@agent-wiki/mcp-server 0.3.0

package/README.md

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+# agent-wiki
+
+[![CI](https://github.com/xinhuagu/agent-wiki/actions/workflows/ci.yml/badge.svg)](https://github.com/xinhuagu/agent-wiki/actions/workflows/ci.yml)
+[![Node](https://img.shields.io/badge/node-%3E%3D18-brightgreen)](https://nodejs.org)
+[![MCP](https://img.shields.io/badge/protocol-MCP-blue)](https://modelcontextprotocol.io)
+[![License: MIT](https://img.shields.io/badge/license-MIT-yellow.svg)](LICENSE)
+
+A structured knowledge base that any AI agent can read, write, and maintain through the [Model Context Protocol](https://modelcontextprotocol.io). No LLM built in — your agent IS the LLM.
+
+```
+npx @agent-wiki/mcp-server
+```
+
+---
+
+## The Idea
+
+Most AI systems treat knowledge as disposable. You ask a question, it retrieves some fragments, generates an answer, and everything is forgotten. Next time you ask, it starts from zero.
+
+agent-wiki takes a different approach: **knowledge compilation**. Instead of retrieving raw documents every time (RAG), the agent incrementally builds and maintains a persistent wiki — structured, interlinked, and continuously refined. Every interaction makes the knowledge base smarter.
+
+The key insight: **LLMs are better editors than search engines.** Let them curate, synthesize, and maintain knowledge over time, not just retrieve it on demand.
+
+### RAG vs Knowledge Compilation
+
+| | RAG | agent-wiki |
+|---|---|---|
+| **Approach** | Retrieve fragments at query time | Build and maintain compiled knowledge |
+| **Memory** | Stateless — forgets after each query | Persistent — knowledge accumulates |
+| **Quality** | Raw chunks, often noisy | Curated, structured, interlinked |
+| **Cost** | Embedding + retrieval every query | One-time compilation, free reads |
+| **Contradictions** | Invisible — buried in source docs | Detected automatically by lint |
+| **Source tracking** | Lost after retrieval | Full provenance chain (raw -> wiki) |
+
+## Architecture
+
+Three immutability layers, inspired by how compilers work:
+
+```
+raw/      Immutable source documents (write-once, SHA-256 verified)
+            Papers, articles, web pages — the "source code" of knowledge
+
+wiki/     Mutable compiled knowledge (entity pages, synthesis, index)
+            Structured Markdown — the "compiled output"
+
+schemas/  Entity templates (person, concept, event, artifact, ...)
+            Consistent structure across all knowledge
+```
+
+The agent reads from `raw/`, compiles understanding into `wiki/`, and the lint system ensures quality:
+
+<p align="center">
+  <img src="architecture.svg" alt="agent-wiki architecture" width="700" />
+</p>
+
+## Key Features
+
+### Immutable Source Layer (`raw/`)
+
+- **Write-once** — raw files can never be modified or overwritten after creation
+- **SHA-256 integrity** — every file is hashed; corruption or tampering is detected
+- **Provenance tracking** — `.meta.yaml` sidecars record source URL, download time, description
+- **URL fetching** — `raw_fetch` downloads directly from URLs, with smart arXiv handling (`arxiv.org/abs/XXXX` auto-converts to PDF)
+- **Local file copy** — `raw_add` with `source_path` physically copies files into `raw/`
+
+### Mutable Knowledge Layer (`wiki/`)
+
+- **Structured Markdown** — YAML frontmatter (title, type, tags, sources) + Markdown body
+- **9 entity types** — person, concept, event, artifact, comparison, summary, how-to, note, synthesis
+- **Auto-classification** — heuristic classifier assigns entity type and suggests tags, zero LLM needed
+- **`[[wiki-links]]`** — interlink pages to build a knowledge graph
+- **Synthesis pages** — higher-order knowledge distilled from combining multiple pages
+- **Auto-timestamps** — `created` and `updated` managed automatically
+- **System pages** — index.md, log.md, timeline.md maintained by the engine
+
+### Self-Checking (`lint`)
+
+No human review needed. The lint system catches problems automatically:
+
+- **Contradictions** — conflicting dates, numbers, and claims across pages
+- **Orphan pages** — pages with no incoming links
+- **Broken links** — `[[page]]` references to non-existent pages
+- **Missing sources** — wiki claims not traceable to raw documents
+- **Stale content** — pages not updated beyond a configurable threshold
+- **Raw integrity** — SHA-256 re-verification of all source files
+- **Synthesis integrity** — checks that source pages of synthesis still exist
+
+### Workspace Separation
+
+Code and data live in separate directories. The tool is stateless; all state lives in the workspace:
+
+```yaml
+# .agent-wiki.yaml
+wiki:
+  workspace: /path/to/data    # all data goes here
+  path: wiki/
+  raw_path: raw/
+  schemas_path: schemas/
+```
+
+Workspace resolution priority: CLI `--workspace` > `AGENT_WIKI_WORKSPACE` env > config file > config root.
+
+### Auto-Classification
+
+Every `wiki_write` automatically classifies content if no type is specified:
+
+```
+Input:  "# YOLO Object Detection\n\nYOLO is a real-time detection model..."
+Output: { type: "concept", tags: ["yolo", "object-detection", "real-time"], confidence: 0.8 }
+```
+
+Pure heuristic — no LLM calls, no API keys, zero latency. Supports English and Chinese keywords.
+
+## Setup
+
+### Claude Code / AceClaw
+
+`~/.aceclaw/mcp-servers.json`:
+
+```json
+{
+  "mcpServers": {
+    "agent-wiki": {
+      "command": "npx",
+      "args": ["-y", "agent-wiki", "serve", "--wiki-path", "/path/to/config", "--workspace", "/path/to/data"]
+    }
+  }
+}
+```
+
+### Cursor / Windsurf / any MCP client
+
+Same pattern — `npx -y @agent-wiki/mcp-server serve --wiki-path /path/to/config`.
+
+### Claude Desktop
+
+`claude_desktop_config.json`:
+
+```json
+{
+  "mcpServers": {
+    "agent-wiki": {
+      "command": "npx",
+      "args": ["-y", "agent-wiki", "serve", "--wiki-path", "/path/to/config"]
+    }
+  }
+}
+```
+
+## MCP Tools (17 total)
+
+### Raw Layer — Immutable Sources
+
+| Tool | Description |
+|------|-------------|
+| `raw_add` | Add a source document (immutable, SHA-256 hashed, .meta.yaml sidecar) |
+| `raw_fetch` | Download from URL to raw/ (smart arXiv handling, auto-provenance) |
+| `raw_list` | List all raw documents with metadata |
+| `raw_read` | Read a raw document's content and metadata |
+| `raw_verify` | Verify integrity of all raw files (SHA-256 check) |
+
+### Wiki Layer — Compiled Knowledge
+
+| Tool | Description |
+|------|-------------|
+| `wiki_read` | Read a page (frontmatter + Markdown) |
+| `wiki_write` | Create or update a page (auto-timestamps, auto-classify) |
+| `wiki_delete` | Delete a page (guards system pages) |
+| `wiki_list` | List pages, filter by type or tag |
+| `wiki_search` | Full-text keyword search with relevance scoring |
+| `wiki_lint` | Health checks: contradictions, orphans, broken links, integrity |
+| `wiki_classify` | Auto-classify content into entity type + suggest tags |
+| `wiki_synthesize` | Prepare context for knowledge distillation across pages |
+| `wiki_log` | Operation history with timestamps |
+| `wiki_init` | Initialize a new knowledge base |
+| `wiki_schemas` | List entity templates |
+| `wiki_rebuild_index` | Rebuild index.md (grouped by type) |
+| `wiki_rebuild_timeline` | Rebuild timeline.md (chronological view) |
+| `wiki_config` | Show current workspace configuration |
+
+## Entity Types
+
+| Type | Use Case | Example |
+|------|----------|---------|
+| `person` | People profiles | Researchers, engineers, historical figures |
+| `concept` | Ideas and definitions | YOLO, attention mechanism, mutex |
+| `event` | Things that happened | Conference talks, releases, incidents |
+| `artifact` | Created things | Papers, tools, models, datasets |
+| `comparison` | Side-by-side analysis | YOLOv8 vs YOLOv9, PyTorch vs TensorFlow |
+| `summary` | Document summaries | Paper summaries, article digests |
+| `how-to` | Procedures and guides | Setup guides, deployment steps |
+| `note` | Freeform knowledge | Anything that doesn't fit other types |
+| `synthesis` | Distilled knowledge | Insights from combining multiple pages |
+
+## Page Format
+
+```markdown
+---
+title: YOLO Object Detection
+type: concept
+tags: [yolo, detection, computer-vision]
+sources: [paper-yolo-v1.pdf]
+created: "2026-04-05T12:00:00.000Z"
+updated: "2026-04-05T14:30:00.000Z"
+---
+
+# YOLO Object Detection
+
+You Only Look Once — real-time object detection.
+
+Related: [[comparison-detectors]], [[person-redmon]]
+```
+
+Synthesis pages track their derivation:
+
+```markdown
+---
+title: Object Detection Overview
+type: synthesis
+derived_from: [concept-yolo.md, concept-ssd.md, concept-rcnn.md]
+---
+```
+
+## CLI
+
+```bash
+npx agent-wiki serve                    # start MCP server (stdio)
+npx agent-wiki serve --workspace ./data # separate data directory
+npx agent-wiki init ./my-kb             # initialize new knowledge base
+npx agent-wiki search "yolo"            # search wiki
+npx agent-wiki list                     # list all pages
+npx agent-wiki list --type concept      # filter by type
+npx agent-wiki raw-list                 # list raw sources
+npx agent-wiki raw-verify               # verify raw file integrity
+npx agent-wiki lint                     # run health checks
+```
+
+## Design Principles
+
+1. **Raw is immutable** — Source documents are write-once, SHA-256 verified. The ground truth never changes.
+2. **Wiki is mutable** — Compiled knowledge improves with every interaction. Pages are refined, not replaced.
+3. **No LLM dependency** — Zero API keys, zero cost per operation. The agent calling the tools IS the intelligence.
+4. **Self-checking** — Lint catches contradictions, broken links, and integrity issues without human review.
+5. **Knowledge compounds** — Every write enriches the whole wiki. Synthesis creates higher-order understanding.
+6. **Provenance matters** — Every wiki claim traces back to raw sources. No hallucination without accountability.
+7. **Code and data separate** — Configurable workspace keeps your knowledge portable and independent.
+8. **Git-native** — Plain Markdown files. Every change is diffable, blameable, and revertable.
+
+## License
+
+MIT

package/dist/cli.d.ts

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+#!/usr/bin/env node
+/**
+ * CLI entry point for agent-wiki.
+ *
+ * Usage:
+ *   npx @agent-wiki/mcp-server                  # start MCP server (stdio)
+ *   npx @agent-wiki/mcp-server --wiki-path /kb  # custom wiki root
+ *   npx @agent-wiki/mcp-server init ./my-kb     # initialize a new knowledge base
+ */
+export {};
+//# sourceMappingURL=cli.d.ts.map

package/dist/cli.d.ts.map

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+{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AAEA;;;;;;;GAOG"}

package/dist/cli.js

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+#!/usr/bin/env node
+/**
+ * CLI entry point for agent-wiki.
+ *
+ * Usage:
+ *   npx @agent-wiki/mcp-server                  # start MCP server (stdio)
+ *   npx @agent-wiki/mcp-server --wiki-path /kb  # custom wiki root
+ *   npx @agent-wiki/mcp-server init ./my-kb     # initialize a new knowledge base
+ */
+import { Command } from "commander";
+import { Wiki } from "./wiki.js";
+import { runServer } from "./server.js";
+const program = new Command();
+program
+    .name("agent-wiki")
+    .description("Agent-driven knowledge base — structured Markdown wiki with MCP server.\n" +
+    "raw/ = immutable sources | wiki/ = mutable knowledge | schemas/ = templates")
+    .version("0.3.0");
+// Default command: start MCP server
+program
+    .command("serve", { isDefault: true })
+    .description("Start MCP server (stdio transport)")
+    .option("-w, --wiki-path <path>", "Path to config root (where .agent-wiki.yaml lives)", ".")
+    .option("--workspace <path>", "Workspace directory for all data (wiki/, raw/, schemas/). Overrides config and env.")
+    .action(async (opts) => {
+    await runServer(opts.wikiPath, opts.workspace);
+});
+// Init
+program
+    .command("init [path]")
+    .description("Initialize a new knowledge base")
+    .option("--workspace <path>", "Separate workspace directory for data (wiki/, raw/, schemas/)")
+    .action((path, opts) => {
+    const target = path ?? ".";
+    const ws = opts.workspace;
+    Wiki.init(target, ws);
+    console.error(`Knowledge base initialized:`);
+    console.error(`  Config:    ${target}/.agent-wiki.yaml`);
+    if (ws) {
+        console.error(`  Workspace: ${ws}/`);
+    }
+    console.error("  wiki/     — Mutable Markdown pages (agent-managed)");
+    console.error("  raw/      — Immutable source documents (write-once)");
+    console.error("  schemas/  — Entity templates (person, concept, event, ...)");
+});
+// Search
+program
+    .command("search <query>")
+    .description("Search wiki pages by keyword")
+    .option("-w, --wiki-path <path>", "Path to config root", ".")
+    .option("--workspace <path>", "Workspace directory override")
+    .option("-n, --limit <n>", "Max results", "10")
+    .action((query, opts) => {
+    const wiki = new Wiki(opts.wikiPath, opts.workspace);
+    const results = wiki.search(query, parseInt(opts.limit));
+    if (results.length === 0) {
+        console.log("No matches.");
+        return;
+    }
+    for (const r of results) {
+        console.log(`  [${r.score}] ${r.path}`);
+        console.log(`       ${r.snippet}`);
+    }
+});
+// List wiki pages
+program
+    .command("list")
+    .description("List all wiki pages")
+    .option("-w, --wiki-path <path>", "Path to config root", ".")
+    .option("--workspace <path>", "Workspace directory override")
+    .option("-t, --type <type>", "Filter by entity type")
+    .option("--tag <tag>", "Filter by tag")
+    .action((opts) => {
+    const wiki = new Wiki(opts.wikiPath, opts.workspace);
+    const pages = wiki.list(opts.type, opts.tag);
+    if (pages.length === 0) {
+        console.log("No pages.");
+        return;
+    }
+    console.log(`${pages.length} pages:`);
+    for (const p of pages) {
+        console.log(`  ${p}`);
+    }
+});
+// List raw sources
+program
+    .command("raw-list")
+    .description("List all raw source documents")
+    .option("-w, --wiki-path <path>", "Path to config root", ".")
+    .option("--workspace <path>", "Workspace directory override")
+    .action((opts) => {
+    const wiki = new Wiki(opts.wikiPath, opts.workspace);
+    const docs = wiki.rawList();
+    if (docs.length === 0) {
+        console.log("No raw documents.");
+        return;
+    }
+    console.log(`${docs.length} raw documents:`);
+    for (const d of docs) {
+        const url = d.sourceUrl ? ` (${d.sourceUrl})` : "";
+        console.log(`  ${d.path} — ${formatBytes(d.size)}${url}`);
+    }
+});
+// Verify raw integrity
+program
+    .command("raw-verify")
+    .description("Verify integrity of raw source documents (SHA-256)")
+    .option("-w, --wiki-path <path>", "Path to config root", ".")
+    .option("--workspace <path>", "Workspace directory override")
+    .action((opts) => {
+    const wiki = new Wiki(opts.wikiPath, opts.workspace);
+    const results = wiki.rawVerify();
+    if (results.length === 0) {
+        console.log("No raw documents to verify.");
+        return;
+    }
+    let ok = 0, bad = 0, noMeta = 0;
+    for (const r of results) {
+        if (r.status === "ok") {
+            ok++;
+        }
+        else if (r.status === "corrupted") {
+            bad++;
+            console.log(`  [CORRUPT] ${r.path}`);
+        }
+        else {
+            noMeta++;
+            console.log(`  [NO META] ${r.path}`);
+        }
+    }
+    console.log(`\n${ok} ok, ${bad} corrupted, ${noMeta} missing metadata`);
+});
+// Lint
+program
+    .command("lint")
+    .description("Run health checks (contradictions, orphans, broken links, integrity)")
+    .option("-w, --wiki-path <path>", "Path to config root", ".")
+    .option("--workspace <path>", "Workspace directory override")
+    .action((opts) => {
+    const wiki = new Wiki(opts.wikiPath, opts.workspace);
+    const report = wiki.lint();
+    if (report.issues.length === 0) {
+        console.log(`All ${report.pagesChecked} pages + ${report.rawChecked} raw files healthy.`);
+        return;
+    }
+    console.log(`Checked ${report.pagesChecked} pages + ${report.rawChecked} raw files\n`);
+    if (report.contradictions.length > 0) {
+        console.log(`Contradictions (${report.contradictions.length}):`);
+        for (const c of report.contradictions) {
+            console.log(`  ${c.pageA} vs ${c.pageB}: ${c.claim}`);
+            console.log(`    "${c.excerptA}" vs "${c.excerptB}"`);
+        }
+        console.log();
+    }
+    const grouped = {};
+    for (const issue of report.issues) {
+        const cat = issue.category ?? "other";
+        if (!grouped[cat])
+            grouped[cat] = [];
+        grouped[cat].push(issue);
+    }
+    for (const [cat, issues] of Object.entries(grouped)) {
+        console.log(`${cat} (${issues.length}):`);
+        for (const issue of issues) {
+            const icon = issue.severity === "error" ? "ERR" : issue.severity === "warning" ? "WARN" : "INFO";
+            console.log(`  [${icon}] ${issue.page}: ${issue.message}`);
+            if (issue.suggestion)
+                console.log(`         -> ${issue.suggestion}`);
+        }
+        console.log();
+    }
+});
+program.parse();
+function formatBytes(bytes) {
+    if (bytes < 1024)
+        return `${bytes} B`;
+    if (bytes < 1024 * 1024)
+        return `${(bytes / 1024).toFixed(1)} KB`;
+    return `${(bytes / (1024 * 1024)).toFixed(1)} MB`;
+}
+//# sourceMappingURL=cli.js.map

package/dist/cli.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,33 @@
+/**
+ * agent-wiki — Agent-driven knowledge base.
+ *
+ * Architecture (Karpathy LLM Wiki pattern):
+ *
+ *   raw/     — Immutable sources. Write-once, never modified. SHA-256 verified.
+ *   wiki/    — Mutable knowledge. System pages, entity pages, synthesis pages.
+ *   schemas/ — Entity templates.
+ *
+ * No LLM dependency. Your agent IS the LLM.
+ * This package provides:
+ *   - Raw document management (immutable, integrity-checked)
+ *   - Wiki CRUD with auto-timestamping
+ *   - Keyword search with relevance scoring
+ *   - Lint with contradiction detection and integrity checks
+ *   - Knowledge synthesis preparation
+ *   - MCP server interface
+ *
+ * Usage as MCP server:
+ *   npx @agent-wiki/mcp-server
+ *
+ * Usage as library:
+ *   import { Wiki } from "@agent-wiki/mcp-server";
+ *   const wiki = new Wiki("/path/to/kb");
+ *   wiki.rawAdd("paper.md", { content: "...", sourceUrl: "..." });
+ *   wiki.write("concept-gil.md", content);
+ *   const results = wiki.search("python");
+ *   const report = wiki.lint();  // contradiction detection included
+ */
+export { Wiki } from "./wiki.js";
+export type { WikiPage, RawDocument, LintIssue, LintReport, Contradiction, TimelineEntry, WikiConfig, } from "./wiki.js";
+export { createServer, runServer } from "./server.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AAEH,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,YAAY,EACV,QAAQ,EACR,WAAW,EACX,SAAS,EACT,UAAU,EACV,aAAa,EACb,aAAa,EACb,UAAU,GACX,MAAM,WAAW,CAAC;AACnB,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC"}

package/dist/index.js

@@ -0,0 +1,32 @@
+/**
+ * agent-wiki — Agent-driven knowledge base.
+ *
+ * Architecture (Karpathy LLM Wiki pattern):
+ *
+ *   raw/     — Immutable sources. Write-once, never modified. SHA-256 verified.
+ *   wiki/    — Mutable knowledge. System pages, entity pages, synthesis pages.
+ *   schemas/ — Entity templates.
+ *
+ * No LLM dependency. Your agent IS the LLM.
+ * This package provides:
+ *   - Raw document management (immutable, integrity-checked)
+ *   - Wiki CRUD with auto-timestamping
+ *   - Keyword search with relevance scoring
+ *   - Lint with contradiction detection and integrity checks
+ *   - Knowledge synthesis preparation
+ *   - MCP server interface
+ *
+ * Usage as MCP server:
+ *   npx @agent-wiki/mcp-server
+ *
+ * Usage as library:
+ *   import { Wiki } from "@agent-wiki/mcp-server";
+ *   const wiki = new Wiki("/path/to/kb");
+ *   wiki.rawAdd("paper.md", { content: "...", sourceUrl: "..." });
+ *   wiki.write("concept-gil.md", content);
+ *   const results = wiki.search("python");
+ *   const report = wiki.lint();  // contradiction detection included
+ */
+export { Wiki } from "./wiki.js";
+export { createServer, runServer } from "./server.js";
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AAEH,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAUjC,OAAO,EAAE,YAAY,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC"}

package/dist/server.d.ts

@@ -0,0 +1,14 @@
+/**
+ * MCP Server — Exposes Agent Wiki as tools to any MCP-compatible agent.
+ *
+ * Architecture (Karpathy LLM Wiki, upgraded):
+ *
+ *   raw/  → Immutable source layer (raw_add, raw_list, raw_read, raw_verify)
+ *   wiki/ → Mutable knowledge layer (read, write, delete, search, lint, synthesize)
+ *
+ * The agent IS the LLM. This server is pure data operations.
+ */
+import { Server } from "@modelcontextprotocol/sdk/server/index.js";
+export declare function createServer(wikiPath?: string, workspace?: string): Server;
+export declare function runServer(wikiPath?: string, workspace?: string): Promise<void>;
+//# sourceMappingURL=server.d.ts.map

package/dist/server.d.ts.map

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