything-plugin/packages/dashboard/src/components/NodeInfo.tsx`
+
+- [ ] **Step 1: Add knowledge node colors to CustomNode.tsx**
+
+In `typeColors` map, add after the `step` entry:
+
+```typescript
+  // Knowledge
+  article: "var(--color-node-article)",
+  entity: "var(--color-node-entity)",
+  topic: "var(--color-node-topic)",
+  claim: "var(--color-node-claim)",
+  source: "var(--color-node-source)",
+```
+
+In `typeTextColors` map, add:
+
+```typescript
+  // Knowledge
+  article: "text-node-article",
+  entity: "text-node-entity",
+  topic: "text-node-topic",
+  claim: "text-node-claim",
+  source: "text-node-source",
+```
+
+- [ ] **Step 2: Add knowledge node badge colors to NodeInfo.tsx**
+
+In `typeBadgeColors` map, add:
+
+```typescript
+  // Knowledge
+  article: "text-node-article border border-node-article/30 bg-node-article/10",
+  entity: "text-node-entity border border-node-entity/30 bg-node-entity/10",
+  topic: "text-node-topic border border-node-topic/30 bg-node-topic/10",
+  claim: "text-node-claim border border-node-claim/30 bg-node-claim/10",
+  source: "text-node-source border border-node-source/30 bg-node-source/10",
+```
+
+- [ ] **Step 3: Add knowledge edge labels to NodeInfo.tsx**
+
+In `EDGE_LABELS` map, add:
+
+```typescript
+  // Knowledge
+  cites: { forward: "cites", backward: "cited by" },
+  contradicts: { forward: "contradicts", backward: "contradicted by" },
+  builds_on: { forward: "builds on", backward: "built upon by" },
+  exemplifies: { forward: "exemplifies", backward: "exemplified by" },
+  categorized_under: { forward: "categorized under", backward: "categorizes" },
+  authored_by: { forward: "authored by", backward: "authored" },
+```
+
+- [ ] **Step 4: Build dashboard and verify**
+
+Run: `pnpm --filter @understand-anything/dashboard build`
+Expected: Clean build, no type errors
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add understand-anything-plugin/packages/dashboard/src/components/CustomNode.tsx understand-anything-plugin/packages/dashboard/src/components/NodeInfo.tsx
+git commit -m "feat(dashboard): add knowledge node colors, badge colors, and edge labels"
+```
+
+---
+
+## Task 6: Dashboard — Knowledge Sidebar Component
+
+**Files:**
+- Create: `understand-anything-plugin/packages/dashboard/src/components/KnowledgeInfo.tsx`
+- Modify: `understand-anything-plugin/packages/dashboard/src/App.tsx`
+
+- [ ] **Step 1: Create KnowledgeInfo.tsx**
+
+Create `understand-anything-plugin/packages/dashboard/src/components/KnowledgeInfo.tsx`:
+
+```tsx
+import { useDashboardStore } from "../store";
+import type { GraphNode, GraphEdge, KnowledgeGraph } from "@understand-anything/core/types";
+
+const KNOWLEDGE_NODE_TYPES = new Set(["article", "entity", "topic", "claim", "source"]);
+
+function getBacklinks(nodeId: string, edges: GraphEdge[]): string[] {
+  return edges
+    .filter((e) => e.target === nodeId)
+    .map((e) => e.source);
+}
+
+function getOutgoingLinks(nodeId: string, edges: GraphEdge[]): string[] {
+  return edges
+    .filter((e) => e.source === nodeId)
+    .map((e) => e.target);
+}
+
+function NodeLink({ nodeId, nodes, onNavigate }: { nodeId: string; nodes: GraphNode[]; onNavigate: (id: string) => void }) {
+  const node = nodes.find((n) => n.id === nodeId);
+  if (!node) return <span className="text-text-muted text-xs">{nodeId}</span>;
+  return (
+    <button
+      className="text-accent-dim hover:text-accent text-xs text-left truncate block w-full"
+      onClick={() => onNavigate(nodeId)}
+    >
+      <span className="text-text-muted mr-1">[{node.type}]</span>
+      {node.name}
+    </button>
+  );
+}
+
+export default function KnowledgeInfo() {
+  const graph = useDashboardStore((s) => s.graph);
+  const selectedNode = useDashboardStore((s) => s.selectedNode);
+  const setSelectedNode = useDashboardStore((s) => s.setSelectedNode);
+
+  if (!graph || !selectedNode) return null;
+
+  const node = graph.nodes.find((n) => n.id === selectedNode);
+  if (!node) return null;
+
+  const backlinks = getBacklinks(node.id, graph.edges);
+  const outgoing = getOutgoingLinks(node.id, graph.edges);
+  const meta = node.knowledgeMeta;
+
+  return (
+    <div className="space-y-4 p-4">
+      {/* Header */}
+      <div>
+        <div className="text-xs text-text-muted uppercase tracking-wider mb-1">{node.type}</div>
+        <h2 className="text-lg font-serif text-text-primary">{node.name}</h2>
+      </div>
+
+      {/* Summary */}
+      <p className="text-sm text-text-secondary leading-relaxed">{node.summary}</p>
+
+      {/* Tags */}
+      {node.tags.length > 0 && (
+        <div className="flex flex-wrap gap-1">
+          {node.tags.map((tag) => (
+            <span key={tag} className="text-[10px] px-2 py-0.5 rounded-full bg-elevated border border-border-subtle text-text-muted">
+              {tag}
+            </span>
+          ))}
+        </div>
+      )}
+
+      {/* Knowledge-specific metadata */}
+      {meta?.sourceUrl && (
+        <div>
+          <div className="text-xs text-text-muted uppercase tracking-wider mb-1">Source</div>
+          <span className="text-xs text-accent-dim break-all">{meta.sourceUrl}</span>
+        </div>
+      )}
+
+      {meta?.confidence !== undefined && (
+        <div>
+          <div className="text-xs text-text-muted uppercase tracking-wider mb-1">Confidence</div>
+          <div className="flex items-center gap-2">
+            <div className="flex-1 h-1.5 bg-elevated rounded-full overflow-hidden">
+              <div
+                className="h-full bg-accent-dim rounded-full"
+                style={{ width: `${meta.confidence * 100}%` }}
+              />
+            </div>
+            <span className="text-xs text-text-muted">{Math.round(meta.confidence * 100)}%</span>
+          </div>
+        </div>
+      )}
+
+      {/* Frontmatter */}
+      {meta?.frontmatter && Object.keys(meta.frontmatter).length > 0 && (
+        <div>
+          <div className="text-xs text-text-muted uppercase tracking-wider mb-1">Frontmatter</div>
+          <div className="space-y-1">
+            {Object.entries(meta.frontmatter).map(([key, value]) => (
+              <div key={key} className="text-xs">
+                <span className="text-text-muted">{key}:</span>{" "}
+                <span className="text-text-secondary">{String(value)}</span>
+              </div>
+            ))}
+          </div>
+        </div>
+      )}
+
+      {/* Backlinks */}
+      {backlinks.length > 0 && (
+        <div>
+          <div className="text-xs text-text-muted uppercase tracking-wider mb-1">
+            Backlinks ({backlinks.length})
+          </div>
+          <div className="space-y-0.5">
+            {backlinks.map((id) => (
+              <NodeLink key={id} nodeId={id} nodes={graph.nodes} onNavigate={setSelectedNode} />
+            ))}
+          </div>
+        </div>
+      )}
+
+      {/* Outgoing */}
+      {outgoing.length > 0 && (
+        <div>
+          <div className="text-xs text-text-muted uppercase tracking-wider mb-1">
+            Outgoing Links ({outgoing.length})
+          </div>
+          <div className="space-y-0.5">
+            {outgoing.map((id) => (
+              <NodeLink key={id} nodeId={id} nodes={graph.nodes} onNavigate={setSelectedNode} />
+            ))}
+          </div>
+        </div>
+      )}
+    </div>
+  );
+}
+```
+
+- [ ] **Step 2: Integrate KnowledgeInfo into App.tsx sidebar rendering**
+
+In `understand-anything-plugin/packages/dashboard/src/App.tsx`, find where the sidebar renders `NodeInfo` and add a condition: if `graph.kind === "knowledge"` and a node is selected, render `KnowledgeInfo` instead of `NodeInfo`.
+
+Import at top:
+```typescript
+import KnowledgeInfo from "./components/KnowledgeInfo";
+```
+
+In the sidebar section, wrap the existing NodeInfo render:
+```tsx
+{graph?.kind === "knowledge" ? <KnowledgeInfo /> : <NodeInfo />}
+```
+
+- [ ] **Step 3: Build dashboard and verify**
+
+Run: `pnpm --filter @understand-anything/dashboard build`
+Expected: Clean build
+
+- [ ] **Step 4: Commit**
+
+```bash
+git add understand-anything-plugin/packages/dashboard/src/components/KnowledgeInfo.tsx understand-anything-plugin/packages/dashboard/src/App.tsx
+git commit -m "feat(dashboard): add KnowledgeInfo sidebar component for knowledge graphs"
+```
+
+---
+
+## Task 7: Dashboard — Reading Panel
+
+**Files:**
+- Create: `understand-anything-plugin/packages/dashboard/src/components/ReadingPanel.tsx`
+- Modify: `understand-anything-plugin/packages/dashboard/src/App.tsx`
+
+- [ ] **Step 1: Create ReadingPanel.tsx**
+
+Create `understand-anything-plugin/packages/dashboard/src/components/ReadingPanel.tsx`:
+
+```tsx
+import { useState } from "react";
+import { useDashboardStore } from "../store";
+
+export default function ReadingPanel() {
+  const graph = useDashboardStore((s) => s.graph);
+  const selectedNode = useDashboardStore((s) => s.selectedNode);
+  const setSelectedNode = useDashboardStore((s) => s.setSelectedNode);
+  const [isExpanded, setIsExpanded] = useState(false);
+
+  if (!graph || graph.kind !== "knowledge" || !selectedNode) return null;
+
+  const node = graph.nodes.find((n) => n.id === selectedNode);
+  if (!node || node.type !== "article") return null;
+
+  // Get backlinks for this article
+  const backlinks = graph.edges
+    .filter((e) => e.target === node.id)
+    .map((e) => {
+      const sourceNode = graph.nodes.find((n) => n.id === e.source);
+      return sourceNode ? { id: sourceNode.id, name: sourceNode.name, type: sourceNode.type } : null;
+    })
+    .filter(Boolean) as { id: string; name: string; type: string }[];
+
+  return (
+    <div
+      className={`absolute bottom-0 left-0 right-0 bg-surface border-t border-border-subtle transition-all duration-300 z-50 ${
+        isExpanded ? "h-[70vh]" : "h-[45vh]"
+      }`}
+    >
+      {/* Header bar */}
+      <div className="flex items-center justify-between px-4 py-2 border-b border-border-subtle bg-elevated">
+        <div className="flex items-center gap-2">
+          <span className="text-xs text-text-muted uppercase tracking-wider">Reading</span>
+          <span className="text-sm font-serif text-text-primary">{node.name}</span>
+        </div>
+        <div className="flex items-center gap-2">
+          <button
+            onClick={() => setIsExpanded(!isExpanded)}
+            className="text-xs text-text-muted hover:text-text-primary px-2 py-1"
+          >
+            {isExpanded ? "Collapse" : "Expand"}
+          </button>
+          <button
+            onClick={() => setSelectedNode(null)}
+            className="text-xs text-text-muted hover:text-text-primary px-2 py-1"
+          >
+            Close
+          </button>
+        </div>
+      </div>
+
+      <div className="flex h-[calc(100%-40px)] overflow-hidden">
+        {/* Main content */}
+        <div className="flex-1 overflow-y-auto p-6">
+          <div className="max-w-3xl mx-auto">
+            <h1 className="text-2xl font-serif text-text-primary mb-4">{node.name}</h1>
+
+            {/* Tags */}
+            {node.tags.length > 0 && (
+              <div className="flex flex-wrap gap-1 mb-4">
+                {node.tags.map((tag) => (
+                  <span key={tag} className="text-[10px] px-2 py-0.5 rounded-full bg-elevated border border-border-subtle text-text-muted">
+                    {tag}
+                  </span>
+                ))}
+              </div>
+            )}
+
+            {/* Article content (summary for now — full markdown rendering is a future enhancement) */}
+            <div className="prose prose-invert prose-sm max-w-none">
+              <p className="text-text-secondary leading-relaxed">{node.summary}</p>
+            </div>
+
+            {/* Frontmatter metadata */}
+            {node.knowledgeMeta?.frontmatter && Object.keys(node.knowledgeMeta.frontmatter).length > 0 && (
+              <div className="mt-6 p-3 rounded-lg bg-elevated border border-border-subtle">
+                <div className="text-xs text-text-muted uppercase tracking-wider mb-2">Metadata</div>
+                {Object.entries(node.knowledgeMeta.frontmatter).map(([key, value]) => (
+                  <div key={key} className="text-xs mb-1">
+                    <span className="text-text-muted">{key}:</span>{" "}
+                    <span className="text-text-secondary">{String(value)}</span>
+                  </div>
+                ))}
+              </div>
+            )}
+          </div>
+        </div>
+
+        {/* Backlinks sidebar */}
+        {backlinks.length > 0 && (
+          <div className="w-56 border-l border-border-subtle overflow-y-auto p-3 bg-elevated">
+            <div className="text-xs text-text-muted uppercase tracking-wider mb-2">
+              Backlinks ({backlinks.length})
+            </div>
+            <div className="space-y-1">
+              {backlinks.map((link) => (
+                <button
+                  key={link.id}
+                  className="text-xs text-accent-dim hover:text-accent text-left truncate block w-full"
+                  onClick={() => setSelectedNode(link.id)}
+                >
+                  <span className="text-text-muted mr-1">[{link.type}]</span>
+                  {link.name}
+                </button>
+              ))}
+            </div>
+          </div>
+        )}
+      </div>
+    </div>
+  );
+}
+```
+
+- [ ] **Step 2: Add ReadingPanel to App.tsx**
+
+Import and render `ReadingPanel` in the main dashboard layout, positioned at the bottom:
+
+```typescript
+import ReadingPanel from "./components/ReadingPanel";
+```
+
+Add `<ReadingPanel />` inside the dashboard container, after the graph view area.
+
+- [ ] **Step 3: Build and verify**
+
+Run: `pnpm --filter @understand-anything/dashboard build`
+Expected: Clean build
+
+- [ ] **Step 4: Commit**
+
+```bash
+git add understand-anything-plugin/packages/dashboard/src/components/ReadingPanel.tsx understand-anything-plugin/packages/dashboard/src/App.tsx
+git commit -m "feat(dashboard): add ReadingPanel for article reading mode in knowledge graphs"
+```
+
+---
+
+## Task 8: Dashboard — Vertical Layout for Knowledge Graphs
+
+**Files:**
+- Modify: `understand-anything-plugin/packages/dashboard/src/components/GraphView.tsx`
+- Modify: `understand-anything-plugin/packages/dashboard/src/utils/layout.ts` (if direction isn't already configurable)
+
+- [ ] **Step 1: Check how layout direction is passed to dagre**
+
+Read `GraphView.tsx` to find where `applyDagreLayout` is called. The layout.ts `applyDagreLayout` already accepts a `direction: "TB" | "LR"` parameter (default `"TB"`).
+
+Find where GraphView calls this function and check what direction it passes.
+
+- [ ] **Step 2: Pass graph kind to layout decision**
+
+In `GraphView.tsx`, where the layout is applied, check the graph's `kind` field. If `kind === "knowledge"`, use `"TB"` (top-to-bottom). If `kind === "codebase"` or undefined, keep the existing default.
+
+The graph object is available via the store. Add:
+
+```typescript
+const graphKind = useDashboardStore((s) => s.graph?.kind);
+const layoutDirection = graphKind === "knowledge" ? "TB" : "LR";
+```
+
+Pass `layoutDirection` to the layout call.
+
+- [ ] **Step 3: Build and verify**
+
+Run: `pnpm --filter @understand-anything/dashboard build`
+Expected: Clean build
+
+- [ ] **Step 4: Commit**
+
+```bash
+git add understand-anything-plugin/packages/dashboard/src/components/GraphView.tsx
+git commit -m "feat(dashboard): use vertical top-down layout for knowledge graphs"
+```
+
+---
+
+## Task 9: Dashboard — Knowledge Edge Styling
+
+**Files:**
+- Modify: `understand-anything-plugin/packages/dashboard/src/components/GraphView.tsx`
+
+- [ ] **Step 1: Add knowledge edge style map**
+
+In `GraphView.tsx`, add a style map for knowledge edge types. Follow the existing pattern from `DomainGraphView.tsx` which uses ReactFlow's `style` prop:
+
+```typescript
+const KNOWLEDGE_EDGE_STYLES: Record<string, React.CSSProperties> = {
+  cites: { strokeDasharray: "6 3", strokeWidth: 1.5 },
+  contradicts: { stroke: "#c97070", strokeWidth: 2 },
+  builds_on: { stroke: "var(--color-accent)", strokeWidth: 2 },
+  categorized_under: { stroke: "rgba(150,150,150,0.5)", strokeWidth: 1 },
+  authored_by: { strokeDasharray: "3 3", stroke: "var(--color-node-entity)", strokeWidth: 1.5 },
+  exemplifies: { strokeDasharray: "3 3", stroke: "var(--color-node-claim)", strokeWidth: 1.5 },
+};
+```
+
+- [ ] **Step 2: Apply styles when building ReactFlow edges**
+
+Where edges are converted to ReactFlow format, check if the graph is `kind === "knowledge"` and the edge type has a knowledge style. Merge the style:
+
+```typescript
+const knowledgeStyle = graph?.kind === "knowledge" ? KNOWLEDGE_EDGE_STYLES[edge.type] : undefined;
+// Merge with existing edge style
+const style = { ...baseEdgeStyle, ...knowledgeStyle };
+```
+
+- [ ] **Step 3: Build and verify**
+
+Run: `pnpm --filter @understand-anything/dashboard build`
+Expected: Clean build
+
+- [ ] **Step 4: Commit**
+
+```bash
+git add understand-anything-plugin/packages/dashboard/src/components/GraphView.tsx
+git commit -m "feat(dashboard): add distinct edge styles for knowledge relationship types"
+```
+
+---
+
+## Task 10: Dashboard — Knowledge-Aware ProjectOverview
+
+**Files:**
+- Modify: `understand-anything-plugin/packages/dashboard/src/components/ProjectOverview.tsx`
+
+- [ ] **Step 1: Add knowledge-specific stats**
+
+In `ProjectOverview.tsx`, detect `graph.kind === "knowledge"` and show knowledge-specific stats:
+
+- Total articles, entities, topics, claims, sources (instead of "code, config, docs, infra, data")
+- Detected format (from the first node's `knowledgeMeta.format`)
+- Remove "Languages" and "Frameworks" sections for knowledge graphs (they'll be empty)
+
+Add after the existing stats grid:
+
+```tsx
+{graph.kind === "knowledge" && (
+  <div className="space-y-2">
+    <div className="text-xs text-text-muted uppercase tracking-wider">Knowledge Stats</div>
+    <div className="grid grid-cols-2 gap-2">
+      <StatBox label="Articles" value={graph.nodes.filter(n => n.type === "article").length} />
+      <StatBox label="Entities" value={graph.nodes.filter(n => n.type === "entity").length} />
+      <StatBox label="Topics" value={graph.nodes.filter(n => n.type === "topic").length} />
+      <StatBox label="Claims" value={graph.nodes.filter(n => n.type === "claim").length} />
+      <StatBox label="Sources" value={graph.nodes.filter(n => n.type === "source").length} />
+    </div>
+  </div>
+)}
+```
+
+Reuse or create a `StatBox` component matching the existing style.
+
+- [ ] **Step 2: Conditionally hide code-specific sections**
+
+Wrap the "Languages", "Frameworks", and code-specific file type breakdown sections in a condition:
+
+```tsx
+{graph.kind !== "knowledge" && (
+  <>
+    {/* existing languages/frameworks/file-types sections */}
+  </>
+)}
+```
+
+- [ ] **Step 3: Build and verify**
+
+Run: `pnpm --filter @understand-anything/dashboard build`
+Expected: Clean build
+
+- [ ] **Step 4: Commit**
+
+```bash
+git add understand-anything-plugin/packages/dashboard/src/components/ProjectOverview.tsx
+git commit -m "feat(dashboard): add knowledge-specific stats to ProjectOverview"
+```
+
+---
+
+## Task 11: Create Agent Definitions
+
+**Files:**
+- Create: `understand-anything-plugin/agents/knowledge-scanner.md`
+- Create: `understand-anything-plugin/agents/format-detector.md`
+- Create: `understand-anything-plugin/agents/article-analyzer.md`
+- Create: `understand-anything-plugin/agents/relationship-builder.md`
+
+- [ ] **Step 1: Create knowledge-scanner agent**
+
+Create `understand-anything-plugin/agents/knowledge-scanner.md`:
+
+```markdown
+---
+name: knowledge-scanner
+description: Scans a directory for markdown files and produces a file manifest for knowledge base analysis
+model: inherit
+---
+
+# Knowledge Scanner Agent
+
+You scan a target directory to discover all markdown files for knowledge base analysis.
+
+## Input
+
+You receive a JSON block with:
+- `targetDir` — absolute path to the knowledge base directory
+
+## Task
+
+1. Use Glob/Bash to find all `.md` files in the target directory (recursive)
+2. Exclude common non-content directories: `.obsidian/`, `logseq/`, `.foam/`, `_meta/`, `node_modules/`, `.git/`
+3. For each file, capture:
+   - `path` — relative path from targetDir
+   - `sizeLines` — number of lines
+   - `preview` — first 20 lines of content
+4. Detect directory structure signatures:
+   - Check for `.obsidian/` directory
+   - Check for `logseq/` + `pages/` directories
+   - Check for `.dendron.yml` or `*.schema.yml`
+   - Check for `.foam/` or `.vscode/foam.json`
+   - Check for `raw/` + `wiki/` + `index.md`
+   - Scan a sample of files for `[[wikilinks]]` and unique ID prefixes
+5. Write results to `$PROJECT_ROOT/.understand-anything/intermediate/knowledge-manifest.json`
+
+## Output Schema
+
+```json
+{
+  "targetDir": "/absolute/path",
+  "totalFiles": 342,
+  "directorySignatures": {
+    "hasObsidianDir": true,
+    "hasLogseqDir": false,
+    "hasDendronConfig": false,
+    "hasFoamConfig": false,
+    "hasKarpathyStructure": false,
+    "hasWikilinks": true,
+    "hasUniqueIdPrefixes": false
+  },
+  "files": [
+    {
+      "path": "notes/topic.md",
+      "sizeLines": 45,
+      "preview": "---\ntags: [ai, ml]\n---\n# Topic Name\n..."
+    }
+  ]
+}
+```
+
+## Rules
+
+- Do NOT read file contents beyond the 20-line preview
+- Sort files by path alphabetically
+- Report total count prominently
+- Write output to `.understand-anything/intermediate/knowledge-manifest.json`
+```
+
+- [ ] **Step 2: Create format-detector agent**
+
+Create `understand-anything-plugin/agents/format-detector.md`:
+
+```markdown
+---
+name: format-detector
+description: Detects the knowledge base format from directory signatures and file samples
+model: inherit
+---
+
+# Format Detector Agent
+
+You analyze the knowledge-manifest.json to determine which knowledge base format is being used.
+
+## Input
+
+Read `.understand-anything/intermediate/knowledge-manifest.json` produced by the knowledge-scanner.
+
+## Detection Priority
+
+Apply these rules in order (first match wins):
+
+| Priority | Signal | Format |
+|----------|--------|--------|
+| 1 | `hasObsidianDir === true` | `obsidian` |
+| 2 | `hasLogseqDir === true` | `logseq` |
+| 3 | `hasDendronConfig === true` | `dendron` |
+| 4 | `hasFoamConfig === true` | `foam` |
+| 5 | `hasKarpathyStructure === true` | `karpathy` |
+| 6 | `hasWikilinks === true` AND `hasUniqueIdPrefixes === true` | `zettelkasten` |
+| 7 | fallback | `plain` |
+
+## Output
+
+Write to `.understand-anything/intermediate/format-detection.json`:
+
+```json
+{
+  "format": "obsidian",
+  "confidence": 0.95,
+  "parsingHints": {
+    "linkStyle": "wikilink",
+    "metadataLocation": "yaml-frontmatter",
+    "folderSemantics": "none",
+    "specialFiles": [".obsidian/app.json"],
+    "tagSyntax": "hashtag-inline"
+  }
+}
+```
+
+## Rules
+
+- Always produce exactly one format
+- Set confidence based on how many signals matched
+- Include parsing hints that will help the article-analyzer
+```
+
+- [ ] **Step 3: Create article-analyzer agent**
+
+Create `understand-anything-plugin/agents/article-analyzer.md`:
+
+```markdown
+---
+name: article-analyzer
+description: Analyzes individual markdown files to extract knowledge nodes and explicit edges
+model: inherit
+---
+
+# Article Analyzer Agent
+
+You analyze batches of markdown files from a knowledge base to extract structured knowledge graph data.
+
+## Input
+
+You receive a JSON block with:
+- `projectRoot` — absolute path to the knowledge base
+- `batchFiles` — array of file objects from the manifest (path, sizeLines, preview)
+- `format` — detected format from format-detection.json
+- `parsingHints` — format-specific parsing guidance
+
+You also receive a **format guide** (injected by the skill) that describes how to parse this specific format.
+
+## Task
+
+For each file in the batch:
+
+### 1. Read the full file content
+
+### 2. Extract the article node
+
+- **id**: `article:<relative-path-without-extension>` (e.g., `article:notes/topic`)
+- **type**: `article`
+- **name**: First heading, or frontmatter title, or filename
+- **filePath**: relative path
+- **summary**: 2-3 sentence summary of the article content
+- **tags**: from frontmatter tags, inline #tags, or inferred from content (3-5 tags)
+- **complexity**: `simple` (<50 lines), `moderate` (50-200 lines), `complex` (>200 lines)
+- **knowledgeMeta**: `{ format, wikilinks, frontmatter }`
+
+### 3. Extract entity nodes
+
+Identify named entities mentioned in the article:
+- People, organizations, tools, papers, projects, datasets
+- **id**: `entity:<normalized-lowercase-name>` (e.g., `entity:andrej-karpathy`)
+- **type**: `entity`
+- **summary**: one-sentence description based on context in the article
+- **tags**: entity category tags like `person`, `tool`, `paper`, `organization`
+
+### 4. Extract claim nodes (for articles with strong assertions)
+
+- Only extract claims that are significant takeaways or insights
+- **id**: `claim:<article-path>:<short-slug>` (e.g., `claim:notes/topic:rag-loses-context`)
+- **type**: `claim`
+- **summary**: the assertion itself
+
+### 5. Extract source nodes (for cited references)
+
+- External URLs, paper references, book citations
+- **id**: `source:<normalized-url-or-title>`
+- **type**: `source`
+- **knowledgeMeta**: `{ sourceUrl }`
+
+### 6. Extract explicit edges
+
+- `[[wikilinks]]` → find target article, create `related` edge
+- Frontmatter references → `categorized_under` or `related` edges
+- Inline citations/URLs → `cites` edges to source nodes
+- Author mentions → `authored_by` edges
+
+## Node ID Conventions
+
+```
+article:<relative-path-without-extension>
+entity:<normalized-lowercase-name>
+topic:<normalized-lowercase-name>
+claim:<article-path>:<short-slug>
+source:<normalized-url-or-title>
+```
+
+Normalize: lowercase, replace spaces with hyphens, remove special characters.
+
+**Deduplicate entities**: If the same entity appears across multiple files in the batch, emit it only once. Use the most informative summary.
+
+## Edge Weight Conventions
+
+```
+contains: 1.0
+authored_by: 0.9
+cites: 0.8
+categorized_under: 0.7
+builds_on: 0.7
+related: 0.5
+exemplifies: 0.5
+contradicts: 0.6
+```
+
+## Output
+
+Write per-batch results to `.understand-anything/intermediate/article-batch-<N>.json`:
+
+```json
+{
+  "nodes": [...],
+  "edges": [...]
+}
+```
+
+## Rules
+
+- One article node per file (always)
+- Entity nodes only for clearly named entities (not generic concepts)
+- Claim nodes only for significant assertions (not every sentence)
+- Source nodes only for explicit external references
+- Deduplicate entities within the batch
+- Respect the format guide for parsing links and metadata
+```
+
+- [ ] **Step 4: Create relationship-builder agent**
+
+Create `understand-anything-plugin/agents/relationship-builder.md`:
+
+```markdown
+---
+name: relationship-builder
+description: Discovers implicit cross-file relationships and builds topic clusters from analyzed knowledge nodes
+model: inherit
+---
+
+# Relationship Builder Agent
+
+You analyze all extracted nodes and edges to discover implicit relationships that explicit links missed.
+
+## Input
+
+Read all `article-batch-*.json` files from `.understand-anything/intermediate/`. Merge all nodes and edges.
+
+## Task
+
+### 1. Deduplicate entities globally
+
+Multiple batches may have emitted the same entity. Merge them:
+- Keep the most detailed summary
+- Union all tags
+- Collapse duplicate IDs
+
+### 2. Discover implicit relationships
+
+For each pair of articles/entities, determine if there's an implicit relationship:
+
+- **builds_on**: Article A extends or deepens ideas from Article B (similar topics, references same entities, but goes further)
+- **contradicts**: Article A makes claims that conflict with Article B
+- **categorized_under**: Group articles into topic clusters
+- **exemplifies**: An entity is a concrete example of a concept/topic
+- **related**: Articles share significant thematic overlap but aren't explicitly linked
+
+Set `confidence` in knowledgeMeta for LLM-inferred edges (0.0-1.0).
+
+### 3. Build topic nodes
+
+Identify thematic clusters across all articles:
+- **id**: `topic:<normalized-name>`
+- **type**: `topic`
+- **summary**: description of what this topic covers
+- Create `categorized_under` edges from articles/entities to their topics
+
+### 4. Build layers
+
+Group nodes into layers by topic:
+- Each topic becomes a layer
+- Articles, entities, claims, and sources are assigned to their primary topic's layer
+- Nodes not clearly belonging to any topic go into an "Uncategorized" layer
+
+### 5. Build tour
+
+Create a guided tour through the knowledge base:
+- Start with the broadest topic overview
+- Walk through key articles in a logical learning order
+- Each step covers 1-3 related nodes
+- 5-10 tour steps total
+
+## Output
+
+Write to `.understand-anything/intermediate/relationships.json`:
+
+```json
+{
+  "nodes": [...],
+  "edges": [...],
+  "layers": [...],
+  "tour": [...]
+}
+```
+
+## Rules
+
+- Only add edges with confidence > 0.4
+- Don't duplicate edges that already exist from article-analyzer
+- Topics should be meaningful clusters (3+ articles), not one-off categories
+- Tour should be navigable by someone new to the knowledge base
+- Keep layers balanced — no layer with 50%+ of all nodes
+```
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add understand-anything-plugin/agents/knowledge-scanner.md understand-anything-plugin/agents/format-detector.md understand-anything-plugin/agents/article-analyzer.md understand-anything-plugin/agents/relationship-builder.md
+git commit -m "feat(agents): add knowledge-scanner, format-detector, article-analyzer, and relationship-builder agents"
+```
+
+---
+
+## Task 12: Create Format Guides
+
+**Files:**
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/obsidian.md`
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/logseq.md`
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/dendron.md`
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/foam.md`
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/karpathy.md`
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/zettelkasten.md`
+- Create: `understand-anything-plugin/skills/understand-knowledge/formats/plain.md`
+
+**IMPORTANT**: Each format guide must be **research-backed**. The implementing agent MUST:
+1. Use WebSearch and WebFetch to read the **official documentation** for each format
+2. Study the actual parsing rules, not assumptions
+3. Include specific syntax examples from real documentation
+
+- [ ] **Step 1: Create obsidian.md format guide**
+
+Research Obsidian's official docs (https://help.obsidian.md/) and create `understand-anything-plugin/skills/understand-knowledge/formats/obsidian.md`:
+
+The guide must cover:
+- Detection: `.obsidian/` directory exists
+- Link syntax: `[[wikilink]]`, `[[note|alias]]`, `[[note#heading]]`, `![[embed]]`
+- Metadata: YAML frontmatter between `---` delimiters
+- Tags: `#tag` inline, `tags:` in frontmatter (both array and space-separated)
+- Properties: Obsidian Properties (frontmatter fields rendered in UI)
+- Folder semantics: Obsidian doesn't assign folder meaning by default
+- Special files: `.obsidian/app.json`, `.obsidian/workspace.json` (ignore these)
+- Canvas: `.canvas` files (JSON format, describe spatial layouts — extract card references)
+- Dataview: inline fields `key:: value`, `[key:: value]`
+
+- [ ] **Step 2: Create logseq.md format guide**
+
+Research Logseq docs (https://docs.logseq.com/) and create `understand-anything-plugin/skills/understand-knowledge/formats/logseq.md`:
+
+Cover:
+- Detection: `logseq/` + `pages/` directories
+- Structure: `journals/YYYY_MM_DD.md` (daily notes), `pages/*.md` (named pages)
+- Link syntax: `[[wikilinks]]`, `((block-references))` by UUID
+- Block-based: Content is organized as bullet-point outlines
+- Properties: `key:: value` syntax on blocks
+- Tags: `#tag` inline, page tags via properties
+- Special: `logseq/config.edn` for configuration
+
+- [ ] **Step 3: Create dendron.md format guide**
+
+Research Dendron wiki (https://wiki.dendron.so/) and create `understand-anything-plugin/skills/understand-knowledge/formats/dendron.md`:
+
+Cover:
+- Detection: `.dendron.yml` or `*.schema.yml` files
+- Hierarchy: dot-delimited filenames (`a.b.c.md`)
+- Link syntax: `[[wikilinks]]` with hierarchy awareness
+- Schemas: `.schema.yml` files define expected hierarchy structure
+- Frontmatter: YAML with required `id` and `title` fields
+- Stubs: auto-created intermediate hierarchy files
+
+- [ ] **Step 4: Create foam.md format guide**
+
+Research Foam docs (https://foambubble.github.io/foam/) and create `understand-anything-plugin/skills/understand-knowledge/formats/foam.md`:
+
+Cover:
+- Detection: `.foam/` directory or `.vscode/foam.json`
+- Link syntax: `[[wikilinks]]` plus link reference definitions at file bottom
+- Placeholder links: links to non-existent files
+- Frontmatter: standard YAML
+- Auto-linking: Foam auto-updates links on file rename/move
+
+- [ ] **Step 5: Create karpathy.md format guide**
+
+Research Karpathy's gist (https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f) and create `understand-anything-plugin/skills/understand-knowledge/formats/karpathy.md`:
+
+Cover:
+- Detection: `raw/` + `wiki/` directories + `index.md`
+- Structure: `raw/` (immutable sources), `wiki/` (compiled articles), `_meta/` (state)
+- Special files: `index.md` (master page list), `log.md` (append-only operations log)
+- Link style: standard markdown links (not wikilinks)
+- Log parsing: `## [YYYY-MM-DD] operation | Title` entries
+- Wiki articles: LLM-compiled, may have cross-references and backlinks
+
+- [ ] **Step 6: Create zettelkasten.md format guide**
+
+Research zettelkasten.de and create `understand-anything-plugin/skills/understand-knowledge/formats/zettelkasten.md`:
+
+Cover:
+- Detection: `[[wikilinks]]` + unique ID prefixes in filenames (timestamps like `202604091234`)
+- Atomic notes: one idea per note
+- Unique IDs: timestamp or alphanumeric prefix in filename
+- Links: `[[wikilinks]]` with optional typed links
+- Frontmatter: YAML with tags, creation date
+- No folder hierarchy: flat structure, connections via links only
+
+- [ ] **Step 7: Create plain.md format guide**
+
+Create `understand-anything-plugin/skills/understand-knowledge/formats/plain.md`:
+
+Cover:
+- Detection: fallback when no other format detected
+- Links: standard markdown `[text](relative/path.md)` links
+- Structure: folder hierarchy provides categorization
+- Headings: `#` hierarchy provides structure within files
+- No special metadata expectations
+- Tags: none expected (LLM infers topics)
+
+- [ ] **Step 8: Commit**
+
+```bash
+git add understand-anything-plugin/skills/understand-knowledge/formats/
+git commit -m "feat(skill): add 7 research-backed format guides for knowledge base parsing"
+```
+
+---
+
+## Task 13: Create SKILL.md
+
+**Files:**
+- Create: `understand-anything-plugin/skills/understand-knowledge/SKILL.md`
+
+- [ ] **Step 1: Create the skill definition**
+
+Create `understand-anything-plugin/skills/understand-knowledge/SKILL.md`:
+
+```markdown
+---
+name: understand-knowledge
+description: Analyze a markdown knowledge base (Obsidian, Logseq, Dendron, Foam, Karpathy-style, Zettelkasten, or plain) to produce an interactive knowledge graph with typed relationships
+argument-hint: [path/to/notes] [--ingest <file-or-folder>]
+---
+
+# /understand-knowledge
+
+Analyze a personal knowledge base of markdown files and produce an interactive knowledge graph.
+
+## Arguments
+
+- `path/to/notes` — (optional) directory containing markdown files. Defaults to current working directory.
+- `--ingest <path>` — (optional) incrementally add new file(s) to an existing knowledge graph.
+
+## Phase 0: Pre-flight
+
+1. Determine the target directory:
+   - If a path argument is provided, use it
+   - Otherwise use the current working directory
+2. Create `.understand-anything/` and `.understand-anything/intermediate/` directories if they don't exist
+3. If `--ingest` flag is present:
+   - Verify `.understand-anything/knowledge-graph.json` exists (error if not — must run full scan first)
+   - Read the existing graph
+   - Skip to Phase 2 with only the new/changed files
+4. Get the current git commit hash (if in a git repo, otherwise use "no-git")
+
+## Phase 1: SCAN
+
+Dispatch the **knowledge-scanner** agent:
+
+```json
+{
+  "targetDir": "<absolute-path-to-target>"
+}
+```
+
+Wait for the agent to write `.understand-anything/intermediate/knowledge-manifest.json`.
+
+Report: "Scanned {totalFiles} markdown files."
+
+## Phase 2: FORMAT DETECTION
+
+Dispatch the **format-detector** agent.
+
+Wait for `.understand-anything/intermediate/format-detection.json`.
+
+Report: "Detected format: {format} (confidence: {confidence})"
+
+## Phase 3: ANALYZE
+
+Read the format detection result. Load the corresponding format guide:
+
+- `obsidian` → inject `skills/understand-knowledge/formats/obsidian.md`
+- `logseq` → inject `skills/understand-knowledge/formats/logseq.md`
+- `dendron` → inject `skills/understand-knowledge/formats/dendron.md`
+- `foam` → inject `skills/understand-knowledge/formats/foam.md`
+- `karpathy` → inject `skills/understand-knowledge/formats/karpathy.md`
+- `zettelkasten` → inject `skills/understand-knowledge/formats/zettelkasten.md`
+- `plain` → inject `skills/understand-knowledge/formats/plain.md`
+
+Batch the files from the manifest into groups of 15-25 files each.
+
+For each batch, dispatch an **article-analyzer** agent with:
+
+```json
+{
+  "projectRoot": "<absolute-path>",
+  "batchFiles": [...],
+  "format": "<detected-format>",
+  "parsingHints": {...}
+}
+```
+
+Inject the format guide content into each agent's context.
+
+Run up to 5 batches concurrently.
+
+Wait for all `article-batch-*.json` files.
+
+Report: "Analyzed {totalFiles} files across {batchCount} batches."
+
+## Phase 4: RELATIONSHIPS
+
+Dispatch the **relationship-builder** agent.
+
+Wait for `.understand-anything/intermediate/relationships.json`.
+
+Report: "Discovered {topicCount} topics, {implicitEdgeCount} implicit relationships."
+
+## Phase 5: ASSEMBLE
+
+Merge all intermediate results into a single knowledge graph:
+
+1. Read all `article-batch-*.json` files — collect all nodes and edges
+2. Read `relationships.json` — merge in topic nodes, implicit edges, layers, and tour
+3. Deduplicate nodes by ID (keep the most complete version)
+4. Deduplicate edges by source+target+type
+5. Assemble into `KnowledgeGraph` format:
+
+```json
+{
+  "version": "1.0",
+  "kind": "knowledge",
+  "project": {
+    "name": "<directory-name>",
+    "languages": [],
+    "frameworks": [],
+    "description": "Knowledge base analyzed from <format> format",
+    "analyzedAt": "<ISO-timestamp>",
+    "gitCommitHash": "<hash>"
+  },
+  "nodes": [...],
+  "edges": [...],
+  "layers": [...],
+  "tour": [...]
+}
+```
+
+## Phase 6: REVIEW
+
+Dispatch the existing **graph-reviewer** agent to validate:
+- All edge source/target IDs reference existing nodes
+- No orphan nodes (nodes with zero edges)
+- No duplicate node IDs
+- All layers reference existing nodes
+- Tour steps reference existing nodes
+
+Apply fixes from the reviewer.
+
+## Phase 7: SAVE
+
+1. Write `.understand-anything/knowledge-graph.json`
+2. Write `.understand-anything/meta.json`:
+   ```json
+   {
+     "lastAnalyzedAt": "<ISO-timestamp>",
+     "gitCommitHash": "<hash>",
+     "version": "1.0",
+     "analyzedFiles": <count>,
+     "knowledgeFormat": "<detected-format>"
+   }
+   ```
+3. Clean up `.understand-anything/intermediate/` directory
+4. Report: "Knowledge graph saved with {nodeCount} nodes and {edgeCount} edges."
+
+## Phase 8: DASHBOARD
+
+Auto-trigger `/understand-dashboard` to launch the visualization.
+
+## Incremental Mode (--ingest)
+
+When `--ingest <path>` is specified:
+
+1. Read the existing `knowledge-graph.json`
+2. Scan only the specified file(s) or folder
+3. Skip format detection (reuse format from existing graph's metadata)
+4. Run article-analyzer on only the new/changed files
+5. Run relationship-builder on new nodes against the full existing graph
+6. Merge new nodes/edges into the existing graph
+7. Re-run graph-reviewer
+8. Save updated graph
+```
+
+- [ ] **Step 2: Commit**
+
+```bash
+git add understand-anything-plugin/skills/understand-knowledge/SKILL.md
+git commit -m "feat(skill): add /understand-knowledge skill definition with 8-phase pipeline"
+```
+
+---
+
+## Task 14: Build, Test & Verify End-to-End
+
+**Files:**
+- All modified files
+
+- [ ] **Step 1: Build core package**
+
+Run: `pnpm --filter @understand-anything/core build`
+Expected: Clean build, no errors
+
+- [ ] **Step 2: Run core tests**
+
+Run: `pnpm --filter @understand-anything/core test -- --run`
+Expected: All tests pass, including new knowledge-schema tests
+
+- [ ] **Step 3: Build dashboard**
+
+Run: `pnpm --filter @understand-anything/dashboard build`
+Expected: Clean build, no errors
+
+- [ ] **Step 4: Run lint**
+
+Run: `pnpm lint`
+Expected: No lint errors
+
+- [ ] **Step 5: Verify skill is discoverable**
+
+Check that the skill file exists and has valid frontmatter:
+
+Run: `head -5 understand-anything-plugin/skills/understand-knowledge/SKILL.md`
+Expected: Valid `---` delimited YAML with name, description, argument-hint
+
+- [ ] **Step 6: Verify all agents are present**
+
+Run: `ls understand-anything-plugin/agents/ | grep knowledge\|format\|article\|relationship`
+Expected: `knowledge-scanner.md`, `format-detector.md`, `article-analyzer.md`, `relationship-builder.md`
+
+- [ ] **Step 7: Verify all format guides are present**
+
+Run: `ls understand-anything-plugin/skills/understand-knowledge/formats/`
+Expected: `obsidian.md`, `logseq.md`, `dendron.md`, `foam.md`, `karpathy.md`, `zettelkasten.md`, `plain.md`
+
+- [ ] **Step 8: Final commit**
+
+```bash
+git add -A
+git commit -m "feat: complete /understand-knowledge implementation — knowledge base analysis skill"
+```

From b3acd5b1d2b0d5ae89c7ddd337a363161a1b1da5 Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Thu, 9 Apr 2026 23:11:44 +0800
Subject: [PATCH 03/15] docs: reorganize docs/ into superpowers/specs/ and
 superpowers/plans/

Move all design docs to docs/superpowers/specs/ and all implementation
plans to docs/superpowers/plans/ for consistent organization.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 docs/{ => superpowers}/plans/2026-03-14-phase1-implementation.md  | 0
 docs/{ => superpowers}/plans/2026-03-14-phase2-implementation.md  | 0
 docs/{ => superpowers}/plans/2026-03-14-phase3-implementation.md  | 0
 docs/{ => superpowers}/plans/2026-03-14-phase4-implementation.md  | 0
 .../{ => superpowers}/plans/2026-03-15-homepage-implementation.md | 0
 .../plans/2026-03-18-multi-platform-simple-implementation.md      | 0
 docs/{ => superpowers}/plans/2026-03-21-language-agnostic-plan.md | 0
 .../plans/2026-03-25-dashboard-robustness-impl.md                 | 0
 .../plans/2026-03-25-dashboard-robustness-plan.md                 | 0
 .../plans/2026-03-26-theme-system-implementation.md               | 0
 docs/{ => superpowers}/plans/2026-03-27-token-reduction-impl.md   | 0
 .../plans/2026-03-28-understand-anything-extension-impl.md        | 0
 docs/{ => superpowers}/plans/2026-03-29-homepage-update-impl.md   | 0
 .../plans/2026-04-01-business-domain-knowledge-impl.md            | 0
 .../specs}/2026-03-14-understand-anything-design.md               | 0
 docs/{plans => superpowers/specs}/2026-03-15-homepage-design.md   | 0
 .../specs}/2026-03-18-multi-platform-simple-design.md             | 0
 .../specs}/2026-03-21-language-agnostic-design.md                 | 0
 .../specs}/2026-03-26-theme-system-design.md                      | 0
 .../specs}/2026-03-27-token-reduction-design.md                   | 0
 .../specs}/2026-03-28-understand-anything-extension-design.md     | 0
 .../specs}/2026-03-29-homepage-update-design.md                   | 0
 .../specs}/2026-04-01-business-domain-knowledge-design.md         | 0
 23 files changed, 0 insertions(+), 0 deletions(-)
 rename docs/{ => superpowers}/plans/2026-03-14-phase1-implementation.md (100%)
 rename docs/{ => superpowers}/plans/2026-03-14-phase2-implementation.md (100%)
 rename docs/{ => superpowers}/plans/2026-03-14-phase3-implementation.md (100%)
 rename docs/{ => superpowers}/plans/2026-03-14-phase4-implementation.md (100%)
 rename docs/{ => superpowers}/plans/2026-03-15-homepage-implementation.md (100%)
 rename docs/{ => superpowers}/plans/2026-03-18-multi-platform-simple-implementation.md (100%)
 rename docs/{ => superpowers}/plans/2026-03-21-language-agnostic-plan.md (100%)
 rename docs/{ => superpowers}/plans/2026-03-25-dashboard-robustness-impl.md (100%)
 rename docs/{ => superpowers}/plans/2026-03-25-dashboard-robustness-plan.md (100%)
 rename docs/{ => superpowers}/plans/2026-03-26-theme-system-implementation.md (100%)
 rename docs/{ => superpowers}/plans/2026-03-27-token-reduction-impl.md (100%)
 rename docs/{ => superpowers}/plans/2026-03-28-understand-anything-extension-impl.md (100%)
 rename docs/{ => superpowers}/plans/2026-03-29-homepage-update-impl.md (100%)
 rename docs/{ => superpowers}/plans/2026-04-01-business-domain-knowledge-impl.md (100%)
 rename docs/{plans => superpowers/specs}/2026-03-14-understand-anything-design.md (100%)
 rename docs/{plans => superpowers/specs}/2026-03-15-homepage-design.md (100%)
 rename docs/{plans => superpowers/specs}/2026-03-18-multi-platform-simple-design.md (100%)
 rename docs/{plans => superpowers/specs}/2026-03-21-language-agnostic-design.md (100%)
 rename docs/{plans => superpowers/specs}/2026-03-26-theme-system-design.md (100%)
 rename docs/{plans => superpowers/specs}/2026-03-27-token-reduction-design.md (100%)
 rename docs/{plans => superpowers/specs}/2026-03-28-understand-anything-extension-design.md (100%)
 rename docs/{plans => superpowers/specs}/2026-03-29-homepage-update-design.md (100%)
 rename docs/{plans => superpowers/specs}/2026-04-01-business-domain-knowledge-design.md (100%)

diff --git a/docs/plans/2026-03-14-phase1-implementation.md b/docs/superpowers/plans/2026-03-14-phase1-implementation.md
similarity index 100%
rename from docs/plans/2026-03-14-phase1-implementation.md
rename to docs/superpowers/plans/2026-03-14-phase1-implementation.md
diff --git a/docs/plans/2026-03-14-phase2-implementation.md b/docs/superpowers/plans/2026-03-14-phase2-implementation.md
similarity index 100%
rename from docs/plans/2026-03-14-phase2-implementation.md
rename to docs/superpowers/plans/2026-03-14-phase2-implementation.md
diff --git a/docs/plans/2026-03-14-phase3-implementation.md b/docs/superpowers/plans/2026-03-14-phase3-implementation.md
similarity index 100%
rename from docs/plans/2026-03-14-phase3-implementation.md
rename to docs/superpowers/plans/2026-03-14-phase3-implementation.md
diff --git a/docs/plans/2026-03-14-phase4-implementation.md b/docs/superpowers/plans/2026-03-14-phase4-implementation.md
similarity index 100%
rename from docs/plans/2026-03-14-phase4-implementation.md
rename to docs/superpowers/plans/2026-03-14-phase4-implementation.md
diff --git a/docs/plans/2026-03-15-homepage-implementation.md b/docs/superpowers/plans/2026-03-15-homepage-implementation.md
similarity index 100%
rename from docs/plans/2026-03-15-homepage-implementation.md
rename to docs/superpowers/plans/2026-03-15-homepage-implementation.md
diff --git a/docs/plans/2026-03-18-multi-platform-simple-implementation.md b/docs/superpowers/plans/2026-03-18-multi-platform-simple-implementation.md
similarity index 100%
rename from docs/plans/2026-03-18-multi-platform-simple-implementation.md
rename to docs/superpowers/plans/2026-03-18-multi-platform-simple-implementation.md
diff --git a/docs/plans/2026-03-21-language-agnostic-plan.md b/docs/superpowers/plans/2026-03-21-language-agnostic-plan.md
similarity index 100%
rename from docs/plans/2026-03-21-language-agnostic-plan.md
rename to docs/superpowers/plans/2026-03-21-language-agnostic-plan.md
diff --git a/docs/plans/2026-03-25-dashboard-robustness-impl.md b/docs/superpowers/plans/2026-03-25-dashboard-robustness-impl.md
similarity index 100%
rename from docs/plans/2026-03-25-dashboard-robustness-impl.md
rename to docs/superpowers/plans/2026-03-25-dashboard-robustness-impl.md
diff --git a/docs/plans/2026-03-25-dashboard-robustness-plan.md b/docs/superpowers/plans/2026-03-25-dashboard-robustness-plan.md
similarity index 100%
rename from docs/plans/2026-03-25-dashboard-robustness-plan.md
rename to docs/superpowers/plans/2026-03-25-dashboard-robustness-plan.md
diff --git a/docs/plans/2026-03-26-theme-system-implementation.md b/docs/superpowers/plans/2026-03-26-theme-system-implementation.md
similarity index 100%
rename from docs/plans/2026-03-26-theme-system-implementation.md
rename to docs/superpowers/plans/2026-03-26-theme-system-implementation.md
diff --git a/docs/plans/2026-03-27-token-reduction-impl.md b/docs/superpowers/plans/2026-03-27-token-reduction-impl.md
similarity index 100%
rename from docs/plans/2026-03-27-token-reduction-impl.md
rename to docs/superpowers/plans/2026-03-27-token-reduction-impl.md
diff --git a/docs/plans/2026-03-28-understand-anything-extension-impl.md b/docs/superpowers/plans/2026-03-28-understand-anything-extension-impl.md
similarity index 100%
rename from docs/plans/2026-03-28-understand-anything-extension-impl.md
rename to docs/superpowers/plans/2026-03-28-understand-anything-extension-impl.md
diff --git a/docs/plans/2026-03-29-homepage-update-impl.md b/docs/superpowers/plans/2026-03-29-homepage-update-impl.md
similarity index 100%
rename from docs/plans/2026-03-29-homepage-update-impl.md
rename to docs/superpowers/plans/2026-03-29-homepage-update-impl.md
diff --git a/docs/plans/2026-04-01-business-domain-knowledge-impl.md b/docs/superpowers/plans/2026-04-01-business-domain-knowledge-impl.md
similarity index 100%
rename from docs/plans/2026-04-01-business-domain-knowledge-impl.md
rename to docs/superpowers/plans/2026-04-01-business-domain-knowledge-impl.md
diff --git a/docs/plans/2026-03-14-understand-anything-design.md b/docs/superpowers/specs/2026-03-14-understand-anything-design.md
similarity index 100%
rename from docs/plans/2026-03-14-understand-anything-design.md
rename to docs/superpowers/specs/2026-03-14-understand-anything-design.md
diff --git a/docs/plans/2026-03-15-homepage-design.md b/docs/superpowers/specs/2026-03-15-homepage-design.md
similarity index 100%
rename from docs/plans/2026-03-15-homepage-design.md
rename to docs/superpowers/specs/2026-03-15-homepage-design.md
diff --git a/docs/plans/2026-03-18-multi-platform-simple-design.md b/docs/superpowers/specs/2026-03-18-multi-platform-simple-design.md
similarity index 100%
rename from docs/plans/2026-03-18-multi-platform-simple-design.md
rename to docs/superpowers/specs/2026-03-18-multi-platform-simple-design.md
diff --git a/docs/plans/2026-03-21-language-agnostic-design.md b/docs/superpowers/specs/2026-03-21-language-agnostic-design.md
similarity index 100%
rename from docs/plans/2026-03-21-language-agnostic-design.md
rename to docs/superpowers/specs/2026-03-21-language-agnostic-design.md
diff --git a/docs/plans/2026-03-26-theme-system-design.md b/docs/superpowers/specs/2026-03-26-theme-system-design.md
similarity index 100%
rename from docs/plans/2026-03-26-theme-system-design.md
rename to docs/superpowers/specs/2026-03-26-theme-system-design.md
diff --git a/docs/plans/2026-03-27-token-reduction-design.md b/docs/superpowers/specs/2026-03-27-token-reduction-design.md
similarity index 100%
rename from docs/plans/2026-03-27-token-reduction-design.md
rename to docs/superpowers/specs/2026-03-27-token-reduction-design.md
diff --git a/docs/plans/2026-03-28-understand-anything-extension-design.md b/docs/superpowers/specs/2026-03-28-understand-anything-extension-design.md
similarity index 100%
rename from docs/plans/2026-03-28-understand-anything-extension-design.md
rename to docs/superpowers/specs/2026-03-28-understand-anything-extension-design.md
diff --git a/docs/plans/2026-03-29-homepage-update-design.md b/docs/superpowers/specs/2026-03-29-homepage-update-design.md
similarity index 100%
rename from docs/plans/2026-03-29-homepage-update-design.md
rename to docs/superpowers/specs/2026-03-29-homepage-update-design.md
diff --git a/docs/plans/2026-04-01-business-domain-knowledge-design.md b/docs/superpowers/specs/2026-04-01-business-domain-knowledge-design.md
similarity index 100%
rename from docs/plans/2026-04-01-business-domain-knowledge-design.md
rename to docs/superpowers/specs/2026-04-01-business-domain-knowledge-design.md

From ce25b61e365b1139059ad1c339a05af385f9444e Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Fri, 10 Apr 2026 11:24:49 +0800
Subject: [PATCH 04/15] docs: add .understandignore design spec

User-configurable file exclusion using .gitignore syntax, with hardcoded
defaults, auto-generated starter file, and pre-analysis review pause.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../2026-04-10-understandignore-design.md     | 258 ++++++++++++++++++
 1 file changed, 258 insertions(+)
 create mode 100644 docs/superpowers/specs/2026-04-10-understandignore-design.md

diff --git a/docs/superpowers/specs/2026-04-10-understandignore-design.md b/docs/superpowers/specs/2026-04-10-understandignore-design.md
new file mode 100644
index 0000000..2d71f51
--- /dev/null
+++ b/docs/superpowers/specs/2026-04-10-understandignore-design.md
@@ -0,0 +1,258 @@
+# .understandignore Design Spec
+
+## Overview
+
+Add user-configurable file exclusion via `.understandignore` files, using `.gitignore` syntax. This makes analysis faster by skipping irrelevant files (vendor code, generated output, test fixtures) without modifying hardcoded defaults.
+
+## Goals
+
+- Let users exclude files/directories from analysis via `.understandignore`
+- Use `.gitignore` syntax (familiar, no learning curve)
+- Keep hardcoded defaults as built-in — `.understandignore` adds patterns on top
+- Allow `!` negation to force-include files excluded by defaults
+- Auto-generate a commented-out starter file on first run (deterministic code, not LLM)
+- Pause before analysis to let user review the ignore file
+
+## Non-Goals
+
+- Replacing `.gitignore` — this is analysis-specific
+- Per-directory `.understandignore` files (project root and `.understand-anything/` only)
+- GUI for editing ignore patterns
+
+---
+
+## IgnoreFilter Module
+
+New file: `packages/core/src/ignore-filter.ts`
+
+Uses the [`ignore`](https://www.npmjs.com/package/ignore) npm package for gitignore-compatible pattern matching.
+
+### API
+
+```typescript
+export interface IgnoreFilter {
+  isIgnored(relativePath: string): boolean;
+}
+
+export function createIgnoreFilter(projectRoot: string): IgnoreFilter;
+```
+
+### Behavior
+
+`createIgnoreFilter` loads patterns in this order (later entries can override earlier ones):
+
+1. **Hardcoded defaults** — the existing exclusion patterns from project-scanner (node_modules/, .git/, dist/, build/, bin/, obj/, *.lock, *.min.js, etc.)
+2. **`.understand-anything/.understandignore`** — project-level, lives alongside the output
+3. **`.understandignore`** at project root — alternative location for visibility
+
+Patterns merge additively. `!` negation in user files can override hardcoded defaults (e.g., `!dist/` force-includes dist/).
+
+### Hardcoded Default Patterns
+
+These are the built-in defaults (matching current project-scanner behavior, plus bin/obj for .NET):
+
+```
+# Dependency directories
+node_modules/
+.git/
+vendor/
+venv/
+.venv/
+__pycache__/
+
+# Build output
+dist/
+build/
+out/
+coverage/
+.next/
+.cache/
+.turbo/
+target/
+bin/
+obj/
+
+# Lock files
+*.lock
+package-lock.json
+yarn.lock
+pnpm-lock.yaml
+
+# Binary/asset files
+*.png
+*.jpg
+*.jpeg
+*.gif
+*.svg
+*.ico
+*.woff
+*.woff2
+*.ttf
+*.eot
+*.mp3
+*.mp4
+*.pdf
+*.zip
+*.tar
+*.gz
+
+# Generated files
+*.min.js
+*.min.css
+*.map
+*.generated.*
+
+# IDE/editor
+.idea/
+.vscode/
+
+# Misc
+LICENSE
+.gitignore
+.editorconfig
+.prettierrc
+.eslintrc*
+*.log
+```
+
+---
+
+## Starter File Generator
+
+New file: `packages/core/src/ignore-generator.ts`
+
+### API
+
+```typescript
+export function generateStarterIgnoreFile(projectRoot: string): string;
+```
+
+### Behavior
+
+- Deterministic code — scans the project directory for common patterns
+- Returns the file content as a string (caller writes it to disk)
+- All suggestions are **commented out** — user must uncomment to activate
+- Header comment explains the file, syntax, and built-in defaults
+
+### Detection Logic
+
+| If exists | Suggest |
+|-----------|---------|
+| `__tests__/` or `*.test.*` files | `# __tests__/`, `# *.test.*`, `# *.spec.*` |
+| `fixtures/` or `testdata/` | `# fixtures/`, `# testdata/` |
+| `test/` or `tests/` | `# test/`, `# tests/` |
+| `.storybook/` | `# .storybook/` |
+| `docs/` | `# docs/` |
+| `examples/` | `# examples/` |
+| `scripts/` | `# scripts/` |
+| `migrations/` | `# migrations/` |
+| `*.snap` files | `# *.snap` |
+| `bin/` (non-.NET, i.e. shell scripts) | `# bin/` |
+| `obj/` | `# obj/` |
+
+### Generated File Format
+
+```
+# .understandignore — patterns for files/dirs to exclude from analysis
+# Syntax: same as .gitignore (globs, # comments, ! negation, trailing / for dirs)
+# Lines below are suggestions — uncomment to activate.
+# Use ! prefix to force-include something excluded by defaults.
+#
+# Built-in defaults (always excluded unless negated):
+#   node_modules/, .git/, dist/, build/, bin/, obj/, *.lock, *.min.js, etc.
+#
+
+# --- Suggested exclusions (uncomment to activate) ---
+
+# Test files
+# __tests__/
+# *.test.*
+# *.spec.*
+
+# Test data
+# fixtures/
+# testdata/
+
+# Documentation
+# docs/
+
+# ... (more suggestions based on detection)
+```
+
+Only generated if `.understand-anything/.understandignore` doesn't already exist.
+
+---
+
+## Skill Integration
+
+### Phase 0.5: Ignore Setup (new phase in SKILL.md)
+
+Added between Pre-flight (Phase 0) and SCAN (Phase 1):
+
+1. Check if `.understand-anything/.understandignore` exists
+2. If not, run `generateStarterIgnoreFile(projectRoot)` and write the result to `.understand-anything/.understandignore`
+3. Report to user:
+   - **First run:** "Generated `.understand-anything/.understandignore` with suggested exclusions. Please review it and uncomment any patterns you'd like to exclude. When ready, confirm to continue."
+   - **Subsequent runs:** "Found `.understand-anything/.understandignore`. Review it if needed, then confirm to continue."
+4. Wait for user confirmation before proceeding
+
+### Phase 1: SCAN changes
+
+The `project-scanner` agent's scan script is updated to:
+
+1. Collect files via `git ls-files` (or fallback)
+2. Apply agent's hardcoded pattern filter (Layer 1 — existing behavior)
+3. Apply `IgnoreFilter` from core (Layer 2 — user patterns)
+4. Add `filteredByIgnore` count to scan output
+5. Report: "Scanned {totalFiles} files ({filteredByIgnore} excluded by .understandignore)"
+
+Two-layer filtering:
+- **Layer 1:** Agent's hardcoded patterns in the prompt (fast, coarse filter)
+- **Layer 2:** `IgnoreFilter` from core (deterministic code, user-configurable)
+
+---
+
+## Project Scanner Agent Update
+
+Changes to `understand-anything-plugin/agents/project-scanner.md`:
+
+- After the file list is built and Layer 1 filtering is applied, the agent runs a Node.js script that imports `createIgnoreFilter` from `@understand-anything/core` and filters the remaining paths
+- The scan result JSON includes a new `filteredByIgnore: number` field
+- Existing hardcoded exclusion patterns in the agent prompt remain for backward compatibility
+
+---
+
+## Testing
+
+### `packages/core/src/__tests__/ignore-filter.test.ts`
+
+- Parses basic glob patterns (`*.log`, `dist/`)
+- Handles `#` comments and blank lines
+- Handles `!` negation (force-include)
+- Handles `**/` recursive matching
+- Handles trailing `/` for directory-only patterns
+- Merges defaults + user patterns correctly
+- `!` in user file overrides hardcoded defaults
+- Returns `false` for paths not matching any pattern
+
+### `packages/core/src/__tests__/ignore-generator.test.ts`
+
+- Generates starter file with header comment
+- Detects existing directories and suggests relevant patterns
+- All suggestions are commented out (prefixed with `# `)
+- Doesn't overwrite existing file
+- Includes bin/obj suggestions when relevant
+
+---
+
+## File Structure
+
+| File | Purpose |
+|------|---------|
+| `packages/core/src/ignore-filter.ts` | Parse .understandignore, merge with defaults, filter paths |
+| `packages/core/src/ignore-generator.ts` | Generate starter file by scanning project structure |
+| `packages/core/src/__tests__/ignore-filter.test.ts` | Filter logic tests |
+| `packages/core/src/__tests__/ignore-generator.test.ts` | Generator tests |
+| `agents/project-scanner.md` | Add Layer 2 filtering via IgnoreFilter |
+| `skills/understand/SKILL.md` | Add Phase 0.5 (generate + pause for review) |
+| `packages/core/package.json` | Add `ignore` npm dependency |

From c0776233898fbbb9f8ee21c63c72d66d18703bb7 Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Fri, 10 Apr 2026 11:27:47 +0800
Subject: [PATCH 05/15] docs: add .understandignore implementation plan (7
 tasks)

TDD-driven plan covering IgnoreFilter module, IgnoreGenerator, core exports,
project-scanner agent update, and skill Phase 0.5 integration.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../plans/2026-04-10-understandignore-impl.md | 776 ++++++++++++++++++
 1 file changed, 776 insertions(+)
 create mode 100644 docs/superpowers/plans/2026-04-10-understandignore-impl.md

diff --git a/docs/superpowers/plans/2026-04-10-understandignore-impl.md b/docs/superpowers/plans/2026-04-10-understandignore-impl.md
new file mode 100644
index 0000000..4bc782d
--- /dev/null
+++ b/docs/superpowers/plans/2026-04-10-understandignore-impl.md
@@ -0,0 +1,776 @@
+# .understandignore Implementation Plan
+
+> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.
+
+**Goal:** Add user-configurable file exclusion via `.understandignore` files using `.gitignore` syntax, with auto-generated starter files and a pre-analysis review pause.
+
+**Architecture:** An `IgnoreFilter` module in `packages/core` uses the `ignore` npm package to parse `.understandignore` files and filter paths. A companion `IgnoreGenerator` scans the project for common patterns and produces a commented-out starter file. The `project-scanner` agent applies the filter as a second pass after its existing hardcoded exclusions. The `/understand` skill adds a Phase 0.5 that generates the starter file and pauses for user review.
+
+**Tech Stack:** TypeScript, `ignore` npm package, Vitest
+
+**Spec:** `docs/superpowers/specs/2026-04-10-understandignore-design.md`
+
+---
+
+## File Structure
+
+### Core package
+- Create: `understand-anything-plugin/packages/core/src/ignore-filter.ts` — parse .understandignore, merge with defaults, filter paths
+- Create: `understand-anything-plugin/packages/core/src/ignore-generator.ts` — generate starter .understandignore by scanning project
+- Create: `understand-anything-plugin/packages/core/src/__tests__/ignore-filter.test.ts` — filter tests
+- Create: `understand-anything-plugin/packages/core/src/__tests__/ignore-generator.test.ts` — generator tests
+- Modify: `understand-anything-plugin/packages/core/src/index.ts` — export new modules
+- Modify: `understand-anything-plugin/packages/core/package.json` — add `ignore` dependency
+
+### Agents & skills
+- Modify: `understand-anything-plugin/agents/project-scanner.md` — add Layer 2 filtering step
+- Modify: `understand-anything-plugin/skills/understand/SKILL.md` — add Phase 0.5
+
+---
+
+## Task 1: Add `ignore` dependency
+
+**Files:**
+- Modify: `understand-anything-plugin/packages/core/package.json`
+
+- [ ] **Step 1: Install the `ignore` npm package**
+
+Run:
+```bash
+cd understand-anything-plugin && pnpm add --filter @understand-anything/core ignore
+```
+
+- [ ] **Step 2: Verify it was added**
+
+Run: `grep ignore understand-anything-plugin/packages/core/package.json`
+Expected: `"ignore": "^7.x.x"` (or similar) in dependencies
+
+- [ ] **Step 3: Commit**
+
+```bash
+git add understand-anything-plugin/packages/core/package.json understand-anything-plugin/pnpm-lock.yaml
+git commit -m "chore(core): add ignore package for .understandignore support"
+```
+
+---
+
+## Task 2: Create IgnoreFilter module with tests (TDD)
+
+**Files:**
+- Create: `understand-anything-plugin/packages/core/src/ignore-filter.ts`
+- Create: `understand-anything-plugin/packages/core/src/__tests__/ignore-filter.test.ts`
+
+- [ ] **Step 1: Write the failing tests**
+
+Create `understand-anything-plugin/packages/core/src/__tests__/ignore-filter.test.ts`:
+
+```typescript
+import { describe, it, expect, beforeEach, afterEach } from "vitest";
+import { createIgnoreFilter, DEFAULT_IGNORE_PATTERNS } from "../ignore-filter";
+import { mkdirSync, writeFileSync, rmSync } from "node:fs";
+import { join } from "node:path";
+import { tmpdir } from "node:os";
+
+describe("IgnoreFilter", () => {
+  let testDir: string;
+
+  beforeEach(() => {
+    testDir = join(tmpdir(), `ignore-filter-test-${Date.now()}`);
+    mkdirSync(testDir, { recursive: true });
+    mkdirSync(join(testDir, ".understand-anything"), { recursive: true });
+  });
+
+  afterEach(() => {
+    rmSync(testDir, { recursive: true, force: true });
+  });
+
+  describe("DEFAULT_IGNORE_PATTERNS", () => {
+    it("contains node_modules", () => {
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("node_modules/");
+    });
+
+    it("contains .git", () => {
+      expect(DEFAULT_IGNORE_PATTERNS).toContain(".git/");
+    });
+
+    it("contains bin and obj for .NET", () => {
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("bin/");
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("obj/");
+    });
+
+    it("contains build output directories", () => {
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("dist/");
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("build/");
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("out/");
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("coverage/");
+    });
+  });
+
+  describe("createIgnoreFilter with no user file", () => {
+    it("ignores files matching default patterns", () => {
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("node_modules/foo/bar.js")).toBe(true);
+      expect(filter.isIgnored("dist/index.js")).toBe(true);
+      expect(filter.isIgnored(".git/config")).toBe(true);
+      expect(filter.isIgnored("bin/Debug/app.dll")).toBe(true);
+      expect(filter.isIgnored("obj/Release/net8.0/app.dll")).toBe(true);
+    });
+
+    it("does not ignore source files", () => {
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("src/index.ts")).toBe(false);
+      expect(filter.isIgnored("README.md")).toBe(false);
+      expect(filter.isIgnored("package.json")).toBe(false);
+    });
+
+    it("ignores lock files", () => {
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("pnpm-lock.yaml")).toBe(true);
+      expect(filter.isIgnored("package-lock.json")).toBe(true);
+      expect(filter.isIgnored("yarn.lock")).toBe(true);
+    });
+
+    it("ignores binary/asset files", () => {
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("logo.png")).toBe(true);
+      expect(filter.isIgnored("font.woff2")).toBe(true);
+      expect(filter.isIgnored("doc.pdf")).toBe(true);
+    });
+
+    it("ignores generated files", () => {
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("bundle.min.js")).toBe(true);
+      expect(filter.isIgnored("style.min.css")).toBe(true);
+      expect(filter.isIgnored("source.map")).toBe(true);
+    });
+
+    it("ignores IDE directories", () => {
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored(".idea/workspace.xml")).toBe(true);
+      expect(filter.isIgnored(".vscode/settings.json")).toBe(true);
+    });
+  });
+
+  describe("createIgnoreFilter with user .understandignore", () => {
+    it("reads patterns from .understand-anything/.understandignore", () => {
+      writeFileSync(
+        join(testDir, ".understand-anything", ".understandignore"),
+        "# Exclude tests\n__tests__/\n*.test.ts\n"
+      );
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("__tests__/foo.test.ts")).toBe(true);
+      expect(filter.isIgnored("src/utils.test.ts")).toBe(true);
+      expect(filter.isIgnored("src/utils.ts")).toBe(false);
+    });
+
+    it("reads patterns from project root .understandignore", () => {
+      writeFileSync(
+        join(testDir, ".understandignore"),
+        "docs/\n"
+      );
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("docs/README.md")).toBe(true);
+      expect(filter.isIgnored("src/index.ts")).toBe(false);
+    });
+
+    it("handles # comments and blank lines", () => {
+      writeFileSync(
+        join(testDir, ".understand-anything", ".understandignore"),
+        "# This is a comment\n\n\nfixtures/\n\n# Another comment\n"
+      );
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("fixtures/data.json")).toBe(true);
+      expect(filter.isIgnored("src/index.ts")).toBe(false);
+    });
+
+    it("supports ! negation to override defaults", () => {
+      writeFileSync(
+        join(testDir, ".understand-anything", ".understandignore"),
+        "!dist/\n"
+      );
+      const filter = createIgnoreFilter(testDir);
+      // dist/ is in defaults but negated by user
+      expect(filter.isIgnored("dist/index.js")).toBe(false);
+    });
+
+    it("supports ** recursive matching", () => {
+      writeFileSync(
+        join(testDir, ".understand-anything", ".understandignore"),
+        "**/snapshots/\n"
+      );
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("src/components/snapshots/Button.snap")).toBe(true);
+      expect(filter.isIgnored("snapshots/foo.snap")).toBe(true);
+    });
+
+    it("merges .understand-anything/ and root .understandignore", () => {
+      writeFileSync(
+        join(testDir, ".understand-anything", ".understandignore"),
+        "__tests__/\n"
+      );
+      writeFileSync(
+        join(testDir, ".understandignore"),
+        "fixtures/\n"
+      );
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("__tests__/foo.ts")).toBe(true);
+      expect(filter.isIgnored("fixtures/data.json")).toBe(true);
+      expect(filter.isIgnored("src/index.ts")).toBe(false);
+    });
+  });
+});
+```
+
+- [ ] **Step 2: Run tests to verify they fail**
+
+Run: `pnpm --filter @understand-anything/core test -- --run src/__tests__/ignore-filter.test.ts`
+Expected: FAIL — module not found
+
+- [ ] **Step 3: Implement IgnoreFilter**
+
+Create `understand-anything-plugin/packages/core/src/ignore-filter.ts`:
+
+```typescript
+import ignore, { type Ignore } from "ignore";
+import { readFileSync, existsSync } from "node:fs";
+import { join } from "node:path";
+
+/**
+ * Hardcoded default ignore patterns matching the project-scanner agent's
+ * exclusion rules, plus bin/obj for .NET projects.
+ */
+export const DEFAULT_IGNORE_PATTERNS: string[] = [
+  // Dependency directories
+  "node_modules/",
+  ".git/",
+  "vendor/",
+  "venv/",
+  ".venv/",
+  "__pycache__/",
+
+  // Build output
+  "dist/",
+  "build/",
+  "out/",
+  "coverage/",
+  ".next/",
+  ".cache/",
+  ".turbo/",
+  "target/",
+  "bin/",
+  "obj/",
+
+  // Lock files
+  "*.lock",
+  "package-lock.json",
+  "yarn.lock",
+  "pnpm-lock.yaml",
+
+  // Binary/asset files
+  "*.png",
+  "*.jpg",
+  "*.jpeg",
+  "*.gif",
+  "*.svg",
+  "*.ico",
+  "*.woff",
+  "*.woff2",
+  "*.ttf",
+  "*.eot",
+  "*.mp3",
+  "*.mp4",
+  "*.pdf",
+  "*.zip",
+  "*.tar",
+  "*.gz",
+
+  // Generated files
+  "*.min.js",
+  "*.min.css",
+  "*.map",
+  "*.generated.*",
+
+  // IDE/editor
+  ".idea/",
+  ".vscode/",
+
+  // Misc
+  "LICENSE",
+  ".gitignore",
+  ".editorconfig",
+  ".prettierrc",
+  ".eslintrc*",
+  "*.log",
+];
+
+export interface IgnoreFilter {
+  /** Returns true if the given relative path should be excluded from analysis. */
+  isIgnored(relativePath: string): boolean;
+}
+
+/**
+ * Creates an IgnoreFilter that merges hardcoded defaults with user-defined
+ * patterns from .understandignore files.
+ *
+ * Pattern load order (later entries can override earlier ones via ! negation):
+ * 1. Hardcoded defaults
+ * 2. .understand-anything/.understandignore (if exists)
+ * 3. .understandignore at project root (if exists)
+ */
+export function createIgnoreFilter(projectRoot: string): IgnoreFilter {
+  const ig: Ignore = ignore();
+
+  // Layer 1: hardcoded defaults
+  ig.add(DEFAULT_IGNORE_PATTERNS);
+
+  // Layer 2: .understand-anything/.understandignore
+  const projectIgnorePath = join(projectRoot, ".understand-anything", ".understandignore");
+  if (existsSync(projectIgnorePath)) {
+    const content = readFileSync(projectIgnorePath, "utf-8");
+    ig.add(content);
+  }
+
+  // Layer 3: .understandignore at project root
+  const rootIgnorePath = join(projectRoot, ".understandignore");
+  if (existsSync(rootIgnorePath)) {
+    const content = readFileSync(rootIgnorePath, "utf-8");
+    ig.add(content);
+  }
+
+  return {
+    isIgnored(relativePath: string): boolean {
+      return ig.ignores(relativePath);
+    },
+  };
+}
+```
+
+- [ ] **Step 4: Run tests to verify they pass**
+
+Run: `pnpm --filter @understand-anything/core test -- --run src/__tests__/ignore-filter.test.ts`
+Expected: All tests PASS
+
+- [ ] **Step 5: Build to verify no type errors**
+
+Run: `pnpm --filter @understand-anything/core build`
+Expected: Clean build
+
+- [ ] **Step 6: Commit**
+
+```bash
+git add understand-anything-plugin/packages/core/src/ignore-filter.ts understand-anything-plugin/packages/core/src/__tests__/ignore-filter.test.ts
+git commit -m "feat(core): add IgnoreFilter module with .understandignore parsing and tests"
+```
+
+---
+
+## Task 3: Create IgnoreGenerator module with tests (TDD)
+
+**Files:**
+- Create: `understand-anything-plugin/packages/core/src/ignore-generator.ts`
+- Create: `understand-anything-plugin/packages/core/src/__tests__/ignore-generator.test.ts`
+
+- [ ] **Step 1: Write the failing tests**
+
+Create `understand-anything-plugin/packages/core/src/__tests__/ignore-generator.test.ts`:
+
+```typescript
+import { describe, it, expect, beforeEach, afterEach } from "vitest";
+import { generateStarterIgnoreFile } from "../ignore-generator";
+import { mkdirSync, rmSync, writeFileSync } from "node:fs";
+import { join } from "node:path";
+import { tmpdir } from "node:os";
+
+describe("generateStarterIgnoreFile", () => {
+  let testDir: string;
+
+  beforeEach(() => {
+    testDir = join(tmpdir(), `ignore-gen-test-${Date.now()}`);
+    mkdirSync(testDir, { recursive: true });
+  });
+
+  afterEach(() => {
+    rmSync(testDir, { recursive: true, force: true });
+  });
+
+  it("includes a header comment explaining the file", () => {
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain(".understandignore");
+    expect(content).toContain("same as .gitignore");
+    expect(content).toContain("Built-in defaults");
+  });
+
+  it("all suggestions are commented out", () => {
+    // Create some directories to trigger suggestions
+    mkdirSync(join(testDir, "__tests__"), { recursive: true });
+    mkdirSync(join(testDir, "docs"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    const lines = content.split("\n").filter((l) => l.trim() && !l.startsWith("#"));
+    // No active (uncommented) patterns
+    expect(lines).toHaveLength(0);
+  });
+
+  it("suggests __tests__ when __tests__ directory exists", () => {
+    mkdirSync(join(testDir, "__tests__"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# __tests__/");
+  });
+
+  it("suggests docs when docs directory exists", () => {
+    mkdirSync(join(testDir, "docs"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# docs/");
+  });
+
+  it("suggests test directories when they exist", () => {
+    mkdirSync(join(testDir, "test"), { recursive: true });
+    mkdirSync(join(testDir, "tests"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# test/");
+    expect(content).toContain("# tests/");
+  });
+
+  it("suggests fixtures when fixtures directory exists", () => {
+    mkdirSync(join(testDir, "fixtures"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# fixtures/");
+  });
+
+  it("suggests examples when examples directory exists", () => {
+    mkdirSync(join(testDir, "examples"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# examples/");
+  });
+
+  it("suggests .storybook when .storybook directory exists", () => {
+    mkdirSync(join(testDir, ".storybook"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# .storybook/");
+  });
+
+  it("suggests migrations when migrations directory exists", () => {
+    mkdirSync(join(testDir, "migrations"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# migrations/");
+  });
+
+  it("suggests scripts when scripts directory exists", () => {
+    mkdirSync(join(testDir, "scripts"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# scripts/");
+  });
+
+  it("always includes generic suggestions", () => {
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# *.snap");
+    expect(content).toContain("# *.test.*");
+    expect(content).toContain("# *.spec.*");
+  });
+
+  it("does not suggest directories that don't exist", () => {
+    const content = generateStarterIgnoreFile(testDir);
+    // __tests__ doesn't exist, so it shouldn't be in directory suggestions
+    // (it may still be in generic test file patterns)
+    expect(content).not.toContain("# __tests__/");
+    expect(content).not.toContain("# .storybook/");
+  });
+});
+```
+
+- [ ] **Step 2: Run tests to verify they fail**
+
+Run: `pnpm --filter @understand-anything/core test -- --run src/__tests__/ignore-generator.test.ts`
+Expected: FAIL — module not found
+
+- [ ] **Step 3: Implement IgnoreGenerator**
+
+Create `understand-anything-plugin/packages/core/src/ignore-generator.ts`:
+
+```typescript
+import { existsSync } from "node:fs";
+import { join } from "node:path";
+
+const HEADER = `# .understandignore — patterns for files/dirs to exclude from analysis
+# Syntax: same as .gitignore (globs, # comments, ! negation, trailing / for dirs)
+# Lines below are suggestions — uncomment to activate.
+# Use ! prefix to force-include something excluded by defaults.
+#
+# Built-in defaults (always excluded unless negated):
+#   node_modules/, .git/, dist/, build/, bin/, obj/, *.lock, *.min.js, etc.
+#
+`;
+
+/** Directories to check for and suggest excluding. */
+const DETECTABLE_DIRS = [
+  { dir: "__tests__", pattern: "__tests__/" },
+  { dir: "test", pattern: "test/" },
+  { dir: "tests", pattern: "tests/" },
+  { dir: "fixtures", pattern: "fixtures/" },
+  { dir: "testdata", pattern: "testdata/" },
+  { dir: "docs", pattern: "docs/" },
+  { dir: "examples", pattern: "examples/" },
+  { dir: "scripts", pattern: "scripts/" },
+  { dir: "migrations", pattern: "migrations/" },
+  { dir: ".storybook", pattern: ".storybook/" },
+];
+
+/** Always-included generic suggestions. */
+const GENERIC_SUGGESTIONS = [
+  "*.test.*",
+  "*.spec.*",
+  "*.snap",
+];
+
+/**
+ * Generates a starter .understandignore file by scanning the project root
+ * for common directories and suggesting them as commented-out exclusions.
+ *
+ * All suggestions are commented out — the user must uncomment to activate.
+ * Returns the file content as a string.
+ */
+export function generateStarterIgnoreFile(projectRoot: string): string {
+  const sections: string[] = [HEADER];
+
+  // Detected directory suggestions
+  const detected: string[] = [];
+  for (const { dir, pattern } of DETECTABLE_DIRS) {
+    if (existsSync(join(projectRoot, dir))) {
+      detected.push(pattern);
+    }
+  }
+
+  if (detected.length > 0) {
+    sections.push("# --- Detected directories (uncomment to exclude) ---\n");
+    for (const pattern of detected) {
+      sections.push(`# ${pattern}`);
+    }
+    sections.push("");
+  }
+
+  // Generic suggestions (always included)
+  sections.push("# --- Test file patterns (uncomment to exclude) ---\n");
+  for (const pattern of GENERIC_SUGGESTIONS) {
+    sections.push(`# ${pattern}`);
+  }
+  sections.push("");
+
+  return sections.join("\n");
+}
+```
+
+- [ ] **Step 4: Run tests to verify they pass**
+
+Run: `pnpm --filter @understand-anything/core test -- --run src/__tests__/ignore-generator.test.ts`
+Expected: All tests PASS
+
+- [ ] **Step 5: Build**
+
+Run: `pnpm --filter @understand-anything/core build`
+Expected: Clean build
+
+- [ ] **Step 6: Commit**
+
+```bash
+git add understand-anything-plugin/packages/core/src/ignore-generator.ts understand-anything-plugin/packages/core/src/__tests__/ignore-generator.test.ts
+git commit -m "feat(core): add IgnoreGenerator for starter .understandignore file creation"
+```
+
+---
+
+## Task 4: Export new modules from core
+
+**Files:**
+- Modify: `understand-anything-plugin/packages/core/src/index.ts`
+
+- [ ] **Step 1: Add exports**
+
+Add to the end of `understand-anything-plugin/packages/core/src/index.ts`:
+
+```typescript
+export {
+  createIgnoreFilter,
+  DEFAULT_IGNORE_PATTERNS,
+  type IgnoreFilter,
+} from "./ignore-filter.js";
+export { generateStarterIgnoreFile } from "./ignore-generator.js";
+```
+
+- [ ] **Step 2: Build and run all tests**
+
+Run: `pnpm --filter @understand-anything/core build && pnpm --filter @understand-anything/core test -- --run`
+Expected: Clean build, all tests pass
+
+- [ ] **Step 3: Commit**
+
+```bash
+git add understand-anything-plugin/packages/core/src/index.ts
+git commit -m "feat(core): export IgnoreFilter and IgnoreGenerator from core index"
+```
+
+---
+
+## Task 5: Update project-scanner agent
+
+**Files:**
+- Modify: `understand-anything-plugin/agents/project-scanner.md`
+
+- [ ] **Step 1: Read the current project-scanner.md**
+
+Read `understand-anything-plugin/agents/project-scanner.md` to understand the current structure.
+
+- [ ] **Step 2: Add bin/ and obj/ to hardcoded exclusions**
+
+In Step 2 (Exclusion Filtering), add `bin/` and `obj/` to the "Build output" line:
+
+Change:
+```
+- **Build output:** paths with a directory segment matching `dist/`, `build/`, `out/`, `coverage/`, `.next/`, `.cache/`, `.turbo/`, `target/` (Rust)
+```
+
+To:
+```
+- **Build output:** paths with a directory segment matching `dist/`, `build/`, `out/`, `coverage/`, `.next/`, `.cache/`, `.turbo/`, `target/` (Rust), `bin/` (.NET), `obj/` (.NET)
+```
+
+- [ ] **Step 3: Add Layer 2 filtering step**
+
+After Step 2 (Exclusion Filtering), add a new step:
+
+```markdown
+**Step 2.5 -- User-Configured Filtering (.understandignore)**
+
+After applying the hardcoded exclusion filters above, apply user-configured patterns from `.understandignore`:
+
+1. Check if `.understand-anything/.understandignore` exists in the project root. If so, read it.
+2. Check if `.understandignore` exists in the project root. If so, read it.
+3. Parse both files using `.gitignore` syntax (glob patterns, `#` comments, blank lines ignored, `!` prefix for negation, trailing `/` for directories, `**/` for recursive matching).
+4. Filter the remaining file list through these patterns. Files matching any pattern are excluded.
+5. `!` negation patterns override the hardcoded exclusions from Step 2 (e.g., `!dist/` force-includes dist/).
+6. Track the count of files removed by this step as `filteredByIgnore`.
+
+This filtering must be deterministic (not LLM-based). Use a Node.js script with the `ignore` npm package if implementing programmatically, or apply the patterns manually if the file list is small.
+```
+
+- [ ] **Step 4: Update scan output schema**
+
+Find the output JSON schema section and add `filteredByIgnore` field:
+
+```json
+{
+  "name": "...",
+  "description": "...",
+  "languages": ["..."],
+  "frameworks": ["..."],
+  "files": [...],
+  "totalFiles": 123,
+  "filteredByIgnore": 5,
+  "estimatedComplexity": "moderate",
+  "importMap": {}
+}
+```
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add understand-anything-plugin/agents/project-scanner.md
+git commit -m "feat(agent): add .understandignore support and bin/obj exclusions to project-scanner"
+```
+
+---
+
+## Task 6: Update /understand skill with Phase 0.5
+
+**Files:**
+- Modify: `understand-anything-plugin/skills/understand/SKILL.md`
+
+- [ ] **Step 1: Read the current SKILL.md Phase 0 section**
+
+Read `understand-anything-plugin/skills/understand/SKILL.md` lines 22-80 to understand Phase 0.
+
+- [ ] **Step 2: Add Phase 0.5 after Phase 0**
+
+After the Phase 0 section (after the `---` separator before Phase 1), insert:
+
+```markdown
+## Phase 0.5 — Ignore Configuration
+
+Set up and verify the `.understandignore` file before scanning.
+
+1. Check if `$PROJECT_ROOT/.understand-anything/.understandignore` exists.
+2. **If it does NOT exist**, generate a starter file:
+   - Run a Node.js script (or inline logic) that scans `$PROJECT_ROOT` for common directories (`__tests__/`, `test/`, `tests/`, `fixtures/`, `testdata/`, `docs/`, `examples/`, `scripts/`, `migrations/`, `.storybook/`) and generates a `.understandignore` file with commented-out suggestions.
+   - Write the generated content to `$PROJECT_ROOT/.understand-anything/.understandignore`.
+   - Report to the user:
+     > "Generated `.understand-anything/.understandignore` with suggested exclusions based on your project structure. Please review it and uncomment any patterns you'd like to exclude from analysis. When ready, confirm to continue."
+   - **Wait for user confirmation before proceeding.**
+3. **If it already exists**, report:
+   > "Found `.understand-anything/.understandignore`. Review it if needed, then confirm to continue."
+   - **Wait for user confirmation before proceeding.**
+4. After confirmation, proceed to Phase 1.
+
+**Note:** The `.understandignore` file uses `.gitignore` syntax. The user can add patterns to exclude files from analysis, or use `!` prefix to force-include files excluded by built-in defaults (e.g., `!dist/` to analyze dist/ files).
+
+---
+```
+
+- [ ] **Step 3: Update Phase 1 reporting**
+
+In the Phase 1 section, after the gate check (~line 114), add a note about reporting ignore stats:
+
+```markdown
+After scanning, if the scan result includes `filteredByIgnore > 0`, report:
+> "Scanned {totalFiles} files ({filteredByIgnore} excluded by .understandignore)"
+```
+
+- [ ] **Step 4: Commit**
+
+```bash
+git add understand-anything-plugin/skills/understand/SKILL.md
+git commit -m "feat(skill): add Phase 0.5 for .understandignore setup and review pause"
+```
+
+---
+
+## Task 7: Build, test, and verify end-to-end
+
+**Files:**
+- All modified files
+
+- [ ] **Step 1: Build core**
+
+Run: `pnpm --filter @understand-anything/core build`
+Expected: Clean build
+
+- [ ] **Step 2: Run all core tests**
+
+Run: `pnpm --filter @understand-anything/core test -- --run`
+Expected: All tests pass (existing + new ignore-filter + ignore-generator tests)
+
+- [ ] **Step 3: Build skill package**
+
+Run: `pnpm --filter @understand-anything/skill build`
+Expected: Clean build
+
+- [ ] **Step 4: Verify files exist**
+
+Run:
+```bash
+ls understand-anything-plugin/packages/core/src/ignore-filter.ts understand-anything-plugin/packages/core/src/ignore-generator.ts
+```
+Expected: Both files listed
+
+- [ ] **Step 5: Verify exports work**
+
+Run:
+```bash
+node -e "import('@understand-anything/core').then(m => { console.log('IgnoreFilter:', typeof m.createIgnoreFilter); console.log('Generator:', typeof m.generateStarterIgnoreFile); })"
+```
+Expected: Both show `function`
+
+- [ ] **Step 6: Final commit (if any unstaged changes)**
+
+```bash
+git status
+# If clean, skip. If changes exist:
+git add -A && git commit -m "chore: final verification for .understandignore support"
+```

From 07b02d18ae3f8a348a3cde4fcabdf1394f3cf5a4 Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Fri, 10 Apr 2026 11:30:52 +0800
Subject: [PATCH 06/15] chore(core): add ignore package for .understandignore
 support

---
 .../packages/core/package.json                |  1 +
 understand-anything-plugin/pnpm-lock.yaml     | 19 ++++++++++++++++++-
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/understand-anything-plugin/packages/core/package.json b/understand-anything-plugin/packages/core/package.json
index 457aae8..2318ddc 100644
--- a/understand-anything-plugin/packages/core/package.json
+++ b/understand-anything-plugin/packages/core/package.json
@@ -38,6 +38,7 @@
   },
   "dependencies": {
     "fuse.js": "^7.1.0",
+    "ignore": "^7.0.5",
     "tree-sitter-javascript": "^0.25.0",
     "tree-sitter-typescript": "^0.23.2",
     "web-tree-sitter": "^0.26.6",
diff --git a/understand-anything-plugin/pnpm-lock.yaml b/understand-anything-plugin/pnpm-lock.yaml
index 0134903..01e7e07 100644
--- a/understand-anything-plugin/pnpm-lock.yaml
+++ b/understand-anything-plugin/pnpm-lock.yaml
@@ -27,6 +27,9 @@ importers:
       fuse.js:
         specifier: ^7.1.0
         version: 7.1.0
+      ignore:
+        specifier: ^7.0.5
+        version: 7.0.5
       tree-sitter-javascript:
         specifier: ^0.25.0
         version: 0.25.0
@@ -998,6 +1001,10 @@ packages:
   html-url-attributes@3.0.1:
     resolution: {integrity: sha512-ol6UPyBWqsrO6EJySPz2O7ZSr856WDrEzM5zMqp+FJJLGMW35cLYmmZnl0vztAZxRUoNZJFTCohfjuIJ8I4QBQ==}
 
+  ignore@7.0.5:
+    resolution: {integrity: sha512-Hs59xBNfUIunMFgWAbGX5cq6893IbWg4KnrjbYwX3tx0ztorVgTDA6B2sxf8ejHJ4wz8BqGUMYlnzNBer5NvGg==}
+    engines: {node: '>= 4'}
+
   inline-style-parser@0.2.7:
     resolution: {integrity: sha512-Nb2ctOyNR8DqQoR0OwRG95uNWIC0C1lCgf5Naz5H6Ji72KZ8OcFZLz2P5sNgwlyoJ8Yif11oMuYs5pBQa86csA==}
 
@@ -2184,6 +2191,14 @@ snapshots:
     optionalDependencies:
       vite: 6.4.1(@types/node@22.19.15)(jiti@2.6.1)(lightningcss@1.32.0)(yaml@2.8.3)
 
+  '@vitest/mocker@3.2.4(vite@6.4.1(@types/node@25.5.0)(jiti@2.6.1)(lightningcss@1.32.0)(yaml@2.8.3))':
+    dependencies:
+      '@vitest/spy': 3.2.4
+      estree-walker: 3.0.3
+      magic-string: 0.30.21
+    optionalDependencies:
+      vite: 6.4.1(@types/node@25.5.0)(jiti@2.6.1)(lightningcss@1.32.0)(yaml@2.8.3)
+
   '@vitest/pretty-format@3.2.4':
     dependencies:
       tinyrainbow: 2.0.0
@@ -2486,6 +2501,8 @@ snapshots:
 
   html-url-attributes@3.0.1: {}
 
+  ignore@7.0.5: {}
+
   inline-style-parser@0.2.7: {}
 
   is-alphabetical@2.0.1: {}
@@ -3256,7 +3273,7 @@ snapshots:
     dependencies:
       '@types/chai': 5.2.3
       '@vitest/expect': 3.2.4
-      '@vitest/mocker': 3.2.4(vite@6.4.1(@types/node@22.19.15)(jiti@2.6.1)(lightningcss@1.32.0)(yaml@2.8.3))
+      '@vitest/mocker': 3.2.4(vite@6.4.1(@types/node@25.5.0)(jiti@2.6.1)(lightningcss@1.32.0)(yaml@2.8.3))
       '@vitest/pretty-format': 3.2.4
       '@vitest/runner': 3.2.4
       '@vitest/snapshot': 3.2.4

From 5e86254b7775b9759dbaa05b667e77241885b1bc Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Fri, 10 Apr 2026 11:33:10 +0800
Subject: [PATCH 07/15] feat(core): add IgnoreFilter module with
 .understandignore parsing and tests

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../core/src/__tests__/ignore-filter.test.ts  | 153 ++++++++++++++++++
 .../packages/core/src/ignore-filter.ts        | 112 +++++++++++++
 2 files changed, 265 insertions(+)
 create mode 100644 understand-anything-plugin/packages/core/src/__tests__/ignore-filter.test.ts
 create mode 100644 understand-anything-plugin/packages/core/src/ignore-filter.ts

diff --git a/understand-anything-plugin/packages/core/src/__tests__/ignore-filter.test.ts b/understand-anything-plugin/packages/core/src/__tests__/ignore-filter.test.ts
new file mode 100644
index 0000000..28c8c7e
--- /dev/null
+++ b/understand-anything-plugin/packages/core/src/__tests__/ignore-filter.test.ts
@@ -0,0 +1,153 @@
+import { describe, it, expect, beforeEach, afterEach } from "vitest";
+import { createIgnoreFilter, DEFAULT_IGNORE_PATTERNS } from "../ignore-filter";
+import { mkdirSync, writeFileSync, rmSync } from "node:fs";
+import { join } from "node:path";
+import { tmpdir } from "node:os";
+
+describe("IgnoreFilter", () => {
+  let testDir: string;
+
+  beforeEach(() => {
+    testDir = join(tmpdir(), `ignore-filter-test-${Date.now()}`);
+    mkdirSync(testDir, { recursive: true });
+    mkdirSync(join(testDir, ".understand-anything"), { recursive: true });
+  });
+
+  afterEach(() => {
+    rmSync(testDir, { recursive: true, force: true });
+  });
+
+  describe("DEFAULT_IGNORE_PATTERNS", () => {
+    it("contains node_modules", () => {
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("node_modules/");
+    });
+
+    it("contains .git", () => {
+      expect(DEFAULT_IGNORE_PATTERNS).toContain(".git/");
+    });
+
+    it("contains bin and obj for .NET", () => {
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("bin/");
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("obj/");
+    });
+
+    it("contains build output directories", () => {
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("dist/");
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("build/");
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("out/");
+      expect(DEFAULT_IGNORE_PATTERNS).toContain("coverage/");
+    });
+  });
+
+  describe("createIgnoreFilter with no user file", () => {
+    it("ignores files matching default patterns", () => {
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("node_modules/foo/bar.js")).toBe(true);
+      expect(filter.isIgnored("dist/index.js")).toBe(true);
+      expect(filter.isIgnored(".git/config")).toBe(true);
+      expect(filter.isIgnored("bin/Debug/app.dll")).toBe(true);
+      expect(filter.isIgnored("obj/Release/net8.0/app.dll")).toBe(true);
+    });
+
+    it("does not ignore source files", () => {
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("src/index.ts")).toBe(false);
+      expect(filter.isIgnored("README.md")).toBe(false);
+      expect(filter.isIgnored("package.json")).toBe(false);
+    });
+
+    it("ignores lock files", () => {
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("pnpm-lock.yaml")).toBe(true);
+      expect(filter.isIgnored("package-lock.json")).toBe(true);
+      expect(filter.isIgnored("yarn.lock")).toBe(true);
+    });
+
+    it("ignores binary/asset files", () => {
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("logo.png")).toBe(true);
+      expect(filter.isIgnored("font.woff2")).toBe(true);
+      expect(filter.isIgnored("doc.pdf")).toBe(true);
+    });
+
+    it("ignores generated files", () => {
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("bundle.min.js")).toBe(true);
+      expect(filter.isIgnored("style.min.css")).toBe(true);
+      expect(filter.isIgnored("source.map")).toBe(true);
+    });
+
+    it("ignores IDE directories", () => {
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored(".idea/workspace.xml")).toBe(true);
+      expect(filter.isIgnored(".vscode/settings.json")).toBe(true);
+    });
+  });
+
+  describe("createIgnoreFilter with user .understandignore", () => {
+    it("reads patterns from .understand-anything/.understandignore", () => {
+      writeFileSync(
+        join(testDir, ".understand-anything", ".understandignore"),
+        "# Exclude tests\n__tests__/\n*.test.ts\n"
+      );
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("__tests__/foo.test.ts")).toBe(true);
+      expect(filter.isIgnored("src/utils.test.ts")).toBe(true);
+      expect(filter.isIgnored("src/utils.ts")).toBe(false);
+    });
+
+    it("reads patterns from project root .understandignore", () => {
+      writeFileSync(
+        join(testDir, ".understandignore"),
+        "docs/\n"
+      );
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("docs/README.md")).toBe(true);
+      expect(filter.isIgnored("src/index.ts")).toBe(false);
+    });
+
+    it("handles # comments and blank lines", () => {
+      writeFileSync(
+        join(testDir, ".understand-anything", ".understandignore"),
+        "# This is a comment\n\n\nfixtures/\n\n# Another comment\n"
+      );
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("fixtures/data.json")).toBe(true);
+      expect(filter.isIgnored("src/index.ts")).toBe(false);
+    });
+
+    it("supports ! negation to override defaults", () => {
+      writeFileSync(
+        join(testDir, ".understand-anything", ".understandignore"),
+        "!dist/\n"
+      );
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("dist/index.js")).toBe(false);
+    });
+
+    it("supports ** recursive matching", () => {
+      writeFileSync(
+        join(testDir, ".understand-anything", ".understandignore"),
+        "**/snapshots/\n"
+      );
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("src/components/snapshots/Button.snap")).toBe(true);
+      expect(filter.isIgnored("snapshots/foo.snap")).toBe(true);
+    });
+
+    it("merges .understand-anything/ and root .understandignore", () => {
+      writeFileSync(
+        join(testDir, ".understand-anything", ".understandignore"),
+        "__tests__/\n"
+      );
+      writeFileSync(
+        join(testDir, ".understandignore"),
+        "fixtures/\n"
+      );
+      const filter = createIgnoreFilter(testDir);
+      expect(filter.isIgnored("__tests__/foo.ts")).toBe(true);
+      expect(filter.isIgnored("fixtures/data.json")).toBe(true);
+      expect(filter.isIgnored("src/index.ts")).toBe(false);
+    });
+  });
+});
diff --git a/understand-anything-plugin/packages/core/src/ignore-filter.ts b/understand-anything-plugin/packages/core/src/ignore-filter.ts
new file mode 100644
index 0000000..88a65b9
--- /dev/null
+++ b/understand-anything-plugin/packages/core/src/ignore-filter.ts
@@ -0,0 +1,112 @@
+import ignore, { type Ignore } from "ignore";
+import { readFileSync, existsSync } from "node:fs";
+import { join } from "node:path";
+
+/**
+ * Hardcoded default ignore patterns matching the project-scanner agent's
+ * exclusion rules, plus bin/obj for .NET projects.
+ */
+export const DEFAULT_IGNORE_PATTERNS: string[] = [
+  // Dependency directories
+  "node_modules/",
+  ".git/",
+  "vendor/",
+  "venv/",
+  ".venv/",
+  "__pycache__/",
+
+  // Build output
+  "dist/",
+  "build/",
+  "out/",
+  "coverage/",
+  ".next/",
+  ".cache/",
+  ".turbo/",
+  "target/",
+  "bin/",
+  "obj/",
+
+  // Lock files
+  "*.lock",
+  "package-lock.json",
+  "yarn.lock",
+  "pnpm-lock.yaml",
+
+  // Binary/asset files
+  "*.png",
+  "*.jpg",
+  "*.jpeg",
+  "*.gif",
+  "*.svg",
+  "*.ico",
+  "*.woff",
+  "*.woff2",
+  "*.ttf",
+  "*.eot",
+  "*.mp3",
+  "*.mp4",
+  "*.pdf",
+  "*.zip",
+  "*.tar",
+  "*.gz",
+
+  // Generated files
+  "*.min.js",
+  "*.min.css",
+  "*.map",
+  "*.generated.*",
+
+  // IDE/editor
+  ".idea/",
+  ".vscode/",
+
+  // Misc
+  "LICENSE",
+  ".gitignore",
+  ".editorconfig",
+  ".prettierrc",
+  ".eslintrc*",
+  "*.log",
+];
+
+export interface IgnoreFilter {
+  /** Returns true if the given relative path should be excluded from analysis. */
+  isIgnored(relativePath: string): boolean;
+}
+
+/**
+ * Creates an IgnoreFilter that merges hardcoded defaults with user-defined
+ * patterns from .understandignore files.
+ *
+ * Pattern load order (later entries can override earlier ones via ! negation):
+ * 1. Hardcoded defaults
+ * 2. .understand-anything/.understandignore (if exists)
+ * 3. .understandignore at project root (if exists)
+ */
+export function createIgnoreFilter(projectRoot: string): IgnoreFilter {
+  const ig: Ignore = ignore();
+
+  // Layer 1: hardcoded defaults
+  ig.add(DEFAULT_IGNORE_PATTERNS);
+
+  // Layer 2: .understand-anything/.understandignore
+  const projectIgnorePath = join(projectRoot, ".understand-anything", ".understandignore");
+  if (existsSync(projectIgnorePath)) {
+    const content = readFileSync(projectIgnorePath, "utf-8");
+    ig.add(content);
+  }
+
+  // Layer 3: .understandignore at project root
+  const rootIgnorePath = join(projectRoot, ".understandignore");
+  if (existsSync(rootIgnorePath)) {
+    const content = readFileSync(rootIgnorePath, "utf-8");
+    ig.add(content);
+  }
+
+  return {
+    isIgnored(relativePath: string): boolean {
+      return ig.ignores(relativePath);
+    },
+  };
+}

From 6f8270fb378a418f7c965627346eaeafbfdf3212 Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Fri, 10 Apr 2026 11:36:23 +0800
Subject: [PATCH 08/15] feat(core): add IgnoreGenerator for starter
 .understandignore file creation

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../src/__tests__/ignore-generator.test.ts    | 97 +++++++++++++++++++
 .../packages/core/src/ignore-generator.ts     | 62 ++++++++++++
 2 files changed, 159 insertions(+)
 create mode 100644 understand-anything-plugin/packages/core/src/__tests__/ignore-generator.test.ts
 create mode 100644 understand-anything-plugin/packages/core/src/ignore-generator.ts

diff --git a/understand-anything-plugin/packages/core/src/__tests__/ignore-generator.test.ts b/understand-anything-plugin/packages/core/src/__tests__/ignore-generator.test.ts
new file mode 100644
index 0000000..8c2189b
--- /dev/null
+++ b/understand-anything-plugin/packages/core/src/__tests__/ignore-generator.test.ts
@@ -0,0 +1,97 @@
+import { describe, it, expect, beforeEach, afterEach } from "vitest";
+import { generateStarterIgnoreFile } from "../ignore-generator";
+import { mkdirSync, rmSync } from "node:fs";
+import { join } from "node:path";
+import { tmpdir } from "node:os";
+
+describe("generateStarterIgnoreFile", () => {
+  let testDir: string;
+
+  beforeEach(() => {
+    testDir = join(tmpdir(), `ignore-gen-test-${Date.now()}`);
+    mkdirSync(testDir, { recursive: true });
+  });
+
+  afterEach(() => {
+    rmSync(testDir, { recursive: true, force: true });
+  });
+
+  it("includes a header comment explaining the file", () => {
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain(".understandignore");
+    expect(content).toContain("same as .gitignore");
+    expect(content).toContain("Built-in defaults");
+  });
+
+  it("all suggestions are commented out", () => {
+    mkdirSync(join(testDir, "__tests__"), { recursive: true });
+    mkdirSync(join(testDir, "docs"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    const lines = content.split("\n").filter((l) => l.trim() && !l.startsWith("#"));
+    expect(lines).toHaveLength(0);
+  });
+
+  it("suggests __tests__ when directory exists", () => {
+    mkdirSync(join(testDir, "__tests__"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# __tests__/");
+  });
+
+  it("suggests docs when directory exists", () => {
+    mkdirSync(join(testDir, "docs"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# docs/");
+  });
+
+  it("suggests test and tests when they exist", () => {
+    mkdirSync(join(testDir, "test"), { recursive: true });
+    mkdirSync(join(testDir, "tests"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# test/");
+    expect(content).toContain("# tests/");
+  });
+
+  it("suggests fixtures when directory exists", () => {
+    mkdirSync(join(testDir, "fixtures"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# fixtures/");
+  });
+
+  it("suggests examples when directory exists", () => {
+    mkdirSync(join(testDir, "examples"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# examples/");
+  });
+
+  it("suggests .storybook when directory exists", () => {
+    mkdirSync(join(testDir, ".storybook"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# .storybook/");
+  });
+
+  it("suggests migrations when directory exists", () => {
+    mkdirSync(join(testDir, "migrations"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# migrations/");
+  });
+
+  it("suggests scripts when directory exists", () => {
+    mkdirSync(join(testDir, "scripts"), { recursive: true });
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# scripts/");
+  });
+
+  it("always includes generic test file suggestions", () => {
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).toContain("# *.snap");
+    expect(content).toContain("# *.test.*");
+    expect(content).toContain("# *.spec.*");
+  });
+
+  it("does not suggest directories that don't exist", () => {
+    const content = generateStarterIgnoreFile(testDir);
+    expect(content).not.toContain("# __tests__/");
+    expect(content).not.toContain("# .storybook/");
+    expect(content).not.toContain("# fixtures/");
+  });
+});
diff --git a/understand-anything-plugin/packages/core/src/ignore-generator.ts b/understand-anything-plugin/packages/core/src/ignore-generator.ts
new file mode 100644
index 0000000..021e170
--- /dev/null
+++ b/understand-anything-plugin/packages/core/src/ignore-generator.ts
@@ -0,0 +1,62 @@
+import { existsSync } from "node:fs";
+import { join } from "node:path";
+
+const HEADER = `# .understandignore — patterns for files/dirs to exclude from analysis
+# Syntax: same as .gitignore (globs, # comments, ! negation, trailing / for dirs)
+# Lines below are suggestions — uncomment to activate.
+# Use ! prefix to force-include something excluded by defaults.
+#
+# Built-in defaults (always excluded unless negated):
+#   node_modules/, .git/, dist/, build/, bin/, obj/, *.lock, *.min.js, etc.
+#
+`;
+
+const DETECTABLE_DIRS = [
+  { dir: "__tests__", pattern: "__tests__/" },
+  { dir: "test", pattern: "test/" },
+  { dir: "tests", pattern: "tests/" },
+  { dir: "fixtures", pattern: "fixtures/" },
+  { dir: "testdata", pattern: "testdata/" },
+  { dir: "docs", pattern: "docs/" },
+  { dir: "examples", pattern: "examples/" },
+  { dir: "scripts", pattern: "scripts/" },
+  { dir: "migrations", pattern: "migrations/" },
+  { dir: ".storybook", pattern: ".storybook/" },
+];
+
+const GENERIC_SUGGESTIONS = [
+  "*.test.*",
+  "*.spec.*",
+  "*.snap",
+];
+
+/**
+ * Generates a starter .understandignore file content by scanning the project
+ * for common directories. All suggestions are commented out.
+ */
+export function generateStarterIgnoreFile(projectRoot: string): string {
+  const sections: string[] = [HEADER];
+
+  const detected: string[] = [];
+  for (const { dir, pattern } of DETECTABLE_DIRS) {
+    if (existsSync(join(projectRoot, dir))) {
+      detected.push(pattern);
+    }
+  }
+
+  if (detected.length > 0) {
+    sections.push("# --- Detected directories (uncomment to exclude) ---\n");
+    for (const pattern of detected) {
+      sections.push(`# ${pattern}`);
+    }
+    sections.push("");
+  }
+
+  sections.push("# --- Test file patterns (uncomment to exclude) ---\n");
+  for (const pattern of GENERIC_SUGGESTIONS) {
+    sections.push(`# ${pattern}`);
+  }
+  sections.push("");
+
+  return sections.join("\n");
+}

From 4201cbcb9e20b48056f22b5012d5a245a0aee622 Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Fri, 10 Apr 2026 11:36:53 +0800
Subject: [PATCH 09/15] feat(core): export IgnoreFilter and IgnoreGenerator
 from core index

---
 understand-anything-plugin/packages/core/src/index.ts | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/understand-anything-plugin/packages/core/src/index.ts b/understand-anything-plugin/packages/core/src/index.ts
index 756284d..0375dad 100644
--- a/understand-anything-plugin/packages/core/src/index.ts
+++ b/understand-anything-plugin/packages/core/src/index.ts
@@ -114,3 +114,9 @@ export {
   ShellParser,
   registerAllParsers,
 } from "./plugins/parsers/index.js";
+export {
+  createIgnoreFilter,
+  DEFAULT_IGNORE_PATTERNS,
+  type IgnoreFilter,
+} from "./ignore-filter.js";
+export { generateStarterIgnoreFile } from "./ignore-generator.js";

From 3e27a4a8d448b81a78eda1ab8c9e9454d7128265 Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Fri, 10 Apr 2026 11:38:23 +0800
Subject: [PATCH 10/15] feat(agent): add .understandignore support and bin/obj
 exclusions to project-scanner

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../agents/project-scanner.md                 | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/understand-anything-plugin/agents/project-scanner.md b/understand-anything-plugin/agents/project-scanner.md
index e8814f9..090c281 100644
--- a/understand-anything-plugin/agents/project-scanner.md
+++ b/understand-anything-plugin/agents/project-scanner.md
@@ -39,7 +39,7 @@ Discover all tracked files. In order of preference:
 
 Remove ALL files matching these patterns:
 - **Dependency directories:** paths containing `node_modules/`, `.git/`, `vendor/`, `venv/`, `.venv/`, `__pycache__/`
-- **Build output:** paths with a directory segment matching `dist/`, `build/`, `out/`, `coverage/`, `.next/`, `.cache/`, `.turbo/`, `target/` (Rust) — match full directory segments only, not substrings (e.g., `buildSrc/` should NOT be excluded)
+- **Build output:** paths with a directory segment matching `dist/`, `build/`, `out/`, `coverage/`, `.next/`, `.cache/`, `.turbo/`, `target/` (Rust), `bin/` (.NET), `obj/` (.NET) — match full directory segments only, not substrings (e.g., `buildSrc/` should NOT be excluded)
 - **Lock files:** `*.lock`, `package-lock.json`, `yarn.lock`, `pnpm-lock.yaml`
 - **Binary/asset files:** `.png`, `.jpg`, `.jpeg`, `.gif`, `.svg`, `.ico`, `.woff`, `.woff2`, `.ttf`, `.eot`, `.mp3`, `.mp4`, `.pdf`, `.zip`, `.tar`, `.gz`
 - **Generated files:** `*.min.js`, `*.min.css`, `*.map`, `*.generated.*` (note: do NOT exclude `*.d.ts` — many projects have hand-written declaration files)
@@ -58,6 +58,19 @@ Remove ALL files matching these patterns:
 
 **Note on package manifests:** Config files read for framework detection (`package.json`, `tsconfig.json`, `Cargo.toml`, `go.mod`, `pyproject.toml`, etc.) should also appear in the file list with `fileCategory: "config"`.
 
+**Step 2.5 -- User-Configured Filtering (.understandignore)**
+
+After applying the hardcoded exclusion filters above, apply user-configured patterns from `.understandignore`:
+
+1. Check if `$PROJECT_ROOT/.understand-anything/.understandignore` exists. If so, read it.
+2. Check if `$PROJECT_ROOT/.understandignore` exists. If so, read it.
+3. Parse both files using `.gitignore` syntax (glob patterns, `#` comments, blank lines ignored, `!` prefix for negation, trailing `/` for directories, `**/` for recursive matching).
+4. Filter the remaining file list through these patterns. Files matching any pattern are excluded.
+5. `!` negation patterns override the hardcoded exclusions from Step 2 (e.g., `!dist/` force-includes files from dist/).
+6. Track the count of files removed by this step as `filteredByIgnore`.
+
+This filtering must be deterministic (not LLM-based). Use a Node.js script with the `ignore` npm package from `@understand-anything/core`, or apply the patterns manually if the file list is small.
+
 **Step 3 -- Language Detection**
 
 Map file extensions to language identifiers:
@@ -217,6 +230,7 @@ The script must write this exact JSON structure to the output file:
     {"path": "package.json", "language": "json", "sizeLines": 35, "fileCategory": "config"}
   ],
   "totalFiles": 42,
+  "filteredByIgnore": 0,
   "estimatedComplexity": "moderate",
   "importMap": {
     "src/index.ts": ["src/utils.ts", "src/config.ts"],
@@ -237,6 +251,7 @@ The script must write this exact JSON structure to the output file:
 - `files` (object[]) -- every discovered file, sorted by `path` alphabetically
 - `files[].fileCategory` (string) -- one of: `code`, `config`, `docs`, `infra`, `data`, `script`, `markup`
 - `totalFiles` (integer) -- must equal `files.length`
+- `filteredByIgnore` (integer) -- count of files removed by `.understandignore` patterns in Step 2.5; 0 if no `.understandignore` file exists
 - `estimatedComplexity` (string) -- one of `small`, `moderate`, `large`, `very-large`
 - `importMap` (object) -- map from every file path to its list of resolved project-internal import paths; empty array for non-code files and files with no resolved imports; external packages excluded
 
@@ -281,6 +296,7 @@ Then assemble the final output JSON:
     {"path": "Dockerfile", "language": "dockerfile", "sizeLines": 22, "fileCategory": "infra"}
   ],
   "totalFiles": 42,
+  "filteredByIgnore": 0,
   "estimatedComplexity": "moderate",
   "importMap": {
     "src/index.ts": ["src/utils.ts"]
@@ -295,6 +311,7 @@ Then assemble the final output JSON:
 - `frameworks` (string[]): directly from script output
 - `files` (object[]): directly from script output, including `fileCategory` per file
 - `totalFiles` (integer): directly from script output
+- `filteredByIgnore` (integer): directly from script output
 - `estimatedComplexity` (string): directly from script output
 - `importMap` (object): directly from script output
 

From 59a6f56bfea046fb0b766916ba5fa09a8b6fd5f6 Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Fri, 10 Apr 2026 11:39:45 +0800
Subject: [PATCH 11/15] feat(skill): add Phase 0.5 for .understandignore setup
 and review pause

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../skills/understand/SKILL.md                | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/understand-anything-plugin/skills/understand/SKILL.md b/understand-anything-plugin/skills/understand/SKILL.md
index be26f59..3ad7fcf 100644
--- a/understand-anything-plugin/skills/understand/SKILL.md
+++ b/understand-anything-plugin/skills/understand/SKILL.md
@@ -77,6 +77,37 @@ Determine whether to run a full analysis or incremental update.
 
 ---
 
+## Phase 0.5 — Ignore Configuration
+
+Set up and verify the `.understandignore` file before scanning.
+
+1. Check if `$PROJECT_ROOT/.understand-anything/.understandignore` exists.
+2. **If it does NOT exist**, generate a starter file:
+   - Run the following Node.js one-liner in `$PROJECT_ROOT`:
+     ```bash
+     node -e "
+     const fs = require('fs');
+     const path = require('path');
+     const root = process.cwd();
+     const dirs = ['__tests__','test','tests','fixtures','testdata','docs','examples','scripts','migrations','.storybook'];
+     const header = '# .understandignore — patterns for files/dirs to exclude from analysis\n# Syntax: same as .gitignore (globs, # comments, ! negation, trailing / for dirs)\n# Lines below are suggestions — uncomment to activate.\n# Use ! prefix to force-include something excluded by defaults.\n#\n# Built-in defaults (always excluded unless negated):\n#   node_modules/, .git/, dist/, build/, bin/, obj/, *.lock, *.min.js, etc.\n#\n';
+     let body = '';
+     const found = dirs.filter(d => fs.existsSync(path.join(root, d)));
+     if (found.length) { body += '# --- Detected directories (uncomment to exclude) ---\n\n' + found.map(d => '# ' + d + '/').join('\n') + '\n\n'; }
+     body += '# --- Test file patterns (uncomment to exclude) ---\n\n# *.test.*\n# *.spec.*\n# *.snap\n';
+     fs.writeFileSync(path.join(root, '.understand-anything', '.understandignore'), header + body);
+     "
+     ```
+   - Report to the user:
+     > Generated `.understand-anything/.understandignore` with suggested exclusions based on your project structure. Please review it and uncomment any patterns you'd like to exclude from analysis. When ready, confirm to continue.
+   - **Wait for user confirmation before proceeding.**
+3. **If it already exists**, report:
+   > Found `.understand-anything/.understandignore`. Review it if needed, then confirm to continue.
+   - **Wait for user confirmation before proceeding.**
+4. After confirmation, proceed to Phase 1.
+
+---
+
 ## Phase 1 — SCAN (Full analysis only)
 
 Dispatch a subagent using the `project-scanner` agent definition (at `agents/project-scanner.md`). Append the following additional context:
@@ -113,6 +144,9 @@ Store the file list as `$FILE_LIST` with `fileCategory` metadata for use in Phas
 
 **Gate check:** If >100 files, inform the user and suggest scoping with a subdirectory argument. Proceed only if user confirms or add guidance that this may take a while.
 
+If the scan result includes `filteredByIgnore > 0`, report:
+> Excluded {filteredByIgnore} files via `.understandignore`.
+
 ---
 
 ## Phase 2 — ANALYZE

From 2104501bc8456ca96a88b919b0bb2aef73482fcf Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Fri, 10 Apr 2026 11:45:05 +0800
Subject: [PATCH 12/15] fix: update pnpm-lock.yaml with ignore dependency

---
 pnpm-lock.yaml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 28627d0..90c1160 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -42,6 +42,9 @@ importers:
       fuse.js:
         specifier: ^7.1.0
         version: 7.1.0
+      ignore:
+        specifier: ^7.0.5
+        version: 7.0.5
       tree-sitter-javascript:
         specifier: ^0.25.0
         version: 0.25.0
@@ -1569,6 +1572,10 @@ packages:
   http-cache-semantics@4.2.0:
     resolution: {integrity: sha512-dTxcvPXqPvXBQpq5dUr6mEMJX4oIEFv6bwom3FDwKRDsuIjjJGANqhBuoAn9c1RQJIdAKav33ED65E2ys+87QQ==}
 
+  ignore@7.0.5:
+    resolution: {integrity: sha512-Hs59xBNfUIunMFgWAbGX5cq6893IbWg4KnrjbYwX3tx0ztorVgTDA6B2sxf8ejHJ4wz8BqGUMYlnzNBer5NvGg==}
+    engines: {node: '>= 4'}
+
   inline-style-parser@0.2.7:
     resolution: {integrity: sha512-Nb2ctOyNR8DqQoR0OwRG95uNWIC0C1lCgf5Naz5H6Ji72KZ8OcFZLz2P5sNgwlyoJ8Yif11oMuYs5pBQa86csA==}
 
@@ -4102,6 +4109,8 @@ snapshots:
 
   http-cache-semantics@4.2.0: {}
 
+  ignore@7.0.5: {}
+
   inline-style-parser@0.2.7: {}
 
   iron-webcrypto@1.2.1: {}

From d3de6dc1fd2b8bd1cab1b9138d8c927eb8893128 Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Fri, 10 Apr 2026 11:51:59 +0800
Subject: [PATCH 13/15] =?UTF-8?q?fix:=20address=20code=20review=20?=
 =?UTF-8?q?=E2=80=94=20remove=20bin/=20from=20defaults,=20fix=20negation?=
 =?UTF-8?q?=20override=20flow?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Remove bin/ from DEFAULT_IGNORE_PATTERNS (Node/Ruby CLI launchers use bin/)
- .NET users can add bin/ to .understandignore manually
- Fix project-scanner Step 2.5 to re-filter from original file list when
  .understandignore exists, ensuring ! negation correctly overrides defaults

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../agents/project-scanner.md                       | 13 ++++++-------
 .../core/src/__tests__/ignore-filter.test.ts        |  8 +++++---
 .../packages/core/src/ignore-filter.ts              |  1 -
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/understand-anything-plugin/agents/project-scanner.md b/understand-anything-plugin/agents/project-scanner.md
index 090c281..2ccc2fe 100644
--- a/understand-anything-plugin/agents/project-scanner.md
+++ b/understand-anything-plugin/agents/project-scanner.md
@@ -39,7 +39,7 @@ Discover all tracked files. In order of preference:
 
 Remove ALL files matching these patterns:
 - **Dependency directories:** paths containing `node_modules/`, `.git/`, `vendor/`, `venv/`, `.venv/`, `__pycache__/`
-- **Build output:** paths with a directory segment matching `dist/`, `build/`, `out/`, `coverage/`, `.next/`, `.cache/`, `.turbo/`, `target/` (Rust), `bin/` (.NET), `obj/` (.NET) — match full directory segments only, not substrings (e.g., `buildSrc/` should NOT be excluded)
+- **Build output:** paths with a directory segment matching `dist/`, `build/`, `out/`, `coverage/`, `.next/`, `.cache/`, `.turbo/`, `target/` (Rust), `obj/` (.NET) — match full directory segments only, not substrings (e.g., `buildSrc/` should NOT be excluded). Note: `bin/` is NOT excluded by default because Node.js and Ruby projects use `bin/` for CLI launchers; .NET users can add `bin/` to `.understandignore`.
 - **Lock files:** `*.lock`, `package-lock.json`, `yarn.lock`, `pnpm-lock.yaml`
 - **Binary/asset files:** `.png`, `.jpg`, `.jpeg`, `.gif`, `.svg`, `.ico`, `.woff`, `.woff2`, `.ttf`, `.eot`, `.mp3`, `.mp4`, `.pdf`, `.zip`, `.tar`, `.gz`
 - **Generated files:** `*.min.js`, `*.min.css`, `*.map`, `*.generated.*` (note: do NOT exclude `*.d.ts` — many projects have hand-written declaration files)
@@ -60,16 +60,15 @@ Remove ALL files matching these patterns:
 
 **Step 2.5 -- User-Configured Filtering (.understandignore)**
 
-After applying the hardcoded exclusion filters above, apply user-configured patterns from `.understandignore`:
+When `.understandignore` files exist, **replace** Step 2's hardcoded filtering with a unified filter that combines defaults and user patterns in a single pass. This ensures `!` negation patterns can override defaults.
 
 1. Check if `$PROJECT_ROOT/.understand-anything/.understandignore` exists. If so, read it.
 2. Check if `$PROJECT_ROOT/.understandignore` exists. If so, read it.
-3. Parse both files using `.gitignore` syntax (glob patterns, `#` comments, blank lines ignored, `!` prefix for negation, trailing `/` for directories, `**/` for recursive matching).
-4. Filter the remaining file list through these patterns. Files matching any pattern are excluded.
-5. `!` negation patterns override the hardcoded exclusions from Step 2 (e.g., `!dist/` force-includes files from dist/).
-6. Track the count of files removed by this step as `filteredByIgnore`.
+3. If neither file exists, skip this step entirely — Step 2's hardcoded filtering is sufficient.
+4. If at least one file exists, re-filter the **original file list from Step 1** (not the Step 2 output) using the `createIgnoreFilter` function from `@understand-anything/core`, which merges hardcoded defaults and user patterns into a single `.gitignore`-compatible matcher. This ensures `!` negation in user files can override hardcoded defaults (e.g., `!dist/` force-includes dist/ files).
+5. Track the count of additional files removed beyond Step 2's baseline as `filteredByIgnore`.
 
-This filtering must be deterministic (not LLM-based). Use a Node.js script with the `ignore` npm package from `@understand-anything/core`, or apply the patterns manually if the file list is small.
+This filtering must be deterministic (not LLM-based). Use a Node.js script with the `ignore` npm package from `@understand-anything/core`.
 
 **Step 3 -- Language Detection**
 
diff --git a/understand-anything-plugin/packages/core/src/__tests__/ignore-filter.test.ts b/understand-anything-plugin/packages/core/src/__tests__/ignore-filter.test.ts
index 28c8c7e..d7f9626 100644
--- a/understand-anything-plugin/packages/core/src/__tests__/ignore-filter.test.ts
+++ b/understand-anything-plugin/packages/core/src/__tests__/ignore-filter.test.ts
@@ -26,11 +26,14 @@ describe("IgnoreFilter", () => {
       expect(DEFAULT_IGNORE_PATTERNS).toContain(".git/");
     });
 
-    it("contains bin and obj for .NET", () => {
-      expect(DEFAULT_IGNORE_PATTERNS).toContain("bin/");
+    it("contains obj for .NET", () => {
       expect(DEFAULT_IGNORE_PATTERNS).toContain("obj/");
     });
 
+    it("does not contain bin (used by Node/Ruby CLI launchers)", () => {
+      expect(DEFAULT_IGNORE_PATTERNS).not.toContain("bin/");
+    });
+
     it("contains build output directories", () => {
       expect(DEFAULT_IGNORE_PATTERNS).toContain("dist/");
       expect(DEFAULT_IGNORE_PATTERNS).toContain("build/");
@@ -45,7 +48,6 @@ describe("IgnoreFilter", () => {
       expect(filter.isIgnored("node_modules/foo/bar.js")).toBe(true);
       expect(filter.isIgnored("dist/index.js")).toBe(true);
       expect(filter.isIgnored(".git/config")).toBe(true);
-      expect(filter.isIgnored("bin/Debug/app.dll")).toBe(true);
       expect(filter.isIgnored("obj/Release/net8.0/app.dll")).toBe(true);
     });
 
diff --git a/understand-anything-plugin/packages/core/src/ignore-filter.ts b/understand-anything-plugin/packages/core/src/ignore-filter.ts
index 88a65b9..a56d2e3 100644
--- a/understand-anything-plugin/packages/core/src/ignore-filter.ts
+++ b/understand-anything-plugin/packages/core/src/ignore-filter.ts
@@ -24,7 +24,6 @@ export const DEFAULT_IGNORE_PATTERNS: string[] = [
   ".cache/",
   ".turbo/",
   "target/",
-  "bin/",
   "obj/",
 
   // Lock files

From 6ef1a21315be673f0377d0ded67cab98d476c84c Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Sun, 12 Apr 2026 11:39:31 +0800
Subject: [PATCH 14/15] feat: seed .understandignore with .gitignore patterns
 on first generation
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Read the project's .gitignore at starter-file generation time and include
non-default patterns as commented suggestions in .understandignore. Patterns
already covered by hardcoded defaults are deduplicated (with trailing-slash
normalization). This is a one-time inclusion — users can later remove patterns
for files they want analyzed without the filter re-reading .gitignore.

Also fixes the starter header listing bin/ as a built-in default when it is
intentionally excluded from DEFAULT_IGNORE_PATTERNS (bin/ is used by Node/Ruby
CLI launchers).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../src/__tests__/ignore-generator.test.ts    | 67 ++++++++++++++++++-
 .../packages/core/src/ignore-generator.ts     | 46 ++++++++++++-
 2 files changed, 109 insertions(+), 4 deletions(-)

diff --git a/understand-anything-plugin/packages/core/src/__tests__/ignore-generator.test.ts b/understand-anything-plugin/packages/core/src/__tests__/ignore-generator.test.ts
index 8c2189b..5d47140 100644
--- a/understand-anything-plugin/packages/core/src/__tests__/ignore-generator.test.ts
+++ b/understand-anything-plugin/packages/core/src/__tests__/ignore-generator.test.ts
@@ -1,6 +1,6 @@
 import { describe, it, expect, beforeEach, afterEach } from "vitest";
 import { generateStarterIgnoreFile } from "../ignore-generator";
-import { mkdirSync, rmSync } from "node:fs";
+import { mkdirSync, rmSync, writeFileSync } from "node:fs";
 import { join } from "node:path";
 import { tmpdir } from "node:os";
 
@@ -94,4 +94,69 @@ describe("generateStarterIgnoreFile", () => {
     expect(content).not.toContain("# .storybook/");
     expect(content).not.toContain("# fixtures/");
   });
+
+  describe(".gitignore integration", () => {
+    it("includes .gitignore patterns not covered by defaults", () => {
+      writeFileSync(join(testDir, ".gitignore"), ".env\nsecrets/\n*.pyc\n");
+      const content = generateStarterIgnoreFile(testDir);
+      expect(content).toContain("From .gitignore");
+      expect(content).toContain("# .env");
+      expect(content).toContain("# secrets/");
+      expect(content).toContain("# *.pyc");
+    });
+
+    it("excludes .gitignore patterns already in defaults", () => {
+      writeFileSync(join(testDir, ".gitignore"), "node_modules/\ndist/\n.env\n");
+      const content = generateStarterIgnoreFile(testDir);
+      // .env is not in defaults, should appear
+      expect(content).toContain("# .env");
+      // node_modules/ and dist/ are in defaults, should not appear in .gitignore section
+      const gitignoreSection = content.split("From .gitignore")[1]?.split("---")[0] ?? "";
+      expect(gitignoreSection).not.toContain("node_modules");
+      expect(gitignoreSection).not.toContain("dist");
+    });
+
+    it("skips .gitignore comments and blank lines", () => {
+      writeFileSync(join(testDir, ".gitignore"), "# a comment\n\n.env\n  \n");
+      const content = generateStarterIgnoreFile(testDir);
+      expect(content).toContain("# .env");
+      // Should not include the original comment as a pattern
+      const gitignoreSection = content.split("From .gitignore")[1]?.split("---")[0] ?? "";
+      expect(gitignoreSection).not.toContain("a comment");
+    });
+
+    it("handles .gitignore with trailing-slash normalization for defaults", () => {
+      // "dist" without trailing slash should still match "dist/" default
+      writeFileSync(join(testDir, ".gitignore"), "dist\ncoverage\n.env\n");
+      const content = generateStarterIgnoreFile(testDir);
+      expect(content).toContain("From .gitignore");
+      // Extract lines between the .gitignore header and the next section header
+      const lines = content.split("\n");
+      const headerIdx = lines.findIndex((l) => l.includes("From .gitignore"));
+      const nextSectionIdx = lines.findIndex((l, i) => i > headerIdx && l.startsWith("# ---"));
+      const sectionLines = lines.slice(headerIdx + 1, nextSectionIdx === -1 ? undefined : nextSectionIdx);
+      const patterns = sectionLines.filter((l) => l.startsWith("# ") && !l.startsWith("# ---")).map((l) => l.slice(2));
+      expect(patterns).toContain(".env");
+      expect(patterns).not.toContain("dist");
+      expect(patterns).not.toContain("coverage");
+    });
+
+    it("omits .gitignore section when no .gitignore exists", () => {
+      const content = generateStarterIgnoreFile(testDir);
+      expect(content).not.toContain("From .gitignore");
+    });
+
+    it("omits .gitignore section when all patterns are covered by defaults", () => {
+      writeFileSync(join(testDir, ".gitignore"), "node_modules/\ndist/\n*.lock\n");
+      const content = generateStarterIgnoreFile(testDir);
+      expect(content).not.toContain("From .gitignore");
+    });
+
+    it("all .gitignore suggestions are commented out", () => {
+      writeFileSync(join(testDir, ".gitignore"), ".env\nsecrets/\n*.pyc\n");
+      const content = generateStarterIgnoreFile(testDir);
+      const lines = content.split("\n").filter((l) => l.trim() && !l.startsWith("#"));
+      expect(lines).toHaveLength(0);
+    });
+  });
 });
diff --git a/understand-anything-plugin/packages/core/src/ignore-generator.ts b/understand-anything-plugin/packages/core/src/ignore-generator.ts
index 021e170..f0e49ac 100644
--- a/understand-anything-plugin/packages/core/src/ignore-generator.ts
+++ b/understand-anything-plugin/packages/core/src/ignore-generator.ts
@@ -1,5 +1,6 @@
-import { existsSync } from "node:fs";
+import { existsSync, readFileSync } from "node:fs";
 import { join } from "node:path";
+import { DEFAULT_IGNORE_PATTERNS } from "./ignore-filter.js";
 
 const HEADER = `# .understandignore — patterns for files/dirs to exclude from analysis
 # Syntax: same as .gitignore (globs, # comments, ! negation, trailing / for dirs)
@@ -7,7 +8,7 @@ const HEADER = `# .understandignore — patterns for files/dirs to exclude from
 # Use ! prefix to force-include something excluded by defaults.
 #
 # Built-in defaults (always excluded unless negated):
-#   node_modules/, .git/, dist/, build/, bin/, obj/, *.lock, *.min.js, etc.
+#   node_modules/, .git/, dist/, build/, obj/, *.lock, *.min.js, etc.
 #
 `;
 
@@ -30,13 +31,51 @@ const GENERIC_SUGGESTIONS = [
   "*.snap",
 ];
 
+/**
+ * Parses a .gitignore file and returns active patterns (no comments, no blanks).
+ */
+function parseGitignorePatterns(gitignorePath: string): string[] {
+  if (!existsSync(gitignorePath)) return [];
+  const content = readFileSync(gitignorePath, "utf-8");
+  return content
+    .split("\n")
+    .map((line) => line.trim())
+    .filter((line) => line.length > 0 && !line.startsWith("#"));
+}
+
+/**
+ * Returns true if a gitignore pattern is already covered by the hardcoded defaults.
+ * Normalizes trailing slashes for comparison.
+ */
+function isCoveredByDefaults(pattern: string): boolean {
+  const normalize = (p: string) => p.replace(/\/+$/, "");
+  const normalized = normalize(pattern);
+  return DEFAULT_IGNORE_PATTERNS.some((d) => normalize(d) === normalized);
+}
+
 /**
  * Generates a starter .understandignore file content by scanning the project
- * for common directories. All suggestions are commented out.
+ * for common directories and reading .gitignore patterns.
+ * All suggestions are commented out — this is a one-time generation.
  */
 export function generateStarterIgnoreFile(projectRoot: string): string {
   const sections: string[] = [HEADER];
 
+  // Section 1: patterns from .gitignore not already in defaults
+  const gitignorePath = join(projectRoot, ".gitignore");
+  const gitignorePatterns = parseGitignorePatterns(gitignorePath).filter(
+    (p) => !isCoveredByDefaults(p),
+  );
+
+  if (gitignorePatterns.length > 0) {
+    sections.push("# --- From .gitignore (uncomment to exclude) ---\n");
+    for (const pattern of gitignorePatterns) {
+      sections.push(`# ${pattern}`);
+    }
+    sections.push("");
+  }
+
+  // Section 2: detected directories
   const detected: string[] = [];
   for (const { dir, pattern } of DETECTABLE_DIRS) {
     if (existsSync(join(projectRoot, dir))) {
@@ -52,6 +91,7 @@ export function generateStarterIgnoreFile(projectRoot: string): string {
     sections.push("");
   }
 
+  // Section 3: generic test patterns
   sections.push("# --- Test file patterns (uncomment to exclude) ---\n");
   for (const pattern of GENERIC_SUGGESTIONS) {
     sections.push(`# ${pattern}`);

From 55fc2ac8488caae5a46d458a042ab27710d8794d Mon Sep 17 00:00:00 2001
From: Lum1104 <linyux1104@163.com>
Date: Sun, 12 Apr 2026 11:47:55 +0800
Subject: [PATCH 15/15] fix: sync Phase 0.5 inline script with .gitignore
 integration and header fix

The skill's inline Node.js generator was duplicated from core and missed
the .gitignore seeding and bin/ header fix. Updated the one-liner to read
.gitignore patterns, deduplicate against defaults with trailing-slash
normalization, and remove bin/ from the built-in defaults header comment.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../skills/understand/SKILL.md                 | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/understand-anything-plugin/skills/understand/SKILL.md b/understand-anything-plugin/skills/understand/SKILL.md
index 3ad7fcf..efebf1e 100644
--- a/understand-anything-plugin/skills/understand/SKILL.md
+++ b/understand-anything-plugin/skills/understand/SKILL.md
@@ -83,19 +83,29 @@ Set up and verify the `.understandignore` file before scanning.
 
 1. Check if `$PROJECT_ROOT/.understand-anything/.understandignore` exists.
 2. **If it does NOT exist**, generate a starter file:
-   - Run the following Node.js one-liner in `$PROJECT_ROOT`:
+   - Run the following Node.js one-liner in `$PROJECT_ROOT` (reads `.gitignore` and deduplicates against built-in defaults):
      ```bash
      node -e "
      const fs = require('fs');
      const path = require('path');
      const root = process.cwd();
-     const dirs = ['__tests__','test','tests','fixtures','testdata','docs','examples','scripts','migrations','.storybook'];
-     const header = '# .understandignore — patterns for files/dirs to exclude from analysis\n# Syntax: same as .gitignore (globs, # comments, ! negation, trailing / for dirs)\n# Lines below are suggestions — uncomment to activate.\n# Use ! prefix to force-include something excluded by defaults.\n#\n# Built-in defaults (always excluded unless negated):\n#   node_modules/, .git/, dist/, build/, bin/, obj/, *.lock, *.min.js, etc.\n#\n';
+     const defaults = ['node_modules/','node_modules','.git/','vendor/','venv/','.venv/','__pycache__/','dist/','dist','build/','build','out/','coverage/','coverage','.next/','.cache/','.turbo/','target/','obj/','*.lock','package-lock.json','yarn.lock','pnpm-lock.yaml','*.png','*.jpg','*.jpeg','*.gif','*.svg','*.ico','*.woff','*.woff2','*.ttf','*.eot','*.mp3','*.mp4','*.pdf','*.zip','*.tar','*.gz','*.min.js','*.min.css','*.map','*.generated.*','.idea/','.vscode/','LICENSE','.gitignore','.editorconfig','.prettierrc','.eslintrc*','*.log'];
+     const norm = p => p.replace(/\/+$/, '');
+     const defaultSet = new Set(defaults.map(norm));
+     const header = '# .understandignore — patterns for files/dirs to exclude from analysis\n# Syntax: same as .gitignore (globs, # comments, ! negation, trailing / for dirs)\n# Lines below are suggestions — uncomment to activate.\n# Use ! prefix to force-include something excluded by defaults.\n#\n# Built-in defaults (always excluded unless negated):\n#   node_modules/, .git/, dist/, build/, obj/, *.lock, *.min.js, etc.\n#\n';
      let body = '';
+     const gitignorePath = path.join(root, '.gitignore');
+     if (fs.existsSync(gitignorePath)) {
+       const gi = fs.readFileSync(gitignorePath, 'utf-8').split('\n').map(l => l.trim()).filter(l => l && !l.startsWith('#')).filter(p => !defaultSet.has(norm(p)));
+       if (gi.length) { body += '# --- From .gitignore (uncomment to exclude) ---\n\n' + gi.map(p => '# ' + p).join('\n') + '\n\n'; }
+     }
+     const dirs = ['__tests__','test','tests','fixtures','testdata','docs','examples','scripts','migrations','.storybook'];
      const found = dirs.filter(d => fs.existsSync(path.join(root, d)));
      if (found.length) { body += '# --- Detected directories (uncomment to exclude) ---\n\n' + found.map(d => '# ' + d + '/').join('\n') + '\n\n'; }
      body += '# --- Test file patterns (uncomment to exclude) ---\n\n# *.test.*\n# *.spec.*\n# *.snap\n';
-     fs.writeFileSync(path.join(root, '.understand-anything', '.understandignore'), header + body);
+     const outDir = path.join(root, '.understand-anything');
+     if (!fs.existsSync(outDir)) fs.mkdirSync(outDir, { recursive: true });
+     fs.writeFileSync(path.join(outDir, '.understandignore'), header + body);
      "
      ```
    - Report to the user: