MCP Knowledge Base Server

A Model Context Protocol (MCP) server providing persistent memory, knowledge base, and project summary capabilities with automatic project detection and an interactive dashboard.

How It Works

┌──────────────────────────────────────────────────────────────┐
│                   AI Assistant (Kiro, Claude, etc.)          │
│                                                              │
│  "Remember we use JWT"    "What do I know about auth?"       │
│  "Init KB from my docs"   "What changed since last summary?" │
└──────────────┬───────────────────────────┬───────────────────┘
               │ MCP Protocol (stdio)      │
               ▼                           ▼
┌──────────────────────────────────────────────────────────────┐
│                    mcp-kb-server                             │
│                                                              │
│  ┌─────────┐ ┌──────────┐ ┌─────────┐ ┌──────────┐          │
│  │ memory  │ │    kb    │ │ summary │ │dashboard │          │
│  │ .store  │ │ .add     │ │.project │ │.projects │          │
│  │ .search │ │ .search  │ │ .delta  │ └──────────┘          │
│  │ .list   │ │ .init ★  │ └─────────┘                       │
│  │ .delete │ └──────────┘                                    │
│  │ .update │   Auto-detect project_id from project_root      │
│  └─────────┘   package.json → git remote → directory name   │
│                                                              │
│  ┌────────────────────┐  ┌─────────────────────┐            │
│  │  memory.sqlite     │  │  kb.sqlite           │            │
│  │  + memory_fts(FTS5)│  │  + kb_fts (FTS5)     │            │
│  │  + wiki_links      │  │  + kb_meta (scoping) │            │
│  │  + expires/TTL     │  │  + sources + fts     │            │
│  └────────────────────┘  └─────────────────────┘            │
└──────────────────────────────────────────────────────────────┘

---

Workflow Diagrams

1. Request Flow

Every tool call follows the same path from AI to database and back.

AI Assistant
    │
    │  JSON-RPC 2.0 over stdio
    ▼
server.js
    │
    ├─ Joi validation ──── invalid ──► error -32602
    │
    ├─ project_id resolution
    │     project_root provided?
    │     ├─ yes → detectProjectId()
    │     │         ├─ package.json name
    │     │         ├─ git remote URL
    │     │         └─ directory basename
    │     └─ no  → use explicit project_id
    │
    ├─ LRU query cache (read-only tools)
    │     hit  ──────────────────────► return cached result
    │     miss ─┐
    │           ▼
    ├─ tool handler (memory / kb / sources / wiki / summary)
    │           │
    │           ▼
    │     better-sqlite3 (synchronous)
    │     memory.sqlite  ──  kb.sqlite
    │           │
    │           ▼
    │     cache invalidated (on mutations)
    │
    └─ JSON-RPC result ──────────────► AI Assistant

---

2. Project Initialization (kb.init)

Run once when starting work on a project to populate the KB from existing docs.

Developer / AI
    │
    │  kb.init({ project_root: "/path/to/project" })
    ▼
Resolve project_id
    │  package.json → git remote → directory name
    ▼
Expand glob patterns
    │  default: ["**/*.md", "**/*.txt"]
    │  skip:    node_modules / .git / dist / build
    ▼
For each file
    ├─ already in KB? (matched by source path)
    │   └─ yes + overwrite=false → skip
    │
    ├─ read file content
    │   └─ binary or empty → skip
    │
    └─ extract title
        ├─ first "# Heading" in content
        └─ fallback: filename without extension
    ▼
Bulk INSERT (single SQLite transaction)
    │  kb_fts  ← title, content, source
    │  kb_meta ← rowid, project_id
    ▼
Return { scanned, added, skipped, added_titles }

---

3. Memory Lifecycle

                    ┌─────────────────────────────┐
                    │         AI Assistant         │
                    └──┬──────────┬───────────┬───┘
                       │          │           │
                  store/update  search      delete
                       │          │           │
                       ▼          ▼           ▼
              ┌────────────────────────────────────┐
              │           memory.sqlite             │
              │                                     │
              │  memory table                       │
              │  ┌──────────────────────────────┐   │
              │  │ id · project_id · scope      │   │
              │  │ content · tags · created_at  │   │
              │  │ updated_at · expires_at      │   │
              │  └──────────────────────────────┘   │
              │           │ FTS5 sync                │
              │  memory_fts (BM25 ranked search)     │
              │                                     │
              │  wiki_links (cross-references)       │
              └────────────────────────────────────┘
                       │
                  TTL purge
                  (auto on access, max 1×/60s/project)
                       │
                       ▼
              expired entries removed

---

4. Knowledge Base Flow

                 ┌──────────────────────────────────┐
                 │           Input sources           │
                 │                                   │
                 │  kb.init        kb.add            │
                 │  (bulk scan)    (single doc)      │
                 │  Dashboard      Dashboard          │
                 │  Import         New Document       │
                 └──────────┬───────────┬────────────┘
                            │           │
                            ▼           ▼
                 ┌──────────────────────────────────┐
                 │           kb.sqlite               │
                 │                                   │
                 │  kb_fts ── title, content, source │
                 │  kb_meta ─ rowid → project_id     │
                 └──────────────────────────────────┘
                            │
              ┌─────────────┼──────────────┐
              │             │              │
         kb.search    dashboard       wiki.link
         (FTS5/BM25   (split-panel    (cross-ref
          + Qdrant     list+detail)    to memory
          optional)                    or source)
              │
              ▼
         AI Assistant

---

5. Summary & Delta Flow

summary.project                        summary.delta
──────────────                         ─────────────

project_root                           project_root
    │                                      │
    ├─ auto-discover files                 ├─ run summary.project
    │   README, ARCHITECTURE,              │   (current snapshot)
    │   .kiro/resources/*.md, etc.         │
    │                                      ├─ search memory for
    ├─ memory.search (recent)              │   last "project-summary"
    │                                      │   scope entry
    ├─ kb.search (relevant docs)           │
    │                                      └─ diff current vs stored
    ▼                                          │
combined snapshot text                         ▼
    │                                  changed files / new memories /
    │  (AI stores result via            updated docs highlighted
    │   memory.store scope=
    │   "project-summary")
    ▼
searchable baseline for next delta

---

6. Dashboard Architecture

Browser                    HTTP Server (Node.js)           SQLite
  │                              │                            │
  │  GET /                       │                            │
  │ ─────────────────────────►   │                            │
  │  ◄── HTML (self-contained) ──│                            │
  │                              │                            │
  │  GET /api/projects           │  SELECT project_id,        │
  │ ─────────────────────────►   │  COUNT(*) FROM memory  ──► │
  │  ◄── [{ project_id, total }] │  ◄─────────────────────── │
  │                              │                            │
  │  GET /api/kb                 │  SELECT kb_fts JOIN        │
  │  ?project_id=x&limit=30      │  kb_meta WHERE             │
  │ ─────────────────────────►   │  project_id=x          ──► │
  │  ◄── { items, total }        │  ◄────────────────────── │
  │                              │                            │
  │  (click item)                │                            │
  │  GET /api/kb/:id         ──► │  SELECT * FROM kb_fts  ──► │
  │  ◄── { title, content, … }   │  ◄─────────────────────── │
  │                              │                            │
  │  GET /api/export/kb          │  SELECT all docs for       │
  │  ?project_id=x           ──► │  project → render .md  ──► │
  │  ◄── kb-x-2026-04-12.md      │  ◄─────────────────────── │
  │                              │                            │
  │  POST /api/kb/import         │  bulk INSERT kb_fts        │
  │  { project_id, docs[] }  ──► │  + kb_meta (transaction)──►│
  │  ◄── { ok, count }           │  ◄─────────────────────── │

---

7. Wiki Links & Lint

Entries (any type)
  memory ──┐
  kb     ──┼──► wiki.link ──► wiki_links table
  source ──┘                  (source_id, source_type,
                               target_id, target_type,
                               relation, project_id)
                                    │
                    ┌───────────────┼───────────────┐
                    │               │               │
               wiki.links      wiki.lint       wiki.export
               (lookup by      (health check)  (dump to .md)
                entry_id)           │
                    │          ┌────┴────────────────┐
                    │          │ orphan_memory        │
                    │          │ (no links at all)    │
                    │          │                      │
                    │          │ broken_links         │
                    │          │ (source or target    │
                    │          │  no longer exists)   │
                    │          │                      │
                    │          │ stale_sources        │
                    │          │ (90+ days, no links) │
                    │          └──────────────────────┘
                    ▼
             { outbound[], inbound[] }

---

Features

🧠 Memory Management

• Long-term Memory: Store, search, list, update, and delete project-specific memory entries
• Full-Text Search: FTS5 with BM25 ranking via use_fts flag, plus substring fallback
• Tag Filtering: Filter memories by tag name, combine with text queries
• Pagination: memory.list with total_count, offset, has_more
• TTL / Expiry: Optional expires_at on entries, auto-purged on access
• Project Isolation: Complete data isolation between projects

📚 Knowledge Base

• Document Storage: Add and search documents with FTS5 full-text search
• Project Scoping: project_id on all KB operations isolates docs per project
• Bulk Init: kb.init scans a project directory and imports all .md/.txt files in one call
• Vector Search: Optional Qdrant integration for semantic search
• Source Tracking: Track document sources and metadata

📂 Sources Layer

• Raw Ingest: Ingest .md, .txt, .csv, .pdf files via source.ingest
• FTS Search: Full-text search across ingested source content
• Project Isolation: Sources scoped per project

🔗 Wiki Links & Lint

• Cross-references: wiki.link creates typed links between memory/KB/source entries
• Link Lookup: wiki.links returns inbound and outbound links for any entry
• Health Check: wiki.lint detects orphan entries, broken links, and stale sources
• Export: wiki.export dumps all data as markdown files to a directory

📊 Project Summaries

• Snapshot Generation: summary.project reads files + memory + KB into a single snapshot
• Delta Summaries: summary.delta compares current state vs. last summary
• Auto-Discovery: Finds instruction files (README, ARCHITECTURE, .kiro/resources/*.md, etc.)

🎨 Interactive Dashboard

• Split-panel UI: KB, Memory, and Sources tabs show a paginated list on the left and a detail view on the right — no more infinite scroll dumps
• Load More: All lists paginate in batches of 30
• Project Management: Create and delete projects directly from the UI
• KB Management: Add, edit, delete, import (JSON/.md), and export KB documents as Markdown
• Memory Management: View and delete individual memory entries; export all as Markdown
• Sources Viewer: Browse and preview ingested source files inline
• Dark / Light mode, responsive layout, markdown rendering

🔒 Safety

• Path validation, mismatch detection, XSS protection, parameterized SQL

Installation

npm install -g mcp-kb-server

Or use directly with npx:

npx mcp-kb-server

Usage

Configure MCP Client

{
  "mcpServers": {
    "kb-server": {
      "command": "npx",
      "args": ["mcp-kb-server"],
      "env": {}
    }
  }
}

With a custom data directory:

{
  "mcpServers": {
    "kb-server": {
      "command": "npx",
      "args": ["mcp-kb-server"],
      "env": {
        "DATA_DIR": "/path/to/your/data",
        "DASHBOARD_PORT": "4242"
      }
    }
  }
}

---

Available Tools

Memory Tools

All memory tools require either project_root (recommended) or project_id.

memory.store

{
  "project_root": "/path/to/project",
  "content": "We use JWT for auth — stateless, works with mobile",
  "scope": "decisions",
  "tags": ["auth", "jwt", "architecture"],
  "expires_at": "2027-01-01T00:00:00Z"
}

memory.search

{
  "project_root": "/path/to/project",
  "query": "authentication",
  "tag": "decision",
  "use_fts": true,
  "limit": 10
}

memory.list

{
  "project_root": "/path/to/project",
  "limit": 50,
  "offset": 0,
  "scope": "decisions"
}

Returns { total_count, offset, limit, has_more, entries }.

memory.update

{
  "project_root": "/path/to/project",
  "id": "uuid",
  "content": "Updated content",
  "tags": ["updated", "auth"],
  "expires_at": ""
}

memory.delete

{
  "project_root": "/path/to/project",
  "id": "uuid"
}

---

Knowledge Base Tools

kb.add

{
  "title": "API Reference",
  "content": "## Endpoints\n...",
  "source": "docs/api.md",
  "project_id": "my-project"
}

kb.search

{
  "query": "authentication",
  "project_id": "my-project",
  "limit": 5
}

kb.init ★ — Scan a project and bulk-import all docs into the KB

{
  "project_root": "/path/to/project",
  "patterns": ["**/*.md", "docs/**/*.txt"],
  "overwrite": false
}

Returns:

{
  "project_id": "my-project",
  "scanned": 42,
  "added": 38,
  "skipped": 4,
  "added_titles": ["Getting Started", "API Reference", "..."],
  "skipped_paths": ["CHANGELOG.md (empty or binary)", "..."]
}

• Auto-detects project_id from project_root
• Default patterns: ["**/*.md", "**/*.txt"]
• Skips node_modules, .git, dist, build automatically
• Uses first # Heading as title, falls back to filename
• Skips already-imported files unless overwrite: true
• Bulk-inserts in a single SQLite transaction

---

Source Tools

source.ingest — Ingest a raw file (md, txt, csv, pdf)

{
  "project_root": "/path/to/project",
  "filename": "spec.md",
  "content": "...",
  "file_type": "md"
}

source.list / source.search

{
  "project_root": "/path/to/project",
  "query": "authentication",
  "limit": 20,
  "offset": 0
}

---

Wiki Tools

wiki.link — Create a typed link between two entries

{
  "project_root": "/path/to/project",
  "source_id": "mem-uuid",
  "source_type": "memory",
  "target_id": "kb-rowid",
  "target_type": "kb",
  "relation": "implements"
}

wiki.links — Look up all links for an entry

{
  "project_root": "/path/to/project",
  "entry_id": "mem-uuid"
}

wiki.lint — Health check

{ "project_root": "/path/to/project" }

Returns { orphan_memory, broken_links, stale_sources, summary }.

wiki.export — Export everything as markdown files

{
  "project_root": "/path/to/project",
  "output_dir": "./wiki-export"
}

---

Summary Tools

summary.project

{
  "project_root": "/path/to/project",
  "auto_discover": true,
  "include_memory": true,
  "include_kb": true
}

summary.delta

{
  "project_root": "/path/to/project",
  "auto_discover": true
}

---

Dashboard Tool

dashboard.projects — Start the dashboard server and return the URL

{ "limit": 10 }

Returns { dashboard_url, file_path }. Open the URL in a browser.

Set DASHBOARD_PORT=4242 in env to auto-start on server boot.

---

Dashboard

The dashboard is a self-contained HTML app served locally.

KB Tab

• Left panel: paginated document list (30/page) with search
• Right panel: full document view with Edit / Delete actions
• Toolbar: New Document, Import (JSON or .md), Export as Markdown

Memory Tab

• Left panel: paginated entry list showing scope + preview
• Right panel: full markdown content with Delete button
• Header: Export all entries as Markdown

Sources Tab

• Left panel: paginated file list with search
• Right panel: inline file content preview (no modal)

Links / Lint Tabs

• Links: look up cross-references by entry ID
• Lint: detect orphans, broken links, stale sources

Project Management

• Project selector in topbar — switches all tabs
• "+" button to create a new project
• "Delete Project" button to wipe all data for the current project

Import Format (JSON)

[
  { "title": "Getting Started", "content": "## Overview\n...", "source": "docs/intro.md" },
  { "title": "API Reference",   "content": "## Endpoints\n..." }
]

Export Format (Markdown)

KB export (kb-{project}-{date}.md):

# Knowledge Base — my-project

> Exported 2026-04-12T... · 38 documents

---

## Getting Started

**Source:** docs/intro.md
**ID:** 1

## Overview
...

Memory export (memory-{project}-{date}.md):

# Memory — my-project

> Exported 2026-04-12T... · 12 entries

---

### [decisions] uuid-here

**Tags:** auth, jwt
**Created:** 2026-03-01T...

We use JWT for auth — stateless, works with mobile.

---

Automatic Project Detection

project_id is auto-detected from project_root in this order:

1. package.json name field
2. Git remote origin URL (repo name)
3. Directory basename

All IDs are sanitized to lowercase alphanumeric + hyphens.

// Auto-detection
memory.store({ project_root: "/Users/me/my-app", content: "test" })
// → project_id: "my-app"

---

Environment Variables

Variable	Default	Purpose
DATA_DIR	./data	SQLite database location
LOG_LEVEL	info	Winston log level
MAX_MEMORY_ENTRIES	1000	Per-project memory cap
MAX_KB_ENTRIES	500	Per-project KB cap
ENABLE_QDRANT	false	Enable vector search
QDRANT_URL	http://localhost:6333	Qdrant endpoint
VACUUM_INTERVAL	86400000	DB vacuum interval (ms)
DASHBOARD_PORT	—	Auto-start dashboard on boot

---

Project Structure

mcp-kb-server/
├── src/
│   ├── server.js              # MCP entry point (JSON-RPC 2.0 over stdio)
│   ├── storage/db.js          # SQLite schema + migrations
│   ├── tools/
│   │   ├── memory.js          # memory.* tools
│   │   ├── kb.js              # kb.add / kb.search / kb.init
│   │   ├── sources.js         # source.ingest / list / search
│   │   ├── summary.js         # summary.project
│   │   ├── summaryDelta.js    # summary.delta
│   │   ├── wikiLinks.js       # wiki.link / wiki.links
│   │   ├── wikiLint.js        # wiki.lint
│   │   ├── wikiExport.js      # wiki.export
│   │   └── dashboard.js       # HTTP server + HTML dashboard
│   └── utils/
│       ├── projectId.js       # Auto-detection logic
│       ├── fileDiscovery.js   # Glob + file reading utilities
│       ├── config.js          # Env config
│       ├── validation.js      # Joi schemas
│       ├── performance.js     # LRU cache + vacuum scheduler
│       └── errors.js          # AppError / handleError
├── config/discovery.json      # Auto-discovery glob patterns
├── data/                      # SQLite databases (auto-created)
└── test/                      # 84 tests (node --test)

---

Database Schema

memory.sqlite

CREATE TABLE memory (
  id TEXT PRIMARY KEY,
  project_id TEXT NOT NULL DEFAULT 'legacy',
  scope TEXT NOT NULL,
  content TEXT NOT NULL,
  tags TEXT,
  created_at TEXT NOT NULL,
  updated_at TEXT,
  expires_at TEXT
);
CREATE VIRTUAL TABLE memory_fts USING fts5(content, tags);
CREATE TABLE wiki_links (
  id TEXT PRIMARY KEY,
  project_id TEXT NOT NULL,
  source_id TEXT, source_type TEXT,
  target_id TEXT, target_type TEXT,
  relation TEXT, created_at TEXT
);

kb.sqlite

CREATE VIRTUAL TABLE kb_fts USING fts5(title, content, source);
CREATE TABLE kb_meta (rowid INTEGER PRIMARY KEY, project_id TEXT);
CREATE TABLE sources (
  id TEXT PRIMARY KEY, project_id TEXT,
  slug TEXT, filename TEXT, file_type TEXT,
  content TEXT, file_path TEXT,
  ingested_at TEXT, size_bytes INTEGER
);
CREATE VIRTUAL TABLE sources_fts USING fts5(slug, content);

---

Development

git clone https://github.com/dereknguyen269/mcp-kb-server.git
cd mcp-kb-server
npm install
npm test        # runs all 84 tests

Run a single test file:

NODE_ENV=test node --test test/memory.test.js

---

Security

• Project Isolation: SQL-level project_id filtering on every query
• Path Validation: Prevents directory traversal
• XSS Protection: All user content HTML-escaped in dashboard
• Parameterized Queries: No SQL injection surface
• No External Resources: Dashboard works fully offline

---

Performance

• FTS5 / BM25: Ranked full-text search on memory, KB, and sources
• LRU Query Cache: 50-entry cache, 5-min TTL, invalidated on mutations
• Throttled Purge: Expired entry cleanup at most once per 60s per project
• SQLite WAL: Concurrent reads without blocking writes
• Bulk Transactions: kb.init and dashboard import use single transactions

---

Error Codes

Code	Meaning
-32602	Invalid params (missing fields, bad paths)
-32601	Method not found
-32000	Server / DB error

---

Version History

v1.2.0 (Current)

• ✅ kb.init — bulk-import project docs from filesystem in one MCP call
• ✅ Dashboard split-panel UI — list + detail for KB, Memory, Sources
• ✅ Paginated lists (30/page, Load more) across all tabs
• ✅ Import KB from JSON array or .md file via dashboard
• ✅ Export KB and Memory as Markdown downloads
• ✅ Create / delete projects from dashboard
• ✅ Delete individual memory entries from dashboard
• ✅ KB list filtered by project_id (was showing all projects)
• ✅ New Document correctly scoped to current project
• ✅ 84 tests

v1.1.0

• ✅ memory.delete / memory.update / memory.list
• ✅ Tag-based filtering, FTS5 on memory
• ✅ KB project scoping, TTL/expiry, LRU cache
• ✅ Sources layer (ingest md/txt/csv/pdf)
• ✅ Wiki links, lint, export tools

v1.0.0

• ✅ Auto project_id detection
• ✅ Interactive HTML dashboard (dark/light)
• ✅ KB management (add/edit/delete)
• ✅ Project scoping, path validation

---

Support

• npm: https://www.npmjs.com/package/mcp-kb-server
• GitHub: https://github.com/dereknguyen269/mcp-kb-server
• Issues: https://github.com/dereknguyen269/mcp-kb-server/issues