mcp-vector-search Library Integration Guide

Comprehensive guide for embedding mcp-vector-search within your own MCP server to provide semantic search capabilities over bundled documentation or resources.

Overview

mcp-vector-search can be used as a library to add semantic search to custom MCP servers. This enables you to bundle documentation with your server and provide semantic search without requiring users to configure vector search separately.

Use cases:

• Bundle documentation with your MCP server
• Provide semantic search over application-specific knowledge bases
• Combine vector search with your own custom tools
• Deliver turnkey MCP servers with integrated search

Adding the Dependency

Add mcp-vector-search to your deps.edn:

{:deps
 {org.hugoduncan/mcp-vector-search
  {:git/url "https://github.com/hugoduncan/mcp-vector-search"
   :git/sha "LATEST_SHA_HERE"}}}

Important: Replace LATEST_SHA_HERE with the latest commit SHA from the repository. You can find this by visiting the repository or running:

git ls-remote https://github.com/hugoduncan/mcp-vector-search HEAD

Classpath vs Filesystem Sources

mcp-vector-search supports two types of source specifications:

Filesystem Sources

Use the :path key with absolute paths:

{:sources [{:path "/Users/me/docs/**/*.md"}]}

Characteristics:

• Absolute paths starting with /
• Files read from the filesystem
• Support file watching for automatic re-indexing
• Used for development and user-specific content

Classpath Sources

Use the :class-path key with relative paths:

{:sources [{:class-path "docs/**/*.md"}]}

Characteristics:

• Relative paths without leading /
• Resources discovered from classpath (JARs, resource directories)
• No file watching (read-only resources)
• Used for bundled, library-embedded content

When to use each:

• Filesystem: Development, user-specific content, files that change
• Classpath: Production, bundled resources, static documentation

You can mix both types in a single configuration to combine bundled resources with user-specific content.

Resource Bundling

Directory Structure

Organize your project to bundle resources:

my-mcp-server/
├── resources/
│   ├── .mcp-vector-search/
│   │   └── config.edn          # Configuration for bundled resources
│   └── docs/
│       ├── guide.md
│       ├── api/
│       │   └── reference.md
│       └── examples/
│           └── usage.md
├── src/
│   └── my_server/
│       └── main.clj
└── deps.edn

Key points:

• Place documentation in resources/ directory
• Configuration goes in resources/.mcp-vector-search/config.edn
• Resources will be bundled in the JAR when you package your server
• Standard Clojure project structure with resources/ on the classpath

Configuration for Classpath Resources

Create resources/.mcp-vector-search/config.edn:

{:description "Search my-server documentation"
 :sources [{:class-path "docs/**/*.md"
            :name "Documentation"
            :type "docs"}]}

Configuration rules:

• Use :class-path instead of :path
• Paths are relative (no leading /)
• All path spec features work: globs (**/*.md), named captures ((?<category>[^/]+))
• Metadata extraction works identically
• File watching (:watch?) has no effect on classpath sources

Starting the Server

In your MCP server's main namespace:

(ns my-server.main
  (:require
    [mcp-vector-search.main :as vector-search]))

(defn -main []
  ;; Start vector search with classpath config
  ;; The config at resources/.mcp-vector-search/config.edn
  ;; will be found automatically on the classpath
  (vector-search/start)

  ;; Your server code here
  ...)

The server will:

1. Search for .mcp-vector-search/config.edn on the classpath
2. Discover and index resources from :class-path sources
3. Provide the search tool via MCP

Configuration Loading Order

When using mcp-vector-search as a library, configuration is loaded from the first location found:

1. Classpath: resources/.mcp-vector-search/config.edn (bundled in JAR)
2. Project directory: ./.mcp-vector-search/config.edn (runtime override)
3. Home directory: ~/.mcp-vector-search/config.edn (user-specific)

This loading order enables:

• Bundling defaults: Ship default configuration in your JAR
• Project overrides: Provide project-specific config during development
• User customization: Allow users to customize via home directory

Example workflow:

Development with project override:

# Create project-specific config during development
mkdir -p .mcp-vector-search
cat > .mcp-vector-search/config.edn <<EOF
{:description "Development search with local files"
 :watch? true
 :sources [{:path "/Users/me/project/docs/**/*.md"}]}
EOF

Production with bundled config:

# Build JAR - includes resources/.mcp-vector-search/config.edn
clojure -T:build uber
# Run - uses bundled config
java -jar target/my-server.jar

JAR Packaging

Build Configuration

Ensure resources/ is in your :paths in deps.edn:

{:paths ["src" "resources"]
 :deps {org.clojure/clojure {:mvn/version "1.12.3"}
        org.hugoduncan/mcp-vector-search
        {:git/url "https://github.com/hugoduncan/mcp-vector-search"
         :git/sha "LATEST_SHA_HERE"}}
 :aliases
 {:build {:deps {io.github.clojure/tools.build {:mvn/version "0.9.6"}}
          :ns-default build}}}

Build Script

Create build.clj:

(ns build
  (:require [clojure.tools.build.api :as b]))

(def class-dir "target/classes")
(def uber-file "target/my-server.jar")

(defn uber [_]
  (b/copy-dir {:src-dirs ["src" "resources"]
               :target-dir class-dir})
  (b/compile-clj {:basis (b/create-basis)
                  :class-dir class-dir})
  (b/uber {:class-dir class-dir
           :uber-file uber-file
           :basis (b/create-basis)
           :main 'my-server.main}))

Important: Include both "src" and "resources" in :src-dirs to bundle all resources.

Building and Running

# Build the JAR
clojure -T:build uber

# Verify resources are included
jar tf target/my-server.jar | grep -E "(docs|.mcp-vector-search)"

# Run the server
java -jar target/my-server.jar

Users can now run your MCP server with semantic search over your bundled documentation, without any configuration needed.

Example Configurations

Bundled API Documentation

;; resources/.mcp-vector-search/config.edn
{:description "Search API documentation and examples"
 :sources [{:class-path "api-docs/**/*.md"
            :category "api"}
           {:class-path "examples/**/*.clj"
            :ingest :namespace-doc
            :category "examples"}]}

Mixed Classpath and Filesystem

Combine bundled resources with filesystem sources:

{:description "Search bundled docs and local project files"
 :sources [
   ;; Bundled documentation (from JAR)
   {:class-path "lib-docs/**/*.md"
    :source "library"
    :type "docs"}

   ;; Local project documentation (filesystem)
   {:path "/Users/me/project/docs/**/*.md"
    :source "project"
    :type "docs"}

   ;; Local source code (filesystem)
   {:path "/Users/me/project/src/**/*.clj"
    :ingest :namespace-doc
    :source "project"
    :type "source"}]}

Multi-Language Documentation

Extract language metadata from paths:

{:description "Search multi-language documentation"
 :sources [{:class-path "docs/(?<lang>en|es|fr)/**/*.md"
            :type "documentation"}]}

For resource docs/en/guide.md:

• Metadata: {:type "documentation", :lang "en"}

Code Analysis for API Discovery

{:description "Search bundled API documentation"
 :sources [{:class-path "src/**/*.clj"
            :ingest :code-analysis
            :visibility :public-only
            :category "api"}]}

Complete Example

Directory Structure

my-mcp-server/
├── resources/
│   ├── .mcp-vector-search/
│   │   └── config.edn
│   └── docs/
│       ├── README.md
│       └── api/
│           └── reference.md
├── src/
│   └── my_server/
│       └── main.clj
├── deps.edn
└── build.clj

Configuration File

;; resources/.mcp-vector-search/config.edn
{:description "Search my-server documentation"
 :sources [{:class-path "docs/**/*.md"
            :project "my-server"
            :type "documentation"}]}

Main Server Code

;; src/my_server/main.clj
(ns my-server.main
  (:require
    [mcp-vector-search.main :as vector-search]
    [mcp-vector-search.server :as mcp-server]))

(defn -main []
  ;; Start vector search (loads classpath config automatically)
  (vector-search/start)

  ;; Add your custom tools here
  ;; ...

  ;; Start MCP server
  (mcp-server/start!))

Dependencies

;; deps.edn
{:paths ["src" "resources"]
 :deps {org.clojure/clojure {:mvn/version "1.12.3"}
        org.hugoduncan/mcp-vector-search
        {:git/url "https://github.com/hugoduncan/mcp-vector-search"
         :git/sha "LATEST_SHA_HERE"}}
 :aliases
 {:build {:deps {io.github.clojure/tools.build {:mvn/version "0.9.6"}}
          :ns-default build}}}

Build Configuration

;; build.clj
(ns build
  (:require [clojure.tools.build.api :as b]))

(def class-dir "target/classes")
(def uber-file "target/my-server.jar")

(defn uber [_]
  (b/copy-dir {:src-dirs ["src" "resources"]
               :target-dir class-dir})
  (b/compile-clj {:basis (b/create-basis)
                  :class-dir class-dir})
  (b/uber {:class-dir class-dir
           :uber-file uber-file
           :basis (b/create-basis)
           :main 'my-server.main}))

Limitations

No File Watching for Classpath Sources

Classpath sources do not support file watching:

• Resources in JARs are read-only
• Classpath resources are indexed once at startup
• The :watch? flag has no effect on :class-path sources

Workaround for development: Use filesystem sources instead:

;; Development config (local file) - with watching
{:watch? true
 :sources [{:path "/Users/me/project/resources/docs/**/*.md"}]}

;; Production config (bundled) - no watching needed
{:sources [{:class-path "docs/**/*.md"}]}

Resource Discovery Performance

Classpath resource discovery walks the entire classpath:

• Use specific base paths to limit scope (e.g., docs/**/*.md not **/*.md)
• Initial indexing may take longer than filesystem sources
• Avoid overly broad patterns for large classpaths

Troubleshooting

Configuration Not Found

Error: No configuration file found

Check:

1. File is in resources/.mcp-vector-search/config.edn
2. resources/ is on the classpath (should be automatic in :paths)
3. File is valid EDN syntax
4. No typos in directory or file name

Verify config is on classpath:

(require '[clojure.java.io :as io])
(io/resource ".mcp-vector-search/config.edn")  ;; Should return URL

Resources Not Indexed

Error: No documents indexed from classpath sources

Check:

1. Resources exist in resources/ directory
2. Path patterns match your directory structure
3. No leading / in :class-path values (should be relative)
4. Resources are included in the JAR (for packaged servers)

Verify resources are on classpath:

(require '[clojure.java.io :as io])
(io/resource "docs/guide.md")  ;; Should return URL

JAR Build Issues

Error: Resources missing from JAR

Check:

1. Ensure resources/ is in :paths in deps.edn:

{:paths ["src" "resources"]
 :deps {...}}

2. Ensure resources/ is in :src-dirs in build.clj:

(b/copy-dir {:src-dirs ["src" "resources"]
             :target-dir class-dir})

3. Verify the JAR contains resources:

jar tf my-server.jar | grep docs
jar tf my-server.jar | grep .mcp-vector-search

Path Pattern Issues

Error: Some resources not matched

Common mistakes:

• Using leading / with :class-path (should be relative)
• Forgetting ** for recursive matching
• Regex special characters not escaped in captures

Test patterns:

;; Wrong - leading slash
{:class-path "/docs/**/*.md"}

;; Correct - relative path
{:class-path "docs/**/*.md"}

;; Wrong - single glob doesn't recurse
{:class-path "docs/*.md"}  ;; only matches docs/file.md

;; Correct - recursive glob
{:class-path "docs/**/*.md"}  ;; matches docs/api/file.md

Tips and Best Practices

Resource organization:

• Place all bundled content in resources/ directory
• Use clear directory structure (e.g., docs/, api/, examples/)
• Include .mcp-vector-search/config.edn in resources/
• Keep resources focused on bundled content

Configuration strategy:

• Ship sensible defaults in resources/.mcp-vector-search/config.edn
• Use relative paths with :class-path for bundled content
• Document how users can override via project or home directory config
• Provide example configs in your server's README

Path specifications:

• Use specific base paths (e.g., docs/**/*.md not **/*.md)
• Leverage named captures for metadata extraction
• Test path patterns during development
• Avoid overly broad patterns for performance

Build process:

• Always include "resources" in both :paths and :src-dirs
• Verify JAR contents after building
• Test the JAR in a clean environment
• Document build requirements in your README

Development workflow:

• Use filesystem sources with :watch? during development
• Switch to classpath sources for production builds
• Keep development and production configs separate
• Test with both config types before releasing

Testing:

• Verify config loading from classpath
• Check resource discovery and indexing
• Test search functionality with bundled resources
• Validate JAR packaging and distribution

See Also

• doc/using.md - Complete configuration reference for all strategies and options
• doc/path-spec.md - Formal syntax for path specifications and captures
• doc/about.md - Project purpose and use cases
• README.md - Quick start guide for mcp-vector-search