diff --git a/.github/workflows/code-health-mcp-server.yml b/.github/workflows/code-health-mcp-server.yml
deleted file mode 100644
index 34240490e3..0000000000
--- a/.github/workflows/code-health-mcp-server.yml
+++ /dev/null
@@ -1,68 +0,0 @@
-name: 'Code Health MCP Server'
-on:
-  push:
-    branches:
-      - main
-    paths: 
-      - 'tools/mcp-server/**'
-      - '.github/workflows/code-health-mcp-server.yml'
-  pull_request:
-    branches:
-      - main
-    paths:
-      - 'tools/mcp-server/**'
-      - '.github/workflows/code-health-mcp-server.yml'
-  workflow_dispatch: {}
-  workflow_call: {}
-
-permissions:
-  contents: read
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-    - name: Checkout MCP Server
-      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
-    - name: Install Go
-      uses: actions/setup-go@4a3601121dd01d1626a1e23e37211e3254c1c06c
-      with:
-        go-version-file: 'tools/mcp-server/go.mod'
-    - name: Build MCP Server
-      working-directory: tools/mcp-server
-      run: make build
-
-  test:
-    needs: build
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
-      - name: Install Go
-        uses: actions/setup-go@4a3601121dd01d1626a1e23e37211e3254c1c06c
-        with:
-          go-version-file: 'tools/mcp-server/go.mod'
-      - name: Run tests
-        working-directory: tools/mcp-server
-        run: make test
-
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
-        with:
-          sparse-checkout: |
-            .github
-            tools
-      - name: Install Go
-        uses: actions/setup-go@4a3601121dd01d1626a1e23e37211e3254c1c06c
-        with:
-          go-version-file: 'tools/mcp-server/go.mod'
-          cache: false # see https://github.com/golangci/golangci-lint-action/issues/807
-      - name: golangci-lint
-        uses: golangci/golangci-lint-action@1e7e51e771db61008b38414a730f564565cf7c20
-        with:
-          version: v2.11.4
-          working-directory: tools/mcp-server
-
diff --git a/.gitignore b/.gitignore
index 9de5acc02b..f765072ace 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,4 +27,3 @@
 **/*metric-collection-results.parquet
 **/*spectral-output.txt
 **/*spectral-report.xml
-tools/go.work.sum
diff --git a/tools/go.work b/tools/go.work
deleted file mode 100644
index 89ae96f07a..0000000000
--- a/tools/go.work
+++ /dev/null
@@ -1,6 +0,0 @@
-go 1.26
-
-use (
-	cli
-	mcp-server
-)
diff --git a/tools/mcp-server/.golangci.yml b/tools/mcp-server/.golangci.yml
deleted file mode 100644
index e3a1f2613c..0000000000
--- a/tools/mcp-server/.golangci.yml
+++ /dev/null
@@ -1,125 +0,0 @@
-version: "2"
-run:
-  modules-download-mode: readonly
-  tests: true
-linters:
-  default: none
-  enable:
-    - copyloopvar
-    - dogsled
-    - errcheck
-    - errorlint
-    - exhaustive
-    - funlen
-    - gocritic
-    - godot
-    - goprintffuncname
-    - gosec
-    - govet
-    - ineffassign
-    - lll
-    - makezero
-    - misspell
-    - nakedret
-    - noctx
-    - nolintlint
-    - perfsprint
-    - prealloc
-    - predeclared
-    - revive
-    - rowserrcheck
-    - staticcheck
-    - testifylint
-    - thelper
-    - unconvert
-    - unused
-    - whitespace
-  settings:
-    funlen:
-      lines: 360
-      statements: 120
-    gocritic:
-      enabled-tags:
-        - diagnostic
-        - experimental
-        - opinionated
-        - performance
-        - style
-    govet:
-      enable:
-        - shadow
-    lll:
-      line-length: 150
-    misspell:
-      locale: US
-    nestif:
-      min-complexity: 7
-    revive:
-      severity: warning
-      rules:
-        - name: blank-imports
-        - name: context-as-argument
-        - name: context-keys-type
-        - name: defer
-        - name: dot-imports
-        - name: error-return
-        - name: error-strings
-        - name: error-naming
-        - name: early-return
-        - name: errorf
-        - name: exported
-        - name: import-shadowing
-        - name: indent-error-flow
-        - name: if-return
-        - name: increment-decrement
-        - name: var-naming
-        - name: var-declaration
-        - name: package-comments
-        - name: range
-        - name: receiver-naming
-        - name: time-naming
-        - name: unexported-return
-        - name: indent-error-flow
-        - name: errorf
-        - name: empty-block
-        - name: superfluous-else
-        - name: struct-tag
-        - name: unused-parameter
-        - name: unreachable-code
-        - name: redefines-builtin-id
-        - name: unused-receiver
-        - name: constant-logical-expr
-        - name: confusing-naming
-        - name: unnecessary-stmt
-        - name: use-any
-        - name: imports-blocklist
-          arguments:
-            - github.com/pkg/errors
-  exclusions:
-    generated: lax
-    presets:
-      - comments
-      - common-false-positives
-      - legacy
-      - std-error-handling
-    paths:
-      - third_party$
-      - builtin$
-      - examples$
-formatters:
-  enable:
-    - gci
-    - gofmt
-    - goimports
-  settings:
-    gci:
-      sections:
-        - standard
-        - default
-  exclusions:
-    generated: lax
-    paths:
-      - third_party$
-      - builtin$
-      - examples$
-
diff --git a/tools/mcp-server/Makefile b/tools/mcp-server/Makefile
deleted file mode 100644
index 2b035d8a06..0000000000
--- a/tools/mcp-server/Makefile
+++ /dev/null
@@ -1,46 +0,0 @@
-.PHONY: build
-build: ## Build the MCP server binary
-	@echo "==> Building mcp-server binary"
-	go build -o bin/mcp-server ./cmd
-
-.PHONY: install
-install: ## Install the MCP server binary to GOPATH/bin
-	@echo "==> Installing mcp-server"
-	go install ./cmd
-
-##@ Development
-
-.PHONY: fmt
-fmt: ## Format Go code
-	@echo "==> Formatting code"
-	gofmt -w -s .
-
-.PHONY: lint
-lint: ## Run linter
-	@echo "==> Running linter"
-	golangci-lint run
-
-.PHONY: test
-test: ## Run tests
-	@echo "==> Running tests"
-	go test -v ./...
-
-##@ Cleanup
-
-.PHONY: clean
-clean: ## Remove build artifacts
-	@echo "==> Cleaning build artifacts"
-	rm -rf bin/
-
-##@ Dependencies
-
-.PHONY: deps
-deps: ## Download dependencies
-	@echo "==> Downloading dependencies"
-	go mod download
-
-.PHONY: tidy
-tidy: ## Tidy go.mod
-	@echo "==> Tidying go.mod"
-	go mod tidy
-
diff --git a/tools/mcp-server/cmd/main.go b/tools/mcp-server/cmd/main.go
deleted file mode 100644
index d0431ed35e..0000000000
--- a/tools/mcp-server/cmd/main.go
+++ /dev/null
@@ -1,48 +0,0 @@
-package main
-
-import (
-	"context"
-	"log"
-	"os"
-
-	"github.com/modelcontextprotocol/go-sdk/mcp"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/resources"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/tools"
-)
-
-const (
-	serverName    = "openapi-mcp-server"
-	serverVersion = "0.1.0"
-)
-
-func main() {
-	if err := run(); err != nil {
-		log.Fatalf("Error: %v", err)
-	}
-}
-
-func run() error {
-	reg := registry.New()
-
-	impl := &mcp.Implementation{
-		Name:    serverName,
-		Version: serverVersion,
-	}
-	server := mcp.NewServer(impl, nil)
-
-	tools.Register(server, reg)
-	resources.Register(server, reg)
-
-	// Log to stderr (stdout is reserved for MCP protocol)
-	log.SetOutput(os.Stderr)
-	log.Printf("Starting %s v%s", serverName, serverVersion)
-
-	transport := &mcp.StdioTransport{}
-	session, err := server.Connect(context.Background(), transport, nil)
-	if err != nil {
-		return err
-	}
-
-	return session.Wait()
-}
diff --git a/tools/mcp-server/go.mod b/tools/mcp-server/go.mod
deleted file mode 100644
index fa68405dbe..0000000000
--- a/tools/mcp-server/go.mod
+++ /dev/null
@@ -1,46 +0,0 @@
-module github.com/mongodb/openapi/tools/mcp-server
-
-go 1.26
-
-require (
-	github.com/getkin/kin-openapi v0.135.0
-	github.com/modelcontextprotocol/go-sdk v1.5.0
-	github.com/mongodb/openapi/tools/cli v0.0.0
-	github.com/spf13/afero v1.15.0
-	github.com/stretchr/testify v1.11.1
-)
-
-require (
-	cloud.google.com/go v0.123.0 // indirect
-	github.com/davecgh/go-spew v1.1.2-0.20180830191138-d8f796af33cc // indirect
-	github.com/go-openapi/jsonpointer v0.22.5 // indirect
-	github.com/go-openapi/swag/jsonname v0.25.5 // indirect
-	github.com/google/jsonschema-go v0.4.2 // indirect
-	github.com/iancoleman/strcase v0.3.0 // indirect
-	github.com/josharian/intern v1.0.0 // indirect
-	github.com/kr/text v0.2.0 // indirect
-	github.com/mailru/easyjson v0.9.2 // indirect
-	github.com/mohae/deepcopy v0.0.0-20170929034955-c48cc78d4826 // indirect
-	github.com/oasdiff/oasdiff v1.14.0 // indirect
-	github.com/oasdiff/yaml v0.0.9 // indirect
-	github.com/oasdiff/yaml3 v0.0.9 // indirect
-	github.com/perimeterx/marshmallow v1.1.5 // indirect
-	github.com/pmezard/go-difflib v1.0.1-0.20181226105442-5d4384ee4fb2 // indirect
-	github.com/segmentio/asm v1.1.3 // indirect
-	github.com/segmentio/encoding v0.5.4 // indirect
-	github.com/tidwall/gjson v1.18.0 // indirect
-	github.com/tidwall/match v1.2.0 // indirect
-	github.com/tidwall/pretty v1.2.1 // indirect
-	github.com/tidwall/sjson v1.2.5 // indirect
-	github.com/wI2L/jsondiff v0.7.1 // indirect
-	github.com/woodsbury/decimal128 v1.4.0 // indirect
-	github.com/yargevad/filepathx v1.0.0 // indirect
-	github.com/yosida95/uritemplate/v3 v3.0.2 // indirect
-	go.uber.org/mock v0.6.0 // indirect
-	golang.org/x/oauth2 v0.35.0 // indirect
-	golang.org/x/sys v0.43.0 // indirect
-	golang.org/x/text v0.36.0 // indirect
-	gopkg.in/yaml.v3 v3.0.1 // indirect
-)
-
-replace github.com/mongodb/openapi/tools/cli => ../cli
diff --git a/tools/mcp-server/go.sum b/tools/mcp-server/go.sum
deleted file mode 100644
index af2d4536cb..0000000000
--- a/tools/mcp-server/go.sum
+++ /dev/null
@@ -1,93 +0,0 @@
-cloud.google.com/go v0.123.0 h1:2NAUJwPR47q+E35uaJeYoNhuNEM9kM8SjgRgdeOJUSE=
-cloud.google.com/go v0.123.0/go.mod h1:xBoMV08QcqUGuPW65Qfm1o9Y4zKZBpGS+7bImXLTAZU=
-github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ33E=
-github.com/davecgh/go-spew v1.1.2-0.20180830191138-d8f796af33cc h1:U9qPSI2PIWSS1VwoXQT9A3Wy9MM3WgvqSxFWenqJduM=
-github.com/davecgh/go-spew v1.1.2-0.20180830191138-d8f796af33cc/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
-github.com/getkin/kin-openapi v0.135.0 h1:751SjYfbiwqukYuVjwYEIKNfrSwS5YpA7DZnKSwQgtg=
-github.com/getkin/kin-openapi v0.135.0/go.mod h1:6dd5FJl6RdX4usBtFBaQhk9q62Yb2J0Mk5IhUO/QqFI=
-github.com/go-openapi/jsonpointer v0.22.5 h1:8on/0Yp4uTb9f4XvTrM2+1CPrV05QPZXu+rvu2o9jcA=
-github.com/go-openapi/jsonpointer v0.22.5/go.mod h1:gyUR3sCvGSWchA2sUBJGluYMbe1zazrYWIkWPjjMUY0=
-github.com/go-openapi/swag/jsonname v0.25.5 h1:8p150i44rv/Drip4vWI3kGi9+4W9TdI3US3uUYSFhSo=
-github.com/go-openapi/swag/jsonname v0.25.5/go.mod h1:jNqqikyiAK56uS7n8sLkdaNY/uq6+D2m2LANat09pKU=
-github.com/go-openapi/testify/v2 v2.4.0 h1:8nsPrHVCWkQ4p8h1EsRVymA2XABB4OT40gcvAu+voFM=
-github.com/go-openapi/testify/v2 v2.4.0/go.mod h1:HCPmvFFnheKK2BuwSA0TbbdxJ3I16pjwMkYkP4Ywn54=
-github.com/go-test/deep v1.0.8 h1:TDsG77qcSprGbC6vTN8OuXp5g+J+b5Pcguhf7Zt61VM=
-github.com/go-test/deep v1.0.8/go.mod h1:5C2ZWiW0ErCdrYzpqxLbTX7MG14M9iiw8DgHncVwcsE=
-github.com/golang-jwt/jwt/v5 v5.3.1 h1:kYf81DTWFe7t+1VvL7eS+jKFVWaUnK9cB1qbwn63YCY=
-github.com/golang-jwt/jwt/v5 v5.3.1/go.mod h1:fxCRLWMO43lRc8nhHWY6LGqRcf+1gQWArsqaEUEa5bE=
-github.com/google/go-cmp v0.7.0 h1:wk8382ETsv4JYUZwIsn6YpYiWiBsYLSJiTsyBybVuN8=
-github.com/google/go-cmp v0.7.0/go.mod h1:pXiqmnSA92OHEEa9HXL2W4E7lf9JzCmGVUdgjX3N/iU=
-github.com/google/jsonschema-go v0.4.2 h1:tmrUohrwoLZZS/P3x7ex0WAVknEkBZM46iALbcqoRA8=
-github.com/google/jsonschema-go v0.4.2/go.mod h1:r5quNTdLOYEz95Ru18zA0ydNbBuYoo9tgaYcxEYhJVE=
-github.com/iancoleman/strcase v0.3.0 h1:nTXanmYxhfFAMjZL34Ov6gkzEsSJZ5DbhxWjvSASxEI=
-github.com/iancoleman/strcase v0.3.0/go.mod h1:iwCmte+B7n89clKwxIoIXy/HfoL7AsD47ZCWhYzw7ho=
-github.com/josharian/intern v1.0.0 h1:vlS4z54oSdjm0bgjRigI+G1HpF+tI+9rE5LLzOg8HmY=
-github.com/josharian/intern v1.0.0/go.mod h1:5DoeVV0s6jJacbCEi61lwdGj/aVlrQvzHFFd8Hwg//Y=
-github.com/kr/pretty v0.3.1 h1:flRD4NNwYAUpkphVc1HcthR4KEIFJ65n8Mw5qdRn3LE=
-github.com/kr/pretty v0.3.1/go.mod h1:hoEshYVHaxMs3cyo3Yncou5ZscifuDolrwPKZanG3xk=
-github.com/kr/text v0.2.0 h1:5Nx0Ya0ZqY2ygV366QzturHI13Jq95ApcVaJBhpS+AY=
-github.com/kr/text v0.2.0/go.mod h1:eLer722TekiGuMkidMxC/pM04lWEeraHUUmBw8l2grE=
-github.com/mailru/easyjson v0.9.2 h1:dX8U45hQsZpxd80nLvDGihsQ/OxlvTkVUXH2r/8cb2M=
-github.com/mailru/easyjson v0.9.2/go.mod h1:1+xMtQp2MRNVL/V1bOzuP3aP8VNwRW55fQUto+XFtTU=
-github.com/modelcontextprotocol/go-sdk v1.5.0 h1:CHU0FIX9kpueNkxuYtfYQn1Z0slhFzBZuq+x6IiblIU=
-github.com/modelcontextprotocol/go-sdk v1.5.0/go.mod h1:gggDIhoemhWs3BGkGwd1umzEXCEMMvAnhTrnbXJKKKA=
-github.com/mohae/deepcopy v0.0.0-20170929034955-c48cc78d4826 h1:RWengNIwukTxcDr9M+97sNutRR1RKhG96O6jWumTTnw=
-github.com/mohae/deepcopy v0.0.0-20170929034955-c48cc78d4826/go.mod h1:TaXosZuwdSHYgviHp1DAtfrULt5eUgsSMsZf+YrPgl8=
-github.com/oasdiff/oasdiff v1.14.0 h1:R9nDNGHDoBpPUs/TthVDHGsJ63mnlL/vWUo252RRCgo=
-github.com/oasdiff/oasdiff v1.14.0/go.mod h1:9Im1HSDZzkao0yWGiy/Crr6cPvUvPBiCRxzVtHtqIKA=
-github.com/oasdiff/yaml v0.0.9 h1:zQOvd2UKoozsSsAknnWoDJlSK4lC0mpmjfDsfqNwX48=
-github.com/oasdiff/yaml v0.0.9/go.mod h1:8lvhgJG4xiKPj3HN5lDow4jZHPlx1i7dIwzkdAo6oAM=
-github.com/oasdiff/yaml3 v0.0.9 h1:rWPrKccrdUm8J0F3sGuU+fuh9+1K/RdJlWF7O/9yw2g=
-github.com/oasdiff/yaml3 v0.0.9/go.mod h1:y5+oSEHCPT/DGrS++Wc/479ERge0zTFxaF8PbGKcg2o=
-github.com/perimeterx/marshmallow v1.1.5 h1:a2LALqQ1BlHM8PZblsDdidgv1mWi1DgC2UmX50IvK2s=
-github.com/perimeterx/marshmallow v1.1.5/go.mod h1:dsXbUu8CRzfYP5a87xpp0xq9S3u0Vchtcl8we9tYaXw=
-github.com/pmezard/go-difflib v1.0.1-0.20181226105442-5d4384ee4fb2 h1:Jamvg5psRIccs7FGNTlIRMkT8wgtp5eCXdBlqhYGL6U=
-github.com/pmezard/go-difflib v1.0.1-0.20181226105442-5d4384ee4fb2/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
-github.com/rogpeppe/go-internal v1.12.0 h1:exVL4IDcn6na9z1rAb56Vxr+CgyK3nn3O+epU5NdKM8=
-github.com/rogpeppe/go-internal v1.12.0/go.mod h1:E+RYuTGaKKdloAfM02xzb0FW3Paa99yedzYV+kq4uf4=
-github.com/segmentio/asm v1.1.3 h1:WM03sfUOENvvKexOLp+pCqgb/WDjsi7EK8gIsICtzhc=
-github.com/segmentio/asm v1.1.3/go.mod h1:Ld3L4ZXGNcSLRg4JBsZ3//1+f/TjYl0Mzen/DQy1EJg=
-github.com/segmentio/encoding v0.5.4 h1:OW1VRern8Nw6ITAtwSZ7Idrl3MXCFwXHPgqESYfvNt0=
-github.com/segmentio/encoding v0.5.4/go.mod h1:HS1ZKa3kSN32ZHVZ7ZLPLXWvOVIiZtyJnO1gPH1sKt0=
-github.com/spf13/afero v1.15.0 h1:b/YBCLWAJdFWJTN9cLhiXXcD7mzKn9Dm86dNnfyQw1I=
-github.com/spf13/afero v1.15.0/go.mod h1:NC2ByUVxtQs4b3sIUphxK0NioZnmxgyCrfzeuq8lxMg=
-github.com/stretchr/testify v1.11.1 h1:7s2iGBzp5EwR7/aIZr8ao5+dra3wiQyKjjFuvgVKu7U=
-github.com/stretchr/testify v1.11.1/go.mod h1:wZwfW3scLgRK+23gO65QZefKpKQRnfz6sD981Nm4B6U=
-github.com/tidwall/gjson v1.14.2/go.mod h1:/wbyibRr2FHMks5tjHJ5F8dMZh3AcwJEMf5vlfC0lxk=
-github.com/tidwall/gjson v1.18.0 h1:FIDeeyB800efLX89e5a8Y0BNH+LOngJyGrIWxG2FKQY=
-github.com/tidwall/gjson v1.18.0/go.mod h1:/wbyibRr2FHMks5tjHJ5F8dMZh3AcwJEMf5vlfC0lxk=
-github.com/tidwall/match v1.1.1/go.mod h1:eRSPERbgtNPcGhD8UCthc6PmLEQXEWd3PRB5JTxsfmM=
-github.com/tidwall/match v1.2.0 h1:0pt8FlkOwjN2fPt4bIl4BoNxb98gGHN2ObFEDkrfZnM=
-github.com/tidwall/match v1.2.0/go.mod h1:eRSPERbgtNPcGhD8UCthc6PmLEQXEWd3PRB5JTxsfmM=
-github.com/tidwall/pretty v1.2.0/go.mod h1:ITEVvHYasfjBbM0u2Pg8T2nJnzm8xPwvNhhsoaGGjNU=
-github.com/tidwall/pretty v1.2.1 h1:qjsOFOWWQl+N3RsoF5/ssm1pHmJJwhjlSbZ51I6wMl4=
-github.com/tidwall/pretty v1.2.1/go.mod h1:ITEVvHYasfjBbM0u2Pg8T2nJnzm8xPwvNhhsoaGGjNU=
-github.com/tidwall/sjson v1.2.5 h1:kLy8mja+1c9jlljvWTlSazM7cKDRfJuR/bOJhcY5NcY=
-github.com/tidwall/sjson v1.2.5/go.mod h1:Fvgq9kS/6ociJEDnK0Fk1cpYF4FIW6ZF7LAe+6jwd28=
-github.com/ugorji/go/codec v1.2.11 h1:BMaWp1Bb6fHwEtbplGBGJ498wD+LKlNSl25MjdZY4dU=
-github.com/ugorji/go/codec v1.2.11/go.mod h1:UNopzCgEMSXjBc6AOMqYvWC1ktqTAfzJZUZgYf6w6lg=
-github.com/wI2L/jsondiff v0.7.1 h1:Fg9+yj+1/x3UtPBJhR91TKEzRkrEEWcAcLbg9dzEaNM=
-github.com/wI2L/jsondiff v0.7.1/go.mod h1:yAt2W7U6Jd4HK0RA8DGSGk0zDtfEtOUUJVnH/xICpjo=
-github.com/woodsbury/decimal128 v1.4.0 h1:xJATj7lLu4f2oObouMt2tgGiElE5gO6mSWUjQsBgUlc=
-github.com/woodsbury/decimal128 v1.4.0/go.mod h1:BP46FUrVjVhdTbKT+XuQh2xfQaGki9LMIRJSFuh6THU=
-github.com/yargevad/filepathx v1.0.0 h1:SYcT+N3tYGi+NvazubCNlvgIPbzAk7i7y2dwg3I5FYc=
-github.com/yargevad/filepathx v1.0.0/go.mod h1:BprfX/gpYNJHJfc35GjRRpVcwWXS89gGulUIU5tK3tA=
-github.com/yosida95/uritemplate/v3 v3.0.2 h1:Ed3Oyj9yrmi9087+NczuL5BwkIc4wvTb5zIM+UJPGz4=
-github.com/yosida95/uritemplate/v3 v3.0.2/go.mod h1:ILOh0sOhIJR3+L/8afwt/kE++YT040gmv5BQTMR2HP4=
-go.uber.org/mock v0.6.0 h1:hyF9dfmbgIX5EfOdasqLsWD6xqpNZlXblLB/Dbnwv3Y=
-go.uber.org/mock v0.6.0/go.mod h1:KiVJ4BqZJaMj4svdfmHM0AUx4NJYO8ZNpPnZn1Z+BBU=
-go.yaml.in/yaml/v3 v3.0.4 h1:tfq32ie2Jv2UxXFdLJdh3jXuOzWiL1fo0bu/FbuKpbc=
-go.yaml.in/yaml/v3 v3.0.4/go.mod h1:DhzuOOF2ATzADvBadXxruRBLzYTpT36CKvDb3+aBEFg=
-golang.org/x/oauth2 v0.35.0 h1:Mv2mzuHuZuY2+bkyWXIHMfhNdJAdwW3FuWeCPYN5GVQ=
-golang.org/x/oauth2 v0.35.0/go.mod h1:lzm5WQJQwKZ3nwavOZ3IS5Aulzxi68dUSgRHujetwEA=
-golang.org/x/sys v0.43.0 h1:Rlag2XtaFTxp19wS8MXlJwTvoh8ArU6ezoyFsMyCTNI=
-golang.org/x/sys v0.43.0/go.mod h1:4GL1E5IUh+htKOUEOaiffhrAeqysfVGipDYzABqnCmw=
-golang.org/x/text v0.36.0 h1:JfKh3XmcRPqZPKevfXVpI1wXPTqbkE5f7JA92a55Yxg=
-golang.org/x/text v0.36.0/go.mod h1:NIdBknypM8iqVmPiuco0Dh6P5Jcdk8lJL0CUebqK164=
-golang.org/x/tools v0.43.0 h1:12BdW9CeB3Z+J/I/wj34VMl8X+fEXBxVR90JeMX5E7s=
-golang.org/x/tools v0.43.0/go.mod h1:uHkMso649BX2cZK6+RpuIPXS3ho2hZo4FVwfoy1vIk0=
-gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
-gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c h1:Hei/4ADfdWqJk1ZMxUNpqntNwaWcugrBjAiHlqqRiVk=
-gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q=
-gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
-gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
diff --git a/tools/mcp-server/internal/registry/registry.go b/tools/mcp-server/internal/registry/registry.go
deleted file mode 100644
index 72a6c7b180..0000000000
--- a/tools/mcp-server/internal/registry/registry.go
+++ /dev/null
@@ -1,185 +0,0 @@
-package registry
-
-import (
-	"crypto/sha256"
-	"encoding/hex"
-	"encoding/json"
-	"fmt"
-	"sort"
-	"sync"
-	"time"
-
-	"github.com/getkin/kin-openapi/openapi3"
-)
-
-// SourceType represents the origin of a spec entry.
-type SourceType string
-
-const (
-	// SourceTypeFile represents a spec loaded from a file.
-	SourceTypeFile SourceType = "file"
-	// SourceTypeVirtual represents a spec created by transformations.
-	SourceTypeVirtual SourceType = "virtual"
-)
-
-// Entry represents a single OpenAPI specification in the registry.
-type Entry struct {
-	Alias      string            // Primary key - unique identifier
-	SourceType SourceType        // Origin: "file" or "virtual"
-	FilePath   string            // Source file path (empty for virtual specs)
-	Checksum   string            // SHA256 hash of spec content
-	Spec       *openapi3.T       // The actual spec
-	Metadata   map[string]string // Custom metadata
-	LoadedAt   time.Time         // When the spec was loaded
-}
-
-// Registry manages a collection of OpenAPI specifications in memory.
-type Registry struct {
-	mu    sync.RWMutex
-	specs map[string]*Entry // Key = alias (unique)
-}
-
-// New creates a new empty registry.
-func New() *Registry {
-	return &Registry{
-		specs: make(map[string]*Entry),
-	}
-}
-
-// Add adds or updates a spec entry in the registry.
-// FilePath should be empty string for virtual specs.
-//
-// Collision detection logic:
-// - Alias must be globally unique (regardless of source type)
-// - File + File with same alias but different path: collision error
-// - File + File with same alias, same path, same checksum: idempotent no-op
-// - File + File with same alias, same path, different checksum: update
-// - Virtual + Virtual with same alias, different checksum: update
-// - Virtual + Virtual with same alias, same checksum: idempotent no-op
-// - File + Virtual or Virtual + File with same alias: collision error.
-func (r *Registry) Add(alias, filePath string, spec *openapi3.T, metadata map[string]string) error {
-	r.mu.Lock()
-	defer r.mu.Unlock()
-
-	sourceType := SourceTypeFile
-	if filePath == "" {
-		sourceType = SourceTypeVirtual
-	}
-
-	checksum, err := calculateChecksum(spec)
-	if err != nil {
-		return fmt.Errorf("failed to calculate checksum: %w", err)
-	}
-
-	if existing, exists := r.specs[alias]; exists {
-		if existing.SourceType != sourceType {
-			return fmt.Errorf("alias '%s' is already in use by a %s spec", alias, existing.SourceType)
-		}
-
-		// File-based specs: check path collision
-		if sourceType == SourceTypeFile {
-			if existing.FilePath != filePath {
-				return fmt.Errorf("alias '%s' is already in use by '%s'", alias, existing.FilePath)
-			}
-		}
-
-		// No changes - idempotent no-op
-		if existing.Checksum == checksum {
-			return nil
-		}
-
-		r.specs[alias] = &Entry{
-			Alias:      alias,
-			SourceType: sourceType,
-			FilePath:   filePath,
-			Checksum:   checksum,
-			Spec:       spec,
-			Metadata:   metadata,
-			LoadedAt:   time.Now(),
-		}
-		return nil
-	}
-
-	r.specs[alias] = &Entry{
-		Alias:      alias,
-		SourceType: sourceType,
-		FilePath:   filePath,
-		Checksum:   checksum,
-		Spec:       spec,
-		Metadata:   metadata,
-		LoadedAt:   time.Now(),
-	}
-	return nil
-}
-
-// GetByAlias retrieves a spec entry by alias.
-// Returns an error if the spec doesn't exist.
-func (r *Registry) GetByAlias(alias string) (*Entry, error) {
-	r.mu.RLock()
-	defer r.mu.RUnlock()
-
-	entry, exists := r.specs[alias]
-	if !exists {
-		return nil, fmt.Errorf("spec with alias '%s' not found", alias)
-	}
-
-	return entry, nil
-}
-
-// Remove removes a spec entry from the registry by alias.
-// Returns an error if the spec doesn't exist.
-func (r *Registry) Remove(alias string) error {
-	r.mu.Lock()
-	defer r.mu.Unlock()
-
-	if _, exists := r.specs[alias]; !exists {
-		return fmt.Errorf("spec with alias '%s' not found", alias)
-	}
-
-	delete(r.specs, alias)
-	return nil
-}
-
-// List returns all spec entries in the registry, sorted by LoadedAt descending (most recent first).
-func (r *Registry) List() []*Entry {
-	r.mu.RLock()
-	defer r.mu.RUnlock()
-
-	entries := make([]*Entry, 0, len(r.specs))
-	for _, entry := range r.specs {
-		entries = append(entries, entry)
-	}
-
-	// Sort by LoadedAt descending (most recent first)
-	sort.Slice(entries, func(i, j int) bool {
-		return entries[i].LoadedAt.After(entries[j].LoadedAt)
-	})
-
-	return entries
-}
-
-// Count returns the number of specs in the registry.
-func (r *Registry) Count() int {
-	r.mu.RLock()
-	defer r.mu.RUnlock()
-
-	return len(r.specs)
-}
-
-// Clear removes all specs from the registry.
-func (r *Registry) Clear() {
-	r.mu.Lock()
-	defer r.mu.Unlock()
-
-	r.specs = make(map[string]*Entry)
-}
-
-// calculateChecksum calculates SHA256 hash of the spec content.
-func calculateChecksum(spec *openapi3.T) (string, error) {
-	data, err := json.Marshal(spec)
-	if err != nil {
-		return "", err
-	}
-	hash := sha256.Sum256(data)
-	return hex.EncodeToString(hash[:]), nil
-}
diff --git a/tools/mcp-server/internal/registry/registry_test.go b/tools/mcp-server/internal/registry/registry_test.go
deleted file mode 100644
index 2a7b14b141..0000000000
--- a/tools/mcp-server/internal/registry/registry_test.go
+++ /dev/null
@@ -1,255 +0,0 @@
-package registry
-
-import (
-	"testing"
-
-	"github.com/getkin/kin-openapi/openapi3"
-)
-
-func TestRegistry_Add_NewEntry(t *testing.T) {
-	reg := New()
-	spec := createTestSpec("Test API", "1.0.0")
-
-	err := reg.Add("test-api", "/path/to/test.yaml", spec, nil)
-	if err != nil {
-		t.Fatalf("Add() failed for new entry: %v", err)
-	}
-
-	if reg.Count() != 1 {
-		t.Errorf("Count() = %d, want 1", reg.Count())
-	}
-
-	entry, err := reg.GetByAlias("test-api")
-	if err != nil {
-		t.Fatalf("GetByAlias() failed: %v", err)
-	}
-
-	if entry.Alias != "test-api" {
-		t.Errorf("entry.Alias = %q, want %q", entry.Alias, "test-api")
-	}
-	if entry.FilePath != "/path/to/test.yaml" {
-		t.Errorf("entry.FilePath = %q, want %q", entry.FilePath, "/path/to/test.yaml")
-	}
-}
-
-func TestRegistry_Add_CollisionDifferentFile(t *testing.T) {
-	reg := New()
-	spec1 := createTestSpec("API 1", "1.0.0")
-	spec2 := createTestSpec("API 2", "2.0.0")
-
-	// Add first spec with alias "my-api"
-	err := reg.Add("my-api", "/path/to/file1.yaml", spec1, nil)
-	if err != nil {
-		t.Fatalf("First Add() failed: %v", err)
-	}
-
-	// Try to add different file with same alias - should error
-	err = reg.Add("my-api", "/path/to/file2.yaml", spec2, nil)
-	if err == nil {
-		t.Fatal("Add() should have returned collision error for different file")
-	}
-
-	// Verify error message mentions collision
-	expectedMsg := "alias 'my-api' is already in use by '/path/to/file1.yaml'"
-	if err.Error() != expectedMsg {
-		t.Errorf("error = %q, want %q", err.Error(), expectedMsg)
-	}
-
-	// Registry should still have only the first entry
-	if reg.Count() != 1 {
-		t.Errorf("Count() = %d, want 1", reg.Count())
-	}
-}
-
-func TestRegistry_Add_SameFileModified(t *testing.T) {
-	reg := New()
-	spec1 := createTestSpec("API", "1.0.0")
-	spec2 := createTestSpec("API", "2.0.0") // Different version = different checksum
-
-	// Add original spec
-	err := reg.Add("my-api", "/path/to/api.yaml", spec1, nil)
-	if err != nil {
-		t.Fatalf("First Add() failed: %v", err)
-	}
-
-	entry1, _ := reg.GetByAlias("my-api")
-	checksum1 := entry1.Checksum
-
-	// Re-add same file with modified content - should update
-	err = reg.Add("my-api", "/path/to/api.yaml", spec2, nil)
-	if err != nil {
-		t.Fatalf("Second Add() should succeed (update): %v", err)
-	}
-
-	// Should still have only 1 entry
-	if reg.Count() != 1 {
-		t.Errorf("Count() = %d, want 1", reg.Count())
-	}
-
-	// Checksum should have changed
-	entry2, _ := reg.GetByAlias("my-api")
-	if entry2.Checksum == checksum1 {
-		t.Error("Checksum should have changed after update")
-	}
-
-	// Version should be updated
-	if entry2.Spec.Info.Version != "2.0.0" {
-		t.Errorf("Spec version = %q, want %q", entry2.Spec.Info.Version, "2.0.0")
-	}
-}
-
-func TestRegistry_Add_SameFileUnchanged(t *testing.T) {
-	reg := New()
-	spec := createTestSpec("API", "1.0.0")
-
-	// Add spec
-	err := reg.Add("my-api", "/path/to/api.yaml", spec, nil)
-	if err != nil {
-		t.Fatalf("First Add() failed: %v", err)
-	}
-
-	entry1, _ := reg.GetByAlias("my-api")
-	loadedAt1 := entry1.LoadedAt
-
-	// Re-add exact same spec - should be idempotent
-	err = reg.Add("my-api", "/path/to/api.yaml", spec, nil)
-	if err != nil {
-		t.Fatalf("Second Add() should succeed (idempotent): %v", err)
-	}
-
-	entry2, _ := reg.GetByAlias("my-api")
-
-	// LoadedAt should NOT change (idempotent operation)
-	if !entry2.LoadedAt.Equal(loadedAt1) {
-		t.Error("LoadedAt should not change for idempotent operation")
-	}
-}
-
-func TestRegistry_Remove(t *testing.T) {
-	reg := New()
-	spec := createTestSpec("Test API", "1.0.0")
-
-	err := reg.Add("test-api", "/path/to/test.yaml", spec, nil)
-	if err != nil {
-		t.Fatalf("Failed to add spec: %v", err)
-	}
-
-	err = reg.Remove("test-api")
-	if err != nil {
-		t.Fatalf("Remove() failed: %v", err)
-	}
-
-	if reg.Count() != 0 {
-		t.Errorf("Count() = %d, want 0", reg.Count())
-	}
-
-	_, err = reg.GetByAlias("test-api")
-	if err == nil {
-		t.Error("GetByAlias() should fail after removal")
-	}
-}
-
-// Helper function to create a test spec.
-func createTestSpec(title, version string) *openapi3.T {
-	return &openapi3.T{
-		OpenAPI: "3.0.0",
-		Info: &openapi3.Info{
-			Title:   title,
-			Version: version,
-		},
-		Paths: &openapi3.Paths{},
-	}
-}
-
-func TestRegistry_Add_VirtualSpec(t *testing.T) {
-	reg := New()
-	spec := createTestSpec("Virtual API", "1.0.0")
-
-	// Add virtual spec (empty file path)
-	err := reg.Add("virtual-api", "", spec, map[string]string{"source": "filter"})
-	if err != nil {
-		t.Fatalf("Add() failed for virtual spec: %v", err)
-	}
-
-	entry, err := reg.GetByAlias("virtual-api")
-	if err != nil {
-		t.Fatalf("GetByAlias() failed: %v", err)
-	}
-
-	if entry.SourceType != SourceTypeVirtual {
-		t.Errorf("entry.SourceType = %q, want %q", entry.SourceType, SourceTypeVirtual)
-	}
-	if entry.FilePath != "" {
-		t.Errorf("entry.FilePath = %q, want empty string", entry.FilePath)
-	}
-}
-
-func TestRegistry_Add_VirtualSpecUpdate(t *testing.T) {
-	reg := New()
-	spec1 := createTestSpec("API", "1.0.0")
-	spec2 := createTestSpec("API", "2.0.0")
-
-	// Add virtual spec
-	err := reg.Add("my-virtual", "", spec1, nil)
-	if err != nil {
-		t.Fatalf("First Add() failed: %v", err)
-	}
-
-	// Update with different spec (different checksum)
-	err = reg.Add("my-virtual", "", spec2, nil)
-	if err != nil {
-		t.Fatalf("Second Add() should succeed (update): %v", err)
-	}
-
-	entry, _ := reg.GetByAlias("my-virtual")
-	if entry.Spec.Info.Version != "2.0.0" {
-		t.Errorf("Spec version = %q, want %q", entry.Spec.Info.Version, "2.0.0")
-	}
-}
-
-func TestRegistry_Add_CollisionFileVsVirtual(t *testing.T) {
-	reg := New()
-	spec1 := createTestSpec("API 1", "1.0.0")
-	spec2 := createTestSpec("API 2", "2.0.0")
-
-	// Add file-based spec
-	err := reg.Add("my-api", "/path/to/file.yaml", spec1, nil)
-	if err != nil {
-		t.Fatalf("File-based Add() failed: %v", err)
-	}
-
-	// Try to add virtual spec with same alias - should error
-	err = reg.Add("my-api", "", spec2, nil)
-	if err == nil {
-		t.Fatal("Add() should return collision error for file vs virtual")
-	}
-
-	// Error message should mention type conflict
-	expectedMsg := "alias 'my-api' is already in use by a file spec"
-	if err.Error() != expectedMsg {
-		t.Errorf("error = %q, want %q", err.Error(), expectedMsg)
-	}
-}
-
-func TestRegistry_Add_CollisionVirtualVsFile(t *testing.T) {
-	reg := New()
-	spec1 := createTestSpec("API 1", "1.0.0")
-	spec2 := createTestSpec("API 2", "2.0.0")
-
-	// Add virtual spec
-	err := reg.Add("my-api", "", spec1, nil)
-	if err != nil {
-		t.Fatalf("Virtual Add() failed: %v", err)
-	}
-
-	// Try to add file-based spec with same alias - should error
-	err = reg.Add("my-api", "/path/to/file.yaml", spec2, nil)
-	if err == nil {
-		t.Fatal("Add() should return collision error for virtual vs file")
-	}
-
-	expectedMsg := "alias 'my-api' is already in use by a virtual spec"
-	if err.Error() != expectedMsg {
-		t.Errorf("error = %q, want %q", err.Error(), expectedMsg)
-	}
-}
diff --git a/tools/mcp-server/internal/resources/alias.go b/tools/mcp-server/internal/resources/alias.go
deleted file mode 100644
index 8026586a07..0000000000
--- a/tools/mcp-server/internal/resources/alias.go
+++ /dev/null
@@ -1,123 +0,0 @@
-package resources
-
-import (
-	"encoding/json"
-	"fmt"
-
-	"github.com/getkin/kin-openapi/openapi3"
-	"github.com/modelcontextprotocol/go-sdk/mcp"
-	"github.com/mongodb/openapi/tools/cli/pkg/apiversion"
-	"github.com/mongodb/openapi/tools/cli/pkg/openapi"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-)
-
-// SpecStats holds counts of the spec's top-level components.
-type SpecStats struct {
-	Paths      int `json:"paths"`
-	Operations int `json:"operations"`
-	Schemas    int `json:"schemas"`
-	Tags       int `json:"tags"`
-}
-
-// SpecOverview is the response body for the openapi://specs/{alias} resource.
-type SpecOverview struct {
-	Alias               string              `json:"alias"`
-	SourceType          registry.SourceType `json:"sourceType"`
-	Title               string              `json:"title,omitempty"`
-	Description         string              `json:"description,omitempty"`
-	Stats               SpecStats           `json:"stats"`
-	LatestStableVersion string              `json:"latestStableVersion"`
-	AvailableVersions   []string            `json:"availableVersions"`
-	HasPreview          bool                `json:"hasPreview"`
-	HasUpcoming         bool                `json:"hasUpcoming"`
-}
-
-func handleAlias(reg *registry.Registry, req *mcp.ReadResourceRequest) (*mcp.ReadResourceResult, error) {
-	alias, err := aliasFromURI(req.Params.URI)
-	if err != nil {
-		return nil, err
-	}
-
-	entry, err := reg.GetByAlias(alias)
-	if err != nil {
-		return nil, fmt.Errorf("spec with alias %q not found", alias)
-	}
-
-	overview := buildSpecOverview(entry)
-
-	data, err := json.Marshal(overview)
-	if err != nil {
-		return nil, err
-	}
-
-	return &mcp.ReadResourceResult{
-		Contents: []*mcp.ResourceContents{
-			{URI: req.Params.URI, MIMEType: mimeTypeJSON, Text: string(data)},
-		},
-	}, nil
-}
-
-func buildSpecOverview(entry *registry.Entry) SpecOverview {
-	overview := SpecOverview{
-		Alias:      entry.Alias,
-		SourceType: entry.SourceType,
-	}
-
-	if entry.Spec == nil {
-		return overview
-	}
-
-	if entry.Spec.Info != nil {
-		overview.Title = entry.Spec.Info.Title
-		overview.Description = entry.Spec.Info.Description
-	}
-
-	if entry.Spec.Paths != nil {
-		overview.Stats.Paths = len(entry.Spec.Paths.Map())
-		overview.Stats.Operations = countOperations(entry.Spec)
-	}
-
-	if entry.Spec.Components != nil {
-		overview.Stats.Schemas = len(entry.Spec.Components.Schemas)
-	}
-
-	overview.Stats.Tags = len(entry.Spec.Tags)
-
-	stable, hasPreview, hasUpcoming := extractVersions(entry.Spec)
-	overview.HasPreview = hasPreview
-	overview.HasUpcoming = hasUpcoming
-	// ExtractVersions returns versions sorted ascending by date string (YYYY-MM-DD).
-	overview.AvailableVersions = stable
-	if len(stable) > 0 {
-		overview.LatestStableVersion = stable[len(stable)-1]
-	}
-
-	return overview
-}
-
-func countOperations(spec *openapi3.T) int {
-	count := 0
-	for _, item := range spec.Paths.Map() {
-		count += len(item.Operations())
-	}
-	return count
-}
-
-func extractVersions(spec *openapi3.T) (stable []string, hasPreview, hasUpcoming bool) {
-	stable = []string{}
-	all, err := openapi.ExtractVersions(spec)
-	if err != nil || len(all) == 0 {
-		return stable, false, false
-	}
-	for _, v := range all {
-		switch {
-		case apiversion.IsPreviewStabilityLevel(v):
-			hasPreview = true
-		case apiversion.IsUpcomingStabilityLevel(v):
-			hasUpcoming = true
-		default:
-			stable = append(stable, v)
-		}
-	}
-	return stable, hasPreview, hasUpcoming
-}
diff --git a/tools/mcp-server/internal/resources/alias_test.go b/tools/mcp-server/internal/resources/alias_test.go
deleted file mode 100644
index 5b3c2a9274..0000000000
--- a/tools/mcp-server/internal/resources/alias_test.go
+++ /dev/null
@@ -1,49 +0,0 @@
-package resources
-
-import (
-	"encoding/json"
-	"testing"
-
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-)
-
-// TestHandleAlias_Overview verifies that the spec overview contains title, stats, and version info.
-func TestHandleAlias_Overview(t *testing.T) {
-	result, err := handleAlias(newTestRegistry(t), makeRequest("openapi://specs/test-api"))
-	require.NoError(t, err)
-
-	var body SpecOverview
-	require.NoError(t, json.Unmarshal([]byte(result.Contents[0].Text), &body))
-
-	assert.Equal(t, "test-api", body.Alias)
-	assert.Equal(t, "Test API", body.Title)
-	assert.Equal(t, registry.SourceTypeFile, body.SourceType)
-	assert.Equal(t, 4, body.Stats.Paths)
-	assert.Equal(t, 6, body.Stats.Operations)
-	assert.Equal(t, 2, body.Stats.Tags)
-	assert.Equal(t, 2, body.Stats.Schemas)
-	assert.Equal(t, "2025-01-01", body.LatestStableVersion)
-	assert.Equal(t, []string{"2024-01-01", "2025-01-01"}, body.AvailableVersions)
-	assert.True(t, body.HasPreview)
-	assert.True(t, body.HasUpcoming)
-}
-
-// TestHandleAlias_NotFound verifies that reading a non-existent alias returns an error.
-func TestHandleAlias_NotFound(t *testing.T) {
-	_, err := handleAlias(registry.New(), makeRequest("openapi://specs/nonexistent"))
-	require.Error(t, err)
-}
-
-// TestHandleAlias_URIMissingAlias verifies that a URI without an alias segment returns an error.
-func TestHandleAlias_URIMissingAlias(t *testing.T) {
-	_, err := handleAlias(registry.New(), makeRequest("not-a-valid-uri"))
-	require.Error(t, err)
-}
-
-// TestHandleAlias_URIExtraSegments verifies that a URI with extra path segments is rejected.
-func TestHandleAlias_URIExtraSegments(t *testing.T) {
-	_, err := handleAlias(registry.New(), makeRequest("openapi://specs/test-api/tags/Clusters"))
-	require.Error(t, err)
-}
diff --git a/tools/mcp-server/internal/resources/resources.go b/tools/mcp-server/internal/resources/resources.go
deleted file mode 100644
index a26f49d213..0000000000
--- a/tools/mcp-server/internal/resources/resources.go
+++ /dev/null
@@ -1,52 +0,0 @@
-package resources
-
-import (
-	"context"
-
-	"github.com/modelcontextprotocol/go-sdk/mcp"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-)
-
-const mimeTypeJSON = "application/json"
-
-// Register registers all static resources and resource template handlers with the server.
-func Register(server *mcp.Server, reg *registry.Registry) {
-	server.AddResource(&mcp.Resource{
-		URI:  "openapi://specs",
-		Name: "specs",
-		Description: "Start here. Lists all OpenAPI specifications currently loaded in the registry. " +
-			"Each entry includes the alias (used to reference the spec in all other resources and tools), " +
-			"sourceType ('file' for specs loaded from disk, 'virtual' for sliced subsets), " +
-			"and filePath (empty for virtual specs). " +
-			"Read this resource first to discover what aliases are available before using other resources or tools.",
-		MIMEType: mimeTypeJSON,
-	}, makeSpecsHandler(reg))
-
-	server.AddResourceTemplate(&mcp.ResourceTemplate{
-		URITemplate: "openapi://specs/{alias}",
-		Name:        "spec-overview",
-		Description: "Returns a structural overview of a single loaded spec identified by {alias}. " +
-			"Includes title, description, and stats (path count, operation count, schema count, tag count). " +
-			"For versioned APIs, also returns: " +
-			"latestStableVersion (the most recent stable YYYY-MM-DD version), " +
-			"availableVersions (all stable date-based versions in ascending order), " +
-			"hasPreview (true if any preview operations exist), " +
-			"hasUpcoming (true if any upcoming operations exist). " +
-			"Use this to understand the scope of a spec before searching or slicing it.",
-		MIMEType: mimeTypeJSON,
-	}, makeAliasHandler(reg))
-}
-
-// makeSpecsHandler creates the handler for the openapi://specs resource.
-func makeSpecsHandler(reg *registry.Registry) mcp.ResourceHandler {
-	return func(_ context.Context, req *mcp.ReadResourceRequest) (*mcp.ReadResourceResult, error) {
-		return handleSpecs(reg, req)
-	}
-}
-
-// makeAliasHandler creates the handler for the openapi://specs/{alias} resource template.
-func makeAliasHandler(reg *registry.Registry) mcp.ResourceHandler {
-	return func(_ context.Context, req *mcp.ReadResourceRequest) (*mcp.ReadResourceResult, error) {
-		return handleAlias(reg, req)
-	}
-}
diff --git a/tools/mcp-server/internal/resources/specs.go b/tools/mcp-server/internal/resources/specs.go
deleted file mode 100644
index 8f87c46bdf..0000000000
--- a/tools/mcp-server/internal/resources/specs.go
+++ /dev/null
@@ -1,45 +0,0 @@
-package resources
-
-import (
-	"encoding/json"
-
-	"github.com/modelcontextprotocol/go-sdk/mcp"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-)
-
-// SpecSummary is a summary of a single spec returned by the openapi://specs resource.
-type SpecSummary struct {
-	Alias      string              `json:"alias"`
-	SourceType registry.SourceType `json:"sourceType"`
-	FilePath   string              `json:"filePath,omitempty"`
-}
-
-// SpecsResource is the response body for the openapi://specs resource.
-type SpecsResource struct {
-	Specs []SpecSummary `json:"specs"`
-	Total int           `json:"total"`
-}
-
-func handleSpecs(reg *registry.Registry, req *mcp.ReadResourceRequest) (*mcp.ReadResourceResult, error) {
-	entries := reg.List()
-
-	summaries := make([]SpecSummary, len(entries))
-	for i, entry := range entries {
-		summaries[i] = SpecSummary{
-			Alias:      entry.Alias,
-			SourceType: entry.SourceType,
-			FilePath:   entry.FilePath,
-		}
-	}
-
-	data, err := json.Marshal(SpecsResource{Specs: summaries, Total: len(summaries)})
-	if err != nil {
-		return nil, err
-	}
-
-	return &mcp.ReadResourceResult{
-		Contents: []*mcp.ResourceContents{
-			{URI: req.Params.URI, MIMEType: mimeTypeJSON, Text: string(data)},
-		},
-	}, nil
-}
diff --git a/tools/mcp-server/internal/resources/specs_test.go b/tools/mcp-server/internal/resources/specs_test.go
deleted file mode 100644
index b484e91461..0000000000
--- a/tools/mcp-server/internal/resources/specs_test.go
+++ /dev/null
@@ -1,51 +0,0 @@
-package resources
-
-import (
-	"encoding/json"
-	"testing"
-
-	"github.com/getkin/kin-openapi/openapi3"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-)
-
-// TestHandleSpecs_EmptyRegistry verifies that an empty registry returns an empty list.
-func TestHandleSpecs_EmptyRegistry(t *testing.T) {
-	result, err := handleSpecs(registry.New(), makeRequest("openapi://specs"))
-	require.NoError(t, err)
-
-	var body SpecsResource
-	require.NoError(t, json.Unmarshal([]byte(result.Contents[0].Text), &body))
-	assert.Equal(t, 0, body.Total)
-	assert.Empty(t, body.Specs)
-}
-
-// TestHandleSpecs_WithEntries verifies that loaded specs are returned with alias, sourceType, and filePath.
-func TestHandleSpecs_WithEntries(t *testing.T) {
-	result, err := handleSpecs(newTestRegistry(t), makeRequest("openapi://specs"))
-	require.NoError(t, err)
-
-	var body SpecsResource
-	require.NoError(t, json.Unmarshal([]byte(result.Contents[0].Text), &body))
-	require.Equal(t, 1, body.Total)
-
-	s := body.Specs[0]
-	assert.Equal(t, "test-api", s.Alias)
-	assert.Equal(t, registry.SourceTypeFile, s.SourceType)
-	assert.Equal(t, "/test/api.yaml", s.FilePath)
-}
-
-// TestHandleSpecs_VirtualSpecHasNoFilePath verifies that virtual specs omit filePath.
-func TestHandleSpecs_VirtualSpecHasNoFilePath(t *testing.T) {
-	reg := registry.New()
-	require.NoError(t, reg.Add("virtual-api", "", &openapi3.T{Info: &openapi3.Info{Title: "Virtual"}}, nil))
-
-	result, err := handleSpecs(reg, makeRequest("openapi://specs"))
-	require.NoError(t, err)
-
-	var body SpecsResource
-	require.NoError(t, json.Unmarshal([]byte(result.Contents[0].Text), &body))
-	assert.Empty(t, body.Specs[0].FilePath)
-	assert.Equal(t, registry.SourceTypeVirtual, body.Specs[0].SourceType)
-}
diff --git a/tools/mcp-server/internal/resources/tags.go b/tools/mcp-server/internal/resources/tags.go
deleted file mode 100644
index 6e957bba14..0000000000
--- a/tools/mcp-server/internal/resources/tags.go
+++ /dev/null
@@ -1,105 +0,0 @@
-package resources
-
-import (
-	"encoding/json"
-	"fmt"
-	"sort"
-
-	"github.com/getkin/kin-openapi/openapi3"
-	"github.com/modelcontextprotocol/go-sdk/mcp"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-)
-
-// TagOperation represents a single operation belonging to a tag.
-type TagOperation struct {
-	OperationID string `json:"operationId"`
-	Method      string `json:"method"`
-	Path        string `json:"path"`
-	Summary     string `json:"summary"`
-}
-
-// TagsResource is the response body for the openapi://specs/{alias}/tags/{tagName} resource.
-type TagsResource struct {
-	Tag        string         `json:"tag"`
-	Total      int            `json:"total"`
-	Operations []TagOperation `json:"operations"`
-}
-
-func handleTags(reg *registry.Registry, req *mcp.ReadResourceRequest) (*mcp.ReadResourceResult, error) {
-	alias, tagName, err := aliasAndTagFromURI(req.Params.URI)
-	if err != nil {
-		return nil, err
-	}
-
-	entry, err := reg.GetByAlias(alias)
-	if err != nil {
-		return nil, fmt.Errorf("spec with alias %q not found", alias)
-	}
-
-	ops, err := operationsByTag(entry.Spec, tagName)
-	if err != nil {
-		return nil, err
-	}
-
-	resource := TagsResource{
-		Tag:        tagName,
-		Total:      len(ops),
-		Operations: ops,
-	}
-
-	data, err := json.Marshal(resource)
-	if err != nil {
-		return nil, err
-	}
-
-	return &mcp.ReadResourceResult{
-		Contents: []*mcp.ResourceContents{
-			{URI: req.Params.URI, MIMEType: mimeTypeJSON, Text: string(data)},
-		},
-	}, nil
-}
-
-// operationsByTag returns all operations in the spec tagged with tagName,
-// sorted by path then method for deterministic output.
-// Returns an error if no operations are found for the given tag.
-func operationsByTag(spec *openapi3.T, tagName string) ([]TagOperation, error) {
-	if spec == nil || spec.Paths == nil {
-		return nil, fmt.Errorf("tag %q not found in spec", tagName)
-	}
-
-	var ops []TagOperation
-	for path, item := range spec.Paths.Map() {
-		if item == nil {
-			continue
-		}
-		for method, op := range item.Operations() {
-			if op == nil {
-				continue
-			}
-			for _, t := range op.Tags {
-				if t == tagName {
-					ops = append(ops, TagOperation{
-						OperationID: op.OperationID,
-						Method:      method,
-						Path:        path,
-						Summary:     op.Summary,
-					})
-					break
-				}
-			}
-		}
-	}
-
-	if len(ops) == 0 {
-		return nil, fmt.Errorf("tag %q not found in spec", tagName)
-	}
-
-	sort.Slice(ops, func(i, j int) bool {
-		if ops[i].Path != ops[j].Path {
-			return ops[i].Path < ops[j].Path
-		}
-		return ops[i].Method < ops[j].Method
-	})
-
-	return ops, nil
-}
diff --git a/tools/mcp-server/internal/resources/tags_test.go b/tools/mcp-server/internal/resources/tags_test.go
deleted file mode 100644
index 16fccbd3d6..0000000000
--- a/tools/mcp-server/internal/resources/tags_test.go
+++ /dev/null
@@ -1,87 +0,0 @@
-package resources
-
-import (
-	"encoding/json"
-	"testing"
-
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-)
-
-type wantOp struct {
-	operationID string
-	method      string
-	path        string
-	summary     string
-}
-
-func assertOp(t *testing.T, got TagOperation, want wantOp) {
-	t.Helper()
-	assert.Equal(t, want.operationID, got.OperationID)
-	assert.Equal(t, want.method, got.Method)
-	assert.Equal(t, want.path, got.Path)
-	assert.Equal(t, want.summary, got.Summary)
-}
-
-// TestHandleTags_Clusters verifies Clusters operations are returned sorted by path then method.
-func TestHandleTags_Clusters(t *testing.T) {
-	result, err := handleTags(newTestRegistry(t), makeRequest("openapi://specs/test-api/tags/Clusters"))
-	require.NoError(t, err)
-
-	var body TagsResource
-	require.NoError(t, json.Unmarshal([]byte(result.Contents[0].Text), &body))
-	assert.Equal(t, "Clusters", body.Tag)
-	require.Equal(t, 4, body.Total)
-
-	assertOp(t, body.Operations[0], wantOp{"listClusterDetails", "GET",
-		"/api/atlas/v2/clusters", "Return All Authorized Clusters in All Projects"})
-	assertOp(t, body.Operations[1], wantOp{"listGroupClusters", "GET",
-		"/api/atlas/v2/groups/{groupId}/clusters", "Return All Clusters in One Project"})
-	assertOp(t, body.Operations[2], wantOp{"createGroupCluster", "POST",
-		"/api/atlas/v2/groups/{groupId}/clusters", "Create One Cluster in One Project"})
-	assertOp(t, body.Operations[3], wantOp{"deleteGroupCluster", "DELETE",
-		"/api/atlas/v2/groups/{groupId}/clusters/{clusterName}", "Remove One Cluster from One Project"})
-}
-
-// TestHandleTags_FlexClusters verifies that tag names containing spaces are resolved correctly.
-// The server decodes the URI automatically so agents can use tag names as they appear in the spec.
-func TestHandleTags_FlexClusters(t *testing.T) {
-	result, err := handleTags(newTestRegistry(t), makeRequest("openapi://specs/test-api/tags/Flex%20Clusters"))
-	require.NoError(t, err)
-
-	var body TagsResource
-	require.NoError(t, json.Unmarshal([]byte(result.Contents[0].Text), &body))
-	assert.Equal(t, "Flex Clusters", body.Tag)
-	require.Equal(t, 2, body.Total)
-
-	// Sorted: GET before POST on the same path.
-	assertOp(t, body.Operations[0], wantOp{"listGroupFlexClusters", "GET",
-		"/api/atlas/v2/groups/{groupId}/flexClusters", "Return All Flex Clusters from One Project"})
-	assertOp(t, body.Operations[1], wantOp{"createGroupFlexCluster", "POST",
-		"/api/atlas/v2/groups/{groupId}/flexClusters", "Create One Flex Cluster in One Project"})
-}
-
-// TestHandleTags_TagNotFound verifies that a non-existent tag returns an error.
-func TestHandleTags_TagNotFound(t *testing.T) {
-	_, err := handleTags(newTestRegistry(t), makeRequest("openapi://specs/test-api/tags/NonExistent"))
-	require.Error(t, err)
-}
-
-// TestHandleTags_TagCaseSensitive verifies that tag matching is case-sensitive.
-func TestHandleTags_TagCaseSensitive(t *testing.T) {
-	_, err := handleTags(newTestRegistry(t), makeRequest("openapi://specs/test-api/tags/clusters"))
-	require.Error(t, err)
-}
-
-// TestHandleTags_AliasNotFound verifies that a non-existent alias returns an error.
-func TestHandleTags_AliasNotFound(t *testing.T) {
-	_, err := handleTags(registry.New(), makeRequest("openapi://specs/nonexistent/tags/Clusters"))
-	require.Error(t, err)
-}
-
-// TestHandleTags_URIInvalid verifies that a URI missing the tag segment returns an error.
-func TestHandleTags_URIInvalid(t *testing.T) {
-	_, err := handleTags(registry.New(), makeRequest("openapi://specs/test-api"))
-	require.Error(t, err)
-}
diff --git a/tools/mcp-server/internal/resources/testhelper_test.go b/tools/mcp-server/internal/resources/testhelper_test.go
deleted file mode 100644
index 32e63416ab..0000000000
--- a/tools/mcp-server/internal/resources/testhelper_test.go
+++ /dev/null
@@ -1,130 +0,0 @@
-package resources
-
-import (
-	"testing"
-
-	"github.com/getkin/kin-openapi/openapi3"
-	"github.com/modelcontextprotocol/go-sdk/mcp"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-)
-
-// makeRequest builds a ReadResourceRequest for the given URI.
-func makeRequest(uri string) *mcp.ReadResourceRequest {
-	return &mcp.ReadResourceRequest{Params: &mcp.ReadResourceParams{URI: uri}}
-}
-
-// newTestRegistry returns a registry pre-loaded with the shared test spec under alias "test-api".
-func newTestRegistry(t *testing.T) *registry.Registry {
-	t.Helper()
-	reg := registry.New()
-	if err := reg.Add("test-api", "/test/api.yaml", newTestSpec(), nil); err != nil {
-		t.Fatalf("newTestRegistry: failed to add spec: %v", err)
-	}
-	return reg
-}
-
-// newTestSpec builds a synthetic OpenAPI spec whose paths, operation IDs, summaries, and tag names
-// are modeled after the real Atlas v2 spec so that test assertions reflect realistic API data.
-func newTestSpec() *openapi3.T {
-	spec := &openapi3.T{
-		Info: &openapi3.Info{
-			Title:       "Test API",
-			Description: "A test API",
-		},
-		Paths: &openapi3.Paths{},
-		Tags: openapi3.Tags{
-			{Name: "Clusters"},
-			{Name: "Flex Clusters"}, // space in name → percent-encoded as "Flex%20Clusters" in URIs
-		},
-		Components: &openapi3.Components{
-			Schemas: map[string]*openapi3.SchemaRef{
-				"Cluster":     {Value: &openapi3.Schema{Type: &openapi3.Types{"object"}}},
-				"FlexCluster": {Value: &openapi3.Schema{Type: &openapi3.Types{"object"}}},
-			},
-		},
-	}
-
-	newStableResp := func() *openapi3.Responses {
-		return openapi3.NewResponses(openapi3.WithStatus(200, &openapi3.ResponseRef{
-			Value: &openapi3.Response{
-				Content: openapi3.Content{
-					"application/vnd.atlas.2024-01-01+json": &openapi3.MediaType{},
-					"application/vnd.atlas.2025-01-01+json": &openapi3.MediaType{},
-				},
-			},
-		}))
-	}
-	newPreviewResp := func() *openapi3.Responses {
-		return openapi3.NewResponses(openapi3.WithStatus(200, &openapi3.ResponseRef{
-			Value: &openapi3.Response{
-				Content: openapi3.Content{
-					"application/vnd.atlas.preview+json": {
-						Extensions: map[string]any{
-							"x-xgen-preview": map[string]any{"public": "true"},
-						},
-					},
-				},
-			},
-		}))
-	}
-	newUpcomingResp := func() *openapi3.Responses {
-		return openapi3.NewResponses(openapi3.WithStatus(200, &openapi3.ResponseRef{
-			Value: &openapi3.Response{
-				Content: openapi3.Content{
-					"application/vnd.atlas.2026-01-01.upcoming+json": &openapi3.MediaType{},
-				},
-			},
-		}))
-	}
-
-	spec.Paths.Set("/api/atlas/v2/clusters", &openapi3.PathItem{
-		Get: &openapi3.Operation{
-			OperationID: "listClusterDetails",
-			Summary:     "Return All Authorized Clusters in All Projects",
-			Tags:        []string{"Clusters"},
-			Responses:   newStableResp(),
-		},
-	})
-
-	spec.Paths.Set("/api/atlas/v2/groups/{groupId}/clusters", &openapi3.PathItem{
-		Get: &openapi3.Operation{
-			OperationID: "listGroupClusters",
-			Summary:     "Return All Clusters in One Project",
-			Tags:        []string{"Clusters"},
-			Responses:   newStableResp(),
-		},
-		Post: &openapi3.Operation{
-			OperationID: "createGroupCluster",
-			Summary:     "Create One Cluster in One Project",
-			Tags:        []string{"Clusters"},
-			Responses:   newStableResp(),
-		},
-	})
-
-	spec.Paths.Set("/api/atlas/v2/groups/{groupId}/clusters/{clusterName}", &openapi3.PathItem{
-		Delete: &openapi3.Operation{
-			OperationID: "deleteGroupCluster",
-			Summary:     "Remove One Cluster from One Project",
-			Tags:        []string{"Clusters"},
-			Responses:   newPreviewResp(),
-		},
-	})
-
-	// Flex Clusters: tag name has a space, exercising percent-encoding in URIs.
-	spec.Paths.Set("/api/atlas/v2/groups/{groupId}/flexClusters", &openapi3.PathItem{
-		Get: &openapi3.Operation{
-			OperationID: "listGroupFlexClusters",
-			Summary:     "Return All Flex Clusters from One Project",
-			Tags:        []string{"Flex Clusters"},
-			Responses:   newStableResp(),
-		},
-		Post: &openapi3.Operation{
-			OperationID: "createGroupFlexCluster",
-			Summary:     "Create One Flex Cluster in One Project",
-			Tags:        []string{"Flex Clusters"},
-			Responses:   newUpcomingResp(),
-		},
-	})
-
-	return spec
-}
diff --git a/tools/mcp-server/internal/resources/uri.go b/tools/mcp-server/internal/resources/uri.go
deleted file mode 100644
index 1fb264c84a..0000000000
--- a/tools/mcp-server/internal/resources/uri.go
+++ /dev/null
@@ -1,52 +0,0 @@
-package resources
-
-import (
-	"fmt"
-	"net/url"
-	"strings"
-)
-
-// parseSpecURI parses a resource URI and validates that it uses the openapi://specs/ base.
-// It is the shared entry point for all URI parsing in this package.
-func parseSpecURI(uri string) (*url.URL, error) {
-	u, err := url.Parse(uri)
-	if err != nil || u.Scheme != "openapi" || u.Host != "specs" {
-		return nil, fmt.Errorf("invalid resource URI %q: must use openapi://specs/ scheme", uri)
-	}
-	return u, nil
-}
-
-// aliasFromURI extracts the alias from openapi://specs/{alias}.
-// Returns an error if the path has extra segments or the alias is empty.
-func aliasFromURI(uri string) (string, error) {
-	u, err := parseSpecURI(uri)
-	if err != nil {
-		return "", fmt.Errorf("invalid resource URI %q: expected openapi://specs/{alias}", uri)
-	}
-	parts := strings.Split(strings.TrimPrefix(u.Path, "/"), "/")
-	if len(parts) != 1 || parts[0] == "" {
-		return "", fmt.Errorf("invalid resource URI %q: expected openapi://specs/{alias}", uri)
-	}
-	return parts[0], nil
-}
-
-// aliasAndTagFromURI extracts the alias and tag name from openapi://specs/{alias}/tags/{tagName}.
-// The tag name is percent-decoded so agents can use tag names as they appear in the spec.
-func aliasAndTagFromURI(uri string) (alias, tagName string, err error) {
-	u, err := parseSpecURI(uri)
-	if err != nil {
-		return "", "", fmt.Errorf("invalid resource URI %q: expected openapi://specs/{alias}/tags/{tagName}", uri)
-	}
-
-	// path: /{alias}/tags/{tagName}
-	parts := strings.SplitN(strings.TrimPrefix(u.Path, "/"), "/", 3)
-	if len(parts) != 3 || parts[0] == "" || parts[1] != "tags" || parts[2] == "" {
-		return "", "", fmt.Errorf("invalid resource URI %q: expected openapi://specs/{alias}/tags/{tagName}", uri)
-	}
-
-	tagName, err = url.PathUnescape(parts[2])
-	if err != nil {
-		return "", "", fmt.Errorf("invalid tag name in URI %q: %w", uri, err)
-	}
-	return parts[0], tagName, nil
-}
diff --git a/tools/mcp-server/internal/resources/uri_test.go b/tools/mcp-server/internal/resources/uri_test.go
deleted file mode 100644
index 5f28569580..0000000000
--- a/tools/mcp-server/internal/resources/uri_test.go
+++ /dev/null
@@ -1,65 +0,0 @@
-package resources
-
-import (
-	"testing"
-
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-)
-
-func TestAliasFromURI(t *testing.T) {
-	tests := []struct {
-		name      string
-		uri       string
-		wantAlias string
-		wantErr   bool
-	}{
-		{
-			name:      "valid URI",
-			uri:       "openapi://specs/atlas",
-			wantAlias: "atlas",
-		},
-		{
-			name:    "wrong scheme",
-			uri:     "https://specs/atlas",
-			wantErr: true,
-		},
-		{
-			name:    "wrong host",
-			uri:     "openapi://other/atlas",
-			wantErr: true,
-		},
-		{
-			name:    "arbitrary https URL",
-			uri:     "https://goodle.com/q",
-			wantErr: true,
-		},
-		{
-			name:    "extra path segments",
-			uri:     "openapi://specs/atlas/tags/Clusters",
-			wantErr: true,
-		},
-		{
-			name:    "missing alias",
-			uri:     "openapi://specs/",
-			wantErr: true,
-		},
-		{
-			name:    "empty string",
-			uri:     "",
-			wantErr: true,
-		},
-	}
-
-	for _, tc := range tests {
-		t.Run(tc.name, func(t *testing.T) {
-			alias, err := aliasFromURI(tc.uri)
-			if tc.wantErr {
-				require.Error(t, err)
-				return
-			}
-			require.NoError(t, err)
-			assert.Equal(t, tc.wantAlias, alias)
-		})
-	}
-}
diff --git a/tools/mcp-server/internal/tools/export.go b/tools/mcp-server/internal/tools/export.go
deleted file mode 100644
index 9b5b623d41..0000000000
--- a/tools/mcp-server/internal/tools/export.go
+++ /dev/null
@@ -1,56 +0,0 @@
-package tools
-
-import (
-	"fmt"
-
-	"github.com/mongodb/openapi/tools/cli/pkg/openapi"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-	"github.com/spf13/afero"
-)
-
-// ExportParams are the parameters for the export tool.
-type ExportParams struct {
-	Alias    string `json:"alias" jsonschema:"Alias of the spec to export"`
-	FilePath string `json:"filePath" jsonschema:"Path where the file should be saved"`
-	Format   string `json:"format,omitempty" jsonschema:"Output format: 'json' or 'yaml' (default: json)"`
-}
-
-// ExportResult is the result of an export operation.
-type ExportResult struct {
-	Success  bool   `json:"success"`
-	Alias    string `json:"alias"`
-	FilePath string `json:"filePath"`
-	Format   string `json:"format"`
-	Message  string `json:"message"`
-}
-
-// handleExport exports a spec from the registry to a file.
-// The SDK handles parameter unmarshaling and validation automatically.
-func handleExport(reg *registry.Registry, params ExportParams) (ExportResult, error) {
-	if params.Format == "" {
-		params.Format = "json"
-	}
-
-	if params.Format != "json" && params.Format != "yaml" {
-		return ExportResult{Success: false}, fmt.Errorf("invalid format %q: must be 'json' or 'yaml'", params.Format)
-	}
-
-	entry, err := reg.GetByAlias(params.Alias)
-	if err != nil {
-		return ExportResult{Success: false}, err
-	}
-
-	fs := afero.NewOsFs()
-
-	if err := openapi.SaveToFile(params.FilePath, params.Format, entry.Spec, fs); err != nil {
-		return ExportResult{Success: false}, fmt.Errorf("failed to export spec: %w", err)
-	}
-
-	return ExportResult{
-		Success:  true,
-		Alias:    params.Alias,
-		FilePath: params.FilePath,
-		Format:   params.Format,
-		Message:  fmt.Sprintf("Exported '%s' to %s", params.Alias, params.FilePath),
-	}, nil
-}
diff --git a/tools/mcp-server/internal/tools/load.go b/tools/mcp-server/internal/tools/load.go
deleted file mode 100644
index 4d27be3be6..0000000000
--- a/tools/mcp-server/internal/tools/load.go
+++ /dev/null
@@ -1,114 +0,0 @@
-package tools
-
-import (
-	"fmt"
-	"path/filepath"
-	"regexp"
-	"strings"
-
-	"github.com/mongodb/openapi/tools/cli/pkg/openapi"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-)
-
-// LoadParams are the parameters for the load tool.
-type LoadParams struct {
-	FilePath string            `json:"filePath" jsonschema:"Path to the OpenAPI file (JSON or YAML)"`
-	Alias    string            `json:"alias,omitempty" jsonschema:"Optional custom alias (auto-generated from filename if not provided)"`
-	Metadata map[string]string `json:"metadata,omitempty" jsonschema:"Optional metadata to attach to the spec"`
-}
-
-// LoadResult is the result of a load operation.
-type LoadResult struct {
-	Success  bool     `json:"success"`
-	Alias    string   `json:"alias"`
-	Message  string   `json:"message"`
-	SpecInfo SpecInfo `json:"specInfo,omitempty"`
-}
-
-// SpecInfo contains metadata about the loaded spec.
-type SpecInfo struct {
-	Title       string `json:"title,omitempty"`
-	Version     string `json:"version,omitempty"`
-	PathCount   int    `json:"pathCount"`
-	SchemaCount int    `json:"schemaCount"`
-}
-
-// handleLoad loads an OpenAPI spec from a file into the registry.
-// The SDK handles parameter unmarshaling and validation automatically.
-func handleLoad(reg *registry.Registry, params LoadParams) (LoadResult, error) {
-	alias := params.Alias
-	if alias == "" {
-		var err error
-		alias, err = generateAliasFromPath(params.FilePath)
-		if err != nil {
-			return LoadResult{Success: false}, fmt.Errorf("failed to generate alias: %w", err)
-		}
-	} else {
-		alias = strings.ToLower(alias)
-		if !isValidAlias(alias) {
-			return LoadResult{Success: false}, fmt.Errorf("invalid alias '%s': only lowercase letters, numbers, and hyphens allowed", alias)
-		}
-	}
-
-	loader := openapi.NewLoader()
-	specInfo, err := loader.LoadFromPath(params.FilePath)
-	if err != nil {
-		return LoadResult{Success: false}, fmt.Errorf("failed to load spec from %q: %w", params.FilePath, err)
-	}
-
-	err = reg.Add(alias, params.FilePath, specInfo.Spec, params.Metadata)
-	if err != nil {
-		return LoadResult{Success: false}, fmt.Errorf("%w. Please use 'unload' first or provide a different alias", err)
-	}
-
-	schemaCount := 0
-	if specInfo.Spec.Components != nil && specInfo.Spec.Components.Schemas != nil {
-		schemaCount = len(specInfo.Spec.Components.Schemas)
-	}
-
-	info := SpecInfo{
-		Title:       specInfo.Spec.Info.Title,
-		Version:     specInfo.Spec.Info.Version,
-		PathCount:   len(specInfo.Spec.Paths.Map()),
-		SchemaCount: schemaCount,
-	}
-
-	return LoadResult{
-		Success:  true,
-		Alias:    alias,
-		Message:  fmt.Sprintf("Loaded '%s' successfully", alias),
-		SpecInfo: info,
-	}, nil
-}
-
-// generateAliasFromPath creates a valid alias from a file path.
-func generateAliasFromPath(filePath string) (string, error) {
-	filename := filepath.Base(filePath)
-	ext := filepath.Ext(filename)
-	name := strings.TrimSuffix(filename, ext)
-
-	name = strings.ToLower(name)
-
-	re := regexp.MustCompile(`[^a-z0-9-]+`)
-	alias := re.ReplaceAllString(name, "-")
-
-	alias = strings.Trim(alias, "-")
-
-	re = regexp.MustCompile(`-+`)
-	alias = re.ReplaceAllString(alias, "-")
-
-	if !isValidAlias(alias) {
-		return "", fmt.Errorf("could not generate valid alias from filename '%s'", filename)
-	}
-
-	return alias, nil
-}
-
-// isValidAlias checks if alias contains only allowed characters.
-func isValidAlias(alias string) bool {
-	if alias == "" {
-		return false
-	}
-	matched, _ := regexp.MatchString(`^[a-z0-9-]+$`, alias)
-	return matched
-}
diff --git a/tools/mcp-server/internal/tools/load_test.go b/tools/mcp-server/internal/tools/load_test.go
deleted file mode 100644
index f9df5eb53e..0000000000
--- a/tools/mcp-server/internal/tools/load_test.go
+++ /dev/null
@@ -1,287 +0,0 @@
-package tools
-
-import (
-	"testing"
-
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-	"github.com/spf13/afero"
-)
-
-func TestGenerateAliasFromPath(t *testing.T) {
-	tests := []struct {
-		name     string
-		filePath string
-		want     string
-		wantErr  bool
-	}{
-		{
-			name:     "simple yaml file",
-			filePath: "/path/to/api.yaml",
-			want:     "api",
-			wantErr:  false,
-		},
-		{
-			name:     "simple json file",
-			filePath: "/path/to/openapi.json",
-			want:     "openapi",
-			wantErr:  false,
-		},
-		{
-			name:     "file with hyphen",
-			filePath: "petstore-api.yaml",
-			want:     "petstore-api",
-			wantErr:  false,
-		},
-		{
-			name:     "file with spaces",
-			filePath: "Pet Store API.yaml",
-			want:     "pet-store-api",
-			wantErr:  false,
-		},
-		{
-			name:     "file with uppercase",
-			filePath: "PetStoreAPI.yaml",
-			want:     "petstoreapi",
-			wantErr:  false,
-		},
-		{
-			name:     "file with mixed case and spaces",
-			filePath: "MongoDB Atlas API.yaml",
-			want:     "mongodb-atlas-api",
-			wantErr:  false,
-		},
-		{
-			name:     "file with underscores",
-			filePath: "my_awesome_api.yaml",
-			want:     "my-awesome-api",
-			wantErr:  false,
-		},
-		{
-			name:     "file with numbers",
-			filePath: "api-v2.yaml",
-			want:     "api-v2",
-			wantErr:  false,
-		},
-		{
-			name:     "file with special characters",
-			filePath: "api@#$%spec.yaml",
-			want:     "api-spec",
-			wantErr:  false,
-		},
-		{
-			name:     "file with multiple consecutive special chars",
-			filePath: "api___---spec.yaml",
-			want:     "api-spec",
-			wantErr:  false,
-		},
-		{
-			name:     "file with leading/trailing hyphens",
-			filePath: "-api-.yaml",
-			want:     "api",
-			wantErr:  false,
-		},
-		{
-			name:     "complex real-world example",
-			filePath: "/Users/me/projects/MongoDB Atlas Admin API v2.0.yaml",
-			want:     "mongodb-atlas-admin-api-v2-0",
-			wantErr:  false,
-		},
-		{
-			name:     "file with dots in name",
-			filePath: "api.spec.v1.yaml",
-			want:     "api-spec-v1",
-			wantErr:  false,
-		},
-		{
-			name:     "only special chars (should error)",
-			filePath: "@#$%.yaml",
-			want:     "",
-			wantErr:  true,
-		},
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.name, func(t *testing.T) {
-			got, err := generateAliasFromPath(tt.filePath)
-			if (err != nil) != tt.wantErr {
-				t.Errorf("generateAliasFromPath() error = %v, wantErr %v", err, tt.wantErr)
-				return
-			}
-			if got != tt.want {
-				t.Errorf("generateAliasFromPath() = %v, want %v", got, tt.want)
-			}
-		})
-	}
-}
-
-func TestIsValidAlias(t *testing.T) {
-	tests := []struct {
-		name  string
-		alias string
-		want  bool
-	}{
-		{"valid simple", "api", true},
-		{"valid with hyphen", "my-api", true},
-		{"valid with numbers", "api-v2", true},
-		{"valid complex", "mongodb-atlas-api-v2", true},
-		{"invalid uppercase", "MyAPI", false},
-		{"invalid underscore", "my_api", false},
-		{"invalid space", "my api", false},
-		{"invalid special char", "api@spec", false},
-		{"invalid empty", "", false},
-		{"invalid just hyphen", "-", true},           // hyphen is allowed
-		{"invalid starts with number", "2api", true}, // numbers are allowed
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.name, func(t *testing.T) {
-			if got := isValidAlias(tt.alias); got != tt.want {
-				t.Errorf("isValidAlias(%q) = %v, want %v", tt.alias, got, tt.want)
-			}
-		})
-	}
-}
-
-func TestHandleLoad_AutoGeneratedAlias(t *testing.T) {
-	reg := registry.New()
-
-	// Create a test YAML file
-	testFile := createTestOpenAPIFile(t, "test-api.yaml")
-	defer cleanupTestFile(t, testFile)
-
-	params := LoadParams{
-		FilePath: testFile,
-		// No alias - should auto-generate
-	}
-
-	result, err := handleLoad(reg, params)
-	if err != nil {
-		t.Fatalf("handleLoad() failed: %v", err)
-	}
-
-	if !result.Success {
-		t.Error("result.Success = false, want true")
-	}
-
-	if result.Alias != "test-api" {
-		t.Errorf("result.Alias = %q, want %q", result.Alias, "test-api")
-	}
-
-	// Verify it's in the registry
-	entry, err := reg.GetByAlias("test-api")
-	if err != nil {
-		t.Fatalf("GetByAlias() failed: %v", err)
-	}
-
-	if entry.FilePath != testFile {
-		t.Errorf("entry.FilePath = %q, want %q", entry.FilePath, testFile)
-	}
-}
-
-func TestHandleLoad_CustomAlias(t *testing.T) {
-	reg := registry.New()
-
-	testFile := createTestOpenAPIFile(t, "api.yaml")
-	defer cleanupTestFile(t, testFile)
-
-	params := LoadParams{
-		FilePath: testFile,
-		Alias:    "my-custom-alias",
-	}
-
-	result, err := handleLoad(reg, params)
-	if err != nil {
-		t.Fatalf("handleLoad() failed: %v", err)
-	}
-
-	if result.Alias != "my-custom-alias" {
-		t.Errorf("result.Alias = %q, want %q", result.Alias, "my-custom-alias")
-	}
-
-	// Verify it's in the registry with custom alias
-	_, err = reg.GetByAlias("my-custom-alias")
-	if err != nil {
-		t.Errorf("GetByAlias() failed: %v", err)
-	}
-}
-
-func TestHandleLoad_InvalidAlias(t *testing.T) {
-	reg := registry.New()
-
-	testFile := createTestOpenAPIFile(t, "api.yaml")
-	defer cleanupTestFile(t, testFile)
-
-	params := LoadParams{
-		FilePath: testFile,
-		Alias:    "Invalid_Alias!", // Contains invalid characters
-	}
-
-	_, err := handleLoad(reg, params)
-	if err == nil {
-		t.Fatal("handleLoad() should fail with invalid alias")
-	}
-}
-
-func TestHandleLoad_Collision(t *testing.T) {
-	reg := registry.New()
-
-	// Load first file
-	testFile1 := createTestOpenAPIFile(t, "api1.yaml")
-	defer cleanupTestFile(t, testFile1)
-
-	params1 := LoadParams{
-		FilePath: testFile1,
-		Alias:    "shared-alias",
-	}
-
-	_, err := handleLoad(reg, params1)
-	if err != nil {
-		t.Fatalf("First load failed: %v", err)
-	}
-
-	// Try to load different file with same alias
-	testFile2 := createTestOpenAPIFile(t, "api2.yaml")
-	defer cleanupTestFile(t, testFile2)
-
-	params2 := LoadParams{
-		FilePath: testFile2,
-		Alias:    "shared-alias",
-	}
-
-	_, err = handleLoad(reg, params2)
-	if err == nil {
-		t.Fatal("handleLoad() should fail with collision error")
-	}
-}
-
-// Helper: creates a temporary OpenAPI file for testing.
-func createTestOpenAPIFile(t *testing.T, filename string) string {
-	t.Helper()
-
-	content := `openapi: 3.0.0
-info:
-  title: Test API
-  version: 1.0.0
-paths:
-  /test:
-    get:
-      summary: Test endpoint
-      responses:
-        '200':
-          description: Success
-`
-
-	tmpFile := t.TempDir() + "/" + filename
-	fs := afero.NewOsFs()
-	err := afero.WriteFile(fs, tmpFile, []byte(content), 0o600)
-	if err != nil {
-		t.Fatalf("Failed to create test file: %v", err)
-	}
-
-	return tmpFile
-}
-
-func cleanupTestFile(t *testing.T, _ string) {
-	t.Helper()
-	// t.TempDir() handles cleanup automatically
-}
diff --git a/tools/mcp-server/internal/tools/search.go b/tools/mcp-server/internal/tools/search.go
deleted file mode 100644
index 061c753944..0000000000
--- a/tools/mcp-server/internal/tools/search.go
+++ /dev/null
@@ -1,487 +0,0 @@
-package tools
-
-import (
-	"fmt"
-	"regexp"
-	"strings"
-
-	"github.com/getkin/kin-openapi/openapi3"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-)
-
-// SearchParams are the parameters for the search tool.
-type SearchParams struct {
-	Alias         string   `json:"alias" jsonschema:"Alias of the spec to search"`
-	Pattern       string   `json:"pattern" jsonschema:"Regular expression pattern to search for"`
-	SearchIn      []string `json:"searchIn,omitempty" jsonschema:"Optional: categories to search"`
-	CaseSensitive bool     `json:"caseSensitive,omitempty" jsonschema:"Optional: case-sensitive search"`
-	Limit         int      `json:"limit,omitempty" jsonschema:"Optional: max results per category"`
-}
-
-// SearchResult is the result of a search operation.
-type SearchResult struct {
-	Success    bool               `json:"success"`
-	Alias      string             `json:"alias"`
-	Pattern    string             `json:"pattern"`
-	Operations []OperationMatch   `json:"operations"`
-	Schemas    []SchemaMatch      `json:"schemas"`
-	Parameters []ParameterMatch   `json:"parameters"`
-	Responses  []ResponseMatch    `json:"responses"`
-	Tags       []TagMatch         `json:"tags"`
-	Paths      []PathMatch        `json:"paths"`
-	Pagination PaginationMetadata `json:"pagination"`
-}
-
-// PaginationMetadata contains pagination information.
-type PaginationMetadata struct {
-	Limit           int             `json:"limit"`
-	TotalMatches    int             `json:"totalMatches"`
-	CategoryCounts  map[string]int  `json:"categoryCounts"`
-	CategoryHasMore map[string]bool `json:"categoryHasMore,omitempty"`
-}
-
-// OperationMatch represents a matched operation.
-type OperationMatch struct {
-	Path        string   `json:"path"`
-	Method      string   `json:"method"`
-	OperationID string   `json:"operationId,omitempty"`
-	Summary     string   `json:"summary,omitempty"`
-	Description string   `json:"description,omitempty"`
-	Tags        []string `json:"tags,omitempty"`
-	MatchedIn   []string `json:"matchedIn"`
-	MatchedText string   `json:"matchedText"`
-}
-
-// SchemaMatch represents a matched schema.
-type SchemaMatch struct {
-	Name              string   `json:"name"`
-	Description       string   `json:"description,omitempty"`
-	MatchedIn         []string `json:"matchedIn"`
-	MatchedText       string   `json:"matchedText"`
-	MatchedProperties []string `json:"matchedProperties,omitempty"`
-}
-
-// ParameterMatch represents a matched parameter.
-type ParameterMatch struct {
-	Name        string   `json:"name"`
-	In          string   `json:"in,omitempty"`
-	Description string   `json:"description,omitempty"`
-	MatchedIn   []string `json:"matchedIn"`
-	MatchedText string   `json:"matchedText"`
-}
-
-// ResponseMatch represents a matched response.
-type ResponseMatch struct {
-	Name        string   `json:"name"`
-	Description string   `json:"description,omitempty"`
-	MatchedIn   []string `json:"matchedIn"`
-	MatchedText string   `json:"matchedText"`
-}
-
-// TagMatch represents a matched tag.
-type TagMatch struct {
-	Name        string   `json:"name"`
-	Description string   `json:"description,omitempty"`
-	MatchedIn   []string `json:"matchedIn"`
-	MatchedText string   `json:"matchedText"`
-}
-
-// PathMatch represents a matched path.
-type PathMatch struct {
-	Path        string   `json:"path"`
-	MatchedIn   []string `json:"matchedIn"`
-	MatchedText string   `json:"matchedText"`
-}
-
-// validSearchCategories defines the valid categories for searchIn parameter.
-var validSearchCategories = map[string]bool{
-	"operations": true,
-	"schemas":    true,
-	"parameters": true,
-	"responses":  true,
-	"tags":       true,
-	"paths":      true,
-}
-
-// Helper methods for SearchResult
-
-// totalCount returns the total number of matches across all categories.
-func (r *SearchResult) totalCount() int {
-	return len(r.Operations) + len(r.Schemas) + len(r.Parameters) +
-		len(r.Responses) + len(r.Tags) + len(r.Paths)
-}
-
-// categoryCounts returns a map of category names to their match counts.
-func (r *SearchResult) categoryCounts() map[string]int {
-	return map[string]int{
-		"operations": len(r.Operations),
-		"schemas":    len(r.Schemas),
-		"parameters": len(r.Parameters),
-		"responses":  len(r.Responses),
-		"tags":       len(r.Tags),
-		"paths":      len(r.Paths),
-	}
-}
-
-// Helper functions for matching
-
-// checkAndRecordMatch checks if a value matches the regex and records the match.
-func checkAndRecordMatch(re *regexp.Regexp, fieldName, value string, matchedIn, matchedTexts *[]string) {
-	if value != "" && re.MatchString(value) {
-		*matchedIn = append(*matchedIn, fieldName)
-		*matchedTexts = append(*matchedTexts, re.FindString(value))
-	}
-}
-
-// handleSearch searches for matches in an OpenAPI spec.
-func handleSearch(reg *registry.Registry, params SearchParams) (SearchResult, error) {
-	// Set defaults
-	if params.Limit == 0 {
-		params.Limit = 100
-	}
-
-	// Validate searchIn categories
-	if len(params.SearchIn) > 0 {
-		var invalidCategories []string
-		for _, category := range params.SearchIn {
-			if !validSearchCategories[category] {
-				invalidCategories = append(invalidCategories, category)
-			}
-		}
-		if len(invalidCategories) > 0 {
-			return SearchResult{Success: false}, fmt.Errorf(
-				"invalid searchIn categories: %v. Valid categories are: operations, schemas, parameters, responses, tags, paths",
-				invalidCategories,
-			)
-		}
-	}
-
-	// Validate and compile regex
-	var re *regexp.Regexp
-	var err error
-	if params.CaseSensitive {
-		re, err = regexp.Compile(params.Pattern)
-	} else {
-		re, err = regexp.Compile("(?i)" + params.Pattern)
-	}
-	if err != nil {
-		return SearchResult{Success: false}, fmt.Errorf("invalid regex pattern: %w", err)
-	}
-
-	// Get spec from registry
-	entry, err := reg.GetByAlias(params.Alias)
-	if err != nil {
-		return SearchResult{Success: false}, err
-	}
-
-	// Determine what to search
-	searchIn := params.SearchIn
-	if len(searchIn) == 0 {
-		searchIn = []string{"operations", "schemas", "parameters", "responses", "tags", "paths"}
-	}
-
-	// Perform search
-	result := SearchResult{
-		Success: true,
-		Alias:   params.Alias,
-		Pattern: params.Pattern,
-	}
-
-	for _, category := range searchIn {
-		switch category {
-		case "operations":
-			result.Operations = searchOperations(entry.Spec, re)
-		case "schemas":
-			result.Schemas = searchSchemas(entry.Spec, re)
-		case "parameters":
-			result.Parameters = searchParameters(entry.Spec, re)
-		case "responses":
-			result.Responses = searchResponses(entry.Spec, re)
-		case "tags":
-			result.Tags = searchTags(entry.Spec, re)
-		case "paths":
-			result.Paths = searchPaths(entry.Spec, re)
-		}
-	}
-
-	// Apply per-category pagination
-	applyPagination(&result, params.Limit)
-
-	return result, nil
-}
-
-// searchOperations searches for matches in operations.
-func searchOperations(spec *openapi3.T, re *regexp.Regexp) []OperationMatch {
-	var matches []OperationMatch
-
-	if spec.Paths == nil {
-		return matches
-	}
-
-	for path, pathItem := range spec.Paths.Map() {
-		for method, operation := range pathItem.Operations() {
-			match := OperationMatch{
-				Path:        path,
-				Method:      strings.ToUpper(method),
-				OperationID: operation.OperationID,
-				Summary:     operation.Summary,
-				Description: operation.Description,
-				Tags:        operation.Tags,
-			}
-
-			var matchedIn []string
-			var matchedTexts []string
-
-			// Search in various fields
-			checkAndRecordMatch(re, "operationId", operation.OperationID, &matchedIn, &matchedTexts)
-			checkAndRecordMatch(re, "summary", operation.Summary, &matchedIn, &matchedTexts)
-			checkAndRecordMatch(re, "description", operation.Description, &matchedIn, &matchedTexts)
-
-			// Search in tags
-			for _, tag := range operation.Tags {
-				if re.MatchString(tag) {
-					matchedIn = append(matchedIn, "tags")
-					matchedTexts = append(matchedTexts, re.FindString(tag))
-					break
-				}
-			}
-
-			if len(matchedIn) > 0 {
-				match.MatchedIn = matchedIn
-				match.MatchedText = strings.Join(matchedTexts, ", ")
-				matches = append(matches, match)
-			}
-		}
-	}
-
-	return matches
-}
-
-// searchSchemas searches for matches in component schemas.
-func searchSchemas(spec *openapi3.T, re *regexp.Regexp) []SchemaMatch {
-	var matches []SchemaMatch
-
-	if spec.Components == nil || spec.Components.Schemas == nil {
-		return matches
-	}
-
-	for name, schemaRef := range spec.Components.Schemas {
-		if schemaRef == nil || schemaRef.Value == nil {
-			continue
-		}
-
-		schema := schemaRef.Value
-		match := SchemaMatch{
-			Name:        name,
-			Description: schema.Description,
-		}
-
-		var matchedIn []string
-		var matchedTexts []string
-		var matchedProps []string
-
-		// Search in schema name and description
-		checkAndRecordMatch(re, "name", name, &matchedIn, &matchedTexts)
-		checkAndRecordMatch(re, "description", schema.Description, &matchedIn, &matchedTexts)
-
-		// Search in property names
-		if schema.Properties != nil {
-			for propName := range schema.Properties {
-				if re.MatchString(propName) {
-					matchedIn = append(matchedIn, "properties")
-					matchedProps = append(matchedProps, propName)
-					matchedTexts = append(matchedTexts, re.FindString(propName))
-				}
-			}
-		}
-
-		if len(matchedIn) > 0 {
-			match.MatchedIn = matchedIn
-			match.MatchedText = strings.Join(matchedTexts, ", ")
-			if len(matchedProps) > 0 {
-				match.MatchedProperties = matchedProps
-			}
-			matches = append(matches, match)
-		}
-	}
-
-	return matches
-}
-
-// searchParameters searches for matches in component parameters.
-func searchParameters(spec *openapi3.T, re *regexp.Regexp) []ParameterMatch {
-	var matches []ParameterMatch
-
-	if spec.Components == nil || spec.Components.Parameters == nil {
-		return matches
-	}
-
-	for name, paramRef := range spec.Components.Parameters {
-		if paramRef == nil || paramRef.Value == nil {
-			continue
-		}
-
-		param := paramRef.Value
-		match := ParameterMatch{
-			Name:        param.Name,
-			In:          param.In,
-			Description: param.Description,
-		}
-
-		var matchedIn []string
-		var matchedTexts []string
-
-		// Search in parameter name (check both component name and param.Name)
-		if re.MatchString(name) || re.MatchString(param.Name) {
-			matchedIn = append(matchedIn, "name")
-			matchedTexts = append(matchedTexts, re.FindString(param.Name))
-		}
-
-		// Search in description
-		checkAndRecordMatch(re, "description", param.Description, &matchedIn, &matchedTexts)
-
-		if len(matchedIn) > 0 {
-			match.MatchedIn = matchedIn
-			match.MatchedText = strings.Join(matchedTexts, ", ")
-			matches = append(matches, match)
-		}
-	}
-
-	return matches
-}
-
-// searchResponses searches for matches in component responses.
-func searchResponses(spec *openapi3.T, re *regexp.Regexp) []ResponseMatch {
-	var matches []ResponseMatch
-
-	if spec.Components == nil || spec.Components.Responses == nil {
-		return matches
-	}
-
-	for name, respRef := range spec.Components.Responses {
-		if respRef == nil || respRef.Value == nil {
-			continue
-		}
-
-		resp := respRef.Value
-		description := ""
-		if resp.Description != nil {
-			description = *resp.Description
-		}
-
-		match := ResponseMatch{
-			Name:        name,
-			Description: description,
-		}
-
-		var matchedIn []string
-		var matchedTexts []string
-
-		// Search in response name and description
-		checkAndRecordMatch(re, "name", name, &matchedIn, &matchedTexts)
-		checkAndRecordMatch(re, "description", description, &matchedIn, &matchedTexts)
-
-		if len(matchedIn) > 0 {
-			match.MatchedIn = matchedIn
-			match.MatchedText = strings.Join(matchedTexts, ", ")
-			matches = append(matches, match)
-		}
-	}
-
-	return matches
-}
-
-// searchTags searches for matches in tags.
-func searchTags(spec *openapi3.T, re *regexp.Regexp) []TagMatch {
-	var matches []TagMatch
-
-	if spec.Tags == nil {
-		return matches
-	}
-
-	for _, tag := range spec.Tags {
-		match := TagMatch{
-			Name:        tag.Name,
-			Description: tag.Description,
-		}
-
-		var matchedIn []string
-		var matchedTexts []string
-
-		// Search in tag name and description
-		checkAndRecordMatch(re, "name", tag.Name, &matchedIn, &matchedTexts)
-		checkAndRecordMatch(re, "description", tag.Description, &matchedIn, &matchedTexts)
-
-		if len(matchedIn) > 0 {
-			match.MatchedIn = matchedIn
-			match.MatchedText = strings.Join(matchedTexts, ", ")
-			matches = append(matches, match)
-		}
-	}
-
-	return matches
-}
-
-// searchPaths searches for matches in path patterns.
-func searchPaths(spec *openapi3.T, re *regexp.Regexp) []PathMatch {
-	var matches []PathMatch
-
-	if spec.Paths == nil {
-		return matches
-	}
-
-	for path := range spec.Paths.Map() {
-		if re.MatchString(path) {
-			match := PathMatch{
-				Path:        path,
-				MatchedIn:   []string{"path"},
-				MatchedText: re.FindString(path),
-			}
-			matches = append(matches, match)
-		}
-	}
-
-	return matches
-}
-
-// applyPagination applies per-category limit to search results.
-func applyPagination(result *SearchResult, limit int) {
-	// Store counts before truncation
-	totalMatches := result.totalCount()
-	categoryCounts := result.categoryCounts()
-	categoryHasMore := make(map[string]bool)
-
-	// Apply limit to each category
-	if len(result.Operations) > limit {
-		result.Operations = result.Operations[:limit]
-		categoryHasMore["operations"] = true
-	}
-	if len(result.Schemas) > limit {
-		result.Schemas = result.Schemas[:limit]
-		categoryHasMore["schemas"] = true
-	}
-	if len(result.Parameters) > limit {
-		result.Parameters = result.Parameters[:limit]
-		categoryHasMore["parameters"] = true
-	}
-	if len(result.Responses) > limit {
-		result.Responses = result.Responses[:limit]
-		categoryHasMore["responses"] = true
-	}
-	if len(result.Tags) > limit {
-		result.Tags = result.Tags[:limit]
-		categoryHasMore["tags"] = true
-	}
-	if len(result.Paths) > limit {
-		result.Paths = result.Paths[:limit]
-		categoryHasMore["paths"] = true
-	}
-
-	// Build pagination metadata
-	result.Pagination = PaginationMetadata{
-		Limit:           limit,
-		TotalMatches:    totalMatches,
-		CategoryCounts:  categoryCounts,
-		CategoryHasMore: categoryHasMore,
-	}
-}
diff --git a/tools/mcp-server/internal/tools/search_test.go b/tools/mcp-server/internal/tools/search_test.go
deleted file mode 100644
index 29a37450ce..0000000000
--- a/tools/mcp-server/internal/tools/search_test.go
+++ /dev/null
@@ -1,497 +0,0 @@
-package tools
-
-import (
-	"strings"
-	"testing"
-
-	"github.com/getkin/kin-openapi/openapi3"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-)
-
-// setupTestRegistry creates a registry with the test spec loaded.
-func setupTestRegistry(t *testing.T) *registry.Registry {
-	t.Helper()
-	reg := registry.New()
-	spec := createTestSpec()
-	err := reg.Add("test-api", "/test/api.yaml", spec, nil)
-	if err != nil {
-		t.Fatalf("Failed to add spec: %v", err)
-	}
-	return reg
-}
-
-// ExpectedResults defines expected search results for table-driven tests.
-type ExpectedResults struct {
-	Operations []string
-	Schemas    []string
-	Parameters []string
-	Paths      []string
-	Tags       []string
-	TotalCount int
-}
-
-// assertSearchResults verifies all aspects of search results.
-func assertSearchResults(t *testing.T, result *SearchResult, expected *ExpectedResults) {
-	t.Helper()
-	assertExactOperationIDs(t, result.Operations, expected.Operations)
-	assertExactSchemaNames(t, result.Schemas, expected.Schemas)
-	assertExactParameterNames(t, result.Parameters, expected.Parameters)
-	assertExactPaths(t, result.Paths, expected.Paths)
-
-	if len(expected.Tags) > 0 {
-		if len(result.Tags) != len(expected.Tags) {
-			t.Errorf("Expected %d tags, got %d", len(expected.Tags), len(result.Tags))
-		}
-		for i, expectedTag := range expected.Tags {
-			if i < len(result.Tags) && result.Tags[i].Name != expectedTag {
-				t.Errorf("Expected tag '%s', got '%s'", expectedTag, result.Tags[i].Name)
-			}
-		}
-	}
-
-	if expected.TotalCount > 0 && result.Pagination.TotalMatches != expected.TotalCount {
-		t.Errorf("Expected totalMatches=%d, got %d", expected.TotalCount, result.Pagination.TotalMatches)
-	}
-}
-
-// assertExactOperationIDs verifies the exact set of operation IDs.
-func assertExactOperationIDs(t *testing.T, operations []OperationMatch, expectedIDs []string) {
-	t.Helper()
-	if len(operations) != len(expectedIDs) {
-		t.Errorf("Expected %d operations, got %d", len(expectedIDs), len(operations))
-		t.Logf("Got: %v", getOperationIDs(operations))
-		t.Logf("Expected: %v", expectedIDs)
-	}
-	found := make(map[string]bool)
-	for i := range operations {
-		found[operations[i].OperationID] = true
-	}
-	for _, expectedID := range expectedIDs {
-		if !found[expectedID] {
-			t.Errorf("Expected operation ID '%s' not found", expectedID)
-		}
-	}
-	expectedSet := make(map[string]bool)
-	for _, id := range expectedIDs {
-		expectedSet[id] = true
-	}
-	for i := range operations {
-		if !expectedSet[operations[i].OperationID] {
-			t.Errorf("Unexpected operation ID '%s' found", operations[i].OperationID)
-		}
-	}
-}
-
-// assertExactSchemaNames verifies the exact set of schema names.
-func assertExactSchemaNames(t *testing.T, schemas []SchemaMatch, expectedNames []string) {
-	t.Helper()
-	if len(schemas) != len(expectedNames) {
-		t.Errorf("Expected %d schemas, got %d", len(expectedNames), len(schemas))
-		t.Logf("Got: %v", getSchemaNames(schemas))
-		t.Logf("Expected: %v", expectedNames)
-	}
-	found := make(map[string]bool)
-	for _, schema := range schemas {
-		found[schema.Name] = true
-	}
-	for _, expectedName := range expectedNames {
-		if !found[expectedName] {
-			t.Errorf("Expected schema '%s' not found", expectedName)
-		}
-	}
-}
-
-// assertExactParameterNames verifies the exact set of parameter names.
-func assertExactParameterNames(t *testing.T, parameters []ParameterMatch, expectedNames []string) {
-	t.Helper()
-	if len(parameters) != len(expectedNames) {
-		t.Errorf("Expected %d parameters, got %d", len(expectedNames), len(parameters))
-		t.Logf("Got: %v", getParameterNames(parameters))
-		t.Logf("Expected: %v", expectedNames)
-	}
-	found := make(map[string]bool)
-	for _, param := range parameters {
-		found[param.Name] = true
-	}
-	for _, expectedName := range expectedNames {
-		if !found[expectedName] {
-			t.Errorf("Expected parameter '%s' not found", expectedName)
-		}
-	}
-}
-
-// assertExactPaths verifies the exact set of paths.
-func assertExactPaths(t *testing.T, paths []PathMatch, expectedPaths []string) {
-	t.Helper()
-	if len(paths) != len(expectedPaths) {
-		t.Errorf("Expected %d paths, got %d", len(expectedPaths), len(paths))
-		t.Logf("Got: %v", getPaths(paths))
-		t.Logf("Expected: %v", expectedPaths)
-	}
-	found := make(map[string]bool)
-	for _, path := range paths {
-		found[path.Path] = true
-	}
-	for _, expectedPath := range expectedPaths {
-		if !found[expectedPath] {
-			t.Errorf("Expected path '%s' not found", expectedPath)
-		}
-	}
-}
-
-// Helper functions to extract names/IDs for logging.
-func getOperationIDs(operations []OperationMatch) []string {
-	ids := make([]string, len(operations))
-	for i := range operations {
-		ids[i] = operations[i].OperationID
-	}
-	return ids
-}
-
-func getSchemaNames(schemas []SchemaMatch) []string {
-	names := make([]string, len(schemas))
-	for i, schema := range schemas {
-		names[i] = schema.Name
-	}
-	return names
-}
-
-func getParameterNames(parameters []ParameterMatch) []string {
-	names := make([]string, len(parameters))
-	for i, param := range parameters {
-		names[i] = param.Name
-	}
-	return names
-}
-
-func getPaths(paths []PathMatch) []string {
-	pathStrs := make([]string, len(paths))
-	for i, path := range paths {
-		pathStrs[i] = path.Path
-	}
-	return pathStrs
-}
-
-func TestHandleSearch_Patterns(t *testing.T) {
-	reg := setupTestRegistry(t)
-
-	tests := []struct {
-		name     string
-		params   SearchParams
-		expected ExpectedResults
-		checkFn  func(*testing.T, SearchResult) // Optional additional checks
-	}{
-		{
-			name: "pattern: user",
-			params: SearchParams{
-				Alias:   "test-api",
-				Pattern: "user",
-			},
-			expected: ExpectedResults{
-				Operations: []string{"getUsers", "createUser", "getUser"},
-				Schemas:    []string{"User"},
-				Parameters: []string{"userId"},
-				Paths:      []string{"/users", "/users/{userId}"},
-				Tags:       []string{"Users"},
-				TotalCount: 8,
-			},
-			checkFn: func(t *testing.T, result SearchResult) {
-				t.Helper()
-				// Verify matchedIn is populated
-				for i := range result.Operations {
-					if len(result.Operations[i].MatchedIn) == 0 {
-						t.Errorf("Expected matchedIn populated for %s", result.Operations[i].OperationID)
-					}
-				}
-			},
-		},
-		{
-			name: "pattern: cluster",
-			params: SearchParams{
-				Alias:   "test-api",
-				Pattern: "cluster",
-			},
-			expected: ExpectedResults{
-				Operations: []string{"createCluster", "listClusters", "getCluster"},
-				Schemas:    []string{"Cluster"},
-				Parameters: []string{"clusterId"},
-				Paths:      []string{"/clusters", "/clusters/{clusterId}"},
-				Tags:       []string{"Clusters"},
-				TotalCount: 8,
-			},
-			checkFn: func(t *testing.T, result SearchResult) {
-				t.Helper()
-				// Verify Cluster schema matched by both name and property
-				if len(result.Schemas) > 0 {
-					schema := result.Schemas[0]
-					hasName := false
-					hasProps := false
-					for _, field := range schema.MatchedIn {
-						if field == "name" {
-							hasName = true
-						}
-						if field == "properties" {
-							hasProps = true
-						}
-					}
-					if !hasName || !hasProps {
-						t.Errorf("Expected Cluster to match by name and properties, got: %v", schema.MatchedIn)
-					}
-				}
-			},
-		},
-		{
-			name: "case-insensitive: USER",
-			params: SearchParams{
-				Alias:   "test-api",
-				Pattern: "USER",
-			},
-			expected: ExpectedResults{
-				Operations: []string{"getUsers", "createUser", "getUser"},
-				Schemas:    []string{"User"},
-				Parameters: []string{"userId"},
-				Paths:      []string{"/users", "/users/{userId}"},
-				Tags:       []string{"Users"},
-				TotalCount: 8,
-			},
-		},
-		{
-			name: "case-sensitive: USER (no match)",
-			params: SearchParams{
-				Alias:         "test-api",
-				Pattern:       "USER",
-				CaseSensitive: true,
-			},
-			expected: ExpectedResults{
-				Operations: []string{},
-				Schemas:    []string{},
-				Parameters: []string{},
-				Paths:      []string{},
-				Tags:       []string{},
-				TotalCount: 0,
-			},
-		},
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.name, func(t *testing.T) {
-			result, err := handleSearch(reg, tt.params)
-			if err != nil {
-				t.Fatalf("handleSearch() failed: %v", err)
-			}
-
-			if !result.Success {
-				t.Error("Expected success=true")
-			}
-
-			assertSearchResults(t, &result, &tt.expected)
-
-			if tt.checkFn != nil {
-				tt.checkFn(t, result)
-			}
-		})
-	}
-}
-
-func TestHandleSearch_InvalidRegex(t *testing.T) {
-	reg := setupTestRegistry(t)
-
-	params := SearchParams{
-		Alias:   "test-api",
-		Pattern: "[invalid(regex",
-	}
-
-	_, err := handleSearch(reg, params)
-	if err == nil {
-		t.Error("Expected error for invalid regex")
-	}
-
-	if !strings.Contains(err.Error(), "invalid regex") && !strings.Contains(err.Error(), "error parsing regexp") {
-		t.Errorf("Expected regex error message, got: %v", err)
-	}
-}
-
-func TestHandleSearch_Pagination(t *testing.T) {
-	reg := registry.New()
-
-	spec := &openapi3.T{
-		OpenAPI: "3.0.0",
-		Info: &openapi3.Info{
-			Title:   "Test API",
-			Version: "1.0.0",
-		},
-		Paths: &openapi3.Paths{},
-	}
-
-	// Add multiple operations (15 to test limit of 5)
-	for i := 0; i < 15; i++ {
-		path := "/endpoint" + string(rune('a'+i))
-		spec.Paths.Set(path, &openapi3.PathItem{
-			Get: &openapi3.Operation{
-				OperationID: "getEndpoint" + string(rune('A'+i)),
-				Summary:     "Test endpoint " + string(rune('A'+i)),
-			},
-		})
-	}
-
-	err := reg.Add("test-api", "/test/api.yaml", spec, nil)
-	if err != nil {
-		t.Fatalf("Failed to add spec: %v", err)
-	}
-
-	// Test with limit=5 per category
-	params := SearchParams{
-		Alias:   "test-api",
-		Pattern: "endpoint",
-		Limit:   5,
-	}
-
-	result, err := handleSearch(reg, params)
-	if err != nil {
-		t.Fatalf("handleSearch() failed: %v", err)
-	}
-
-	// We should get 5 operations and 5 paths (limited)
-	if len(result.Operations) != 5 {
-		t.Errorf("Expected 5 operations (limited), got %d", len(result.Operations))
-	}
-
-	if len(result.Paths) != 5 {
-		t.Errorf("Expected 5 paths (limited), got %d", len(result.Paths))
-	}
-
-	// Total matches should be 30 (15 paths + 15 operations)
-	if result.Pagination.TotalMatches != 30 {
-		t.Errorf("Expected totalMatches=30, got %d", result.Pagination.TotalMatches)
-	}
-
-	// Verify pagination metadata is exact
-	if result.Pagination.Limit != 5 {
-		t.Errorf("Expected limit=5, got %d", result.Pagination.Limit)
-	}
-
-	if result.Pagination.TotalMatches != 30 {
-		t.Errorf("Expected totalMatches=30 (15 paths + 15 operations), got %d", result.Pagination.TotalMatches)
-	}
-
-	// Verify category counts (before truncation)
-	if result.Pagination.CategoryCounts["operations"] != 15 {
-		t.Errorf("Expected categoryCounts['operations']=15, got %d", result.Pagination.CategoryCounts["operations"])
-	}
-
-	if result.Pagination.CategoryCounts["paths"] != 15 {
-		t.Errorf("Expected categoryCounts['paths']=15, got %d", result.Pagination.CategoryCounts["paths"])
-	}
-
-	// Should indicate more available for both categories
-	if !result.Pagination.CategoryHasMore["operations"] {
-		t.Error("Expected categoryHasMore['operations']=true (15 total, limit 5)")
-	}
-
-	if !result.Pagination.CategoryHasMore["paths"] {
-		t.Error("Expected categoryHasMore['paths']=true (15 total, limit 5)")
-	}
-
-	// Other categories should not be in categoryHasMore
-	if result.Pagination.CategoryHasMore["schemas"] {
-		t.Error("Expected categoryHasMore['schemas'] to be false (0 matches)")
-	}
-}
-
-func TestHandleSearch_SearchInFilter(t *testing.T) {
-	reg := setupTestRegistry(t)
-
-	tests := []struct {
-		name     string
-		searchIn []string
-		expected ExpectedResults
-	}{
-		{
-			name:     "only schemas",
-			searchIn: []string{"schemas"},
-			expected: ExpectedResults{
-				Operations: []string{},
-				Schemas:    []string{"User"},
-				Parameters: []string{},
-				Paths:      []string{},
-				Tags:       []string{},
-			},
-		},
-		{
-			name:     "only operations",
-			searchIn: []string{"operations"},
-			expected: ExpectedResults{
-				Operations: []string{"getUsers", "createUser", "getUser"},
-				Schemas:    []string{},
-				Parameters: []string{},
-				Paths:      []string{},
-				Tags:       []string{},
-			},
-		},
-		{
-			name:     "operations and schemas",
-			searchIn: []string{"operations", "schemas"},
-			expected: ExpectedResults{
-				Operations: []string{"getUsers", "createUser", "getUser"},
-				Schemas:    []string{"User"},
-				Parameters: []string{},
-				Paths:      []string{},
-				Tags:       []string{},
-			},
-		},
-		{
-			name:     "empty searchIn (all categories)",
-			searchIn: []string{},
-			expected: ExpectedResults{
-				Operations: []string{"getUsers", "createUser", "getUser"},
-				Schemas:    []string{"User"},
-				Parameters: []string{"userId"},
-				Paths:      []string{"/users", "/users/{userId}"},
-				Tags:       []string{"Users"},
-				TotalCount: 8,
-			},
-		},
-	}
-
-	for _, tt := range tests {
-		t.Run(tt.name, func(t *testing.T) {
-			params := SearchParams{
-				Alias:    "test-api",
-				Pattern:  "user",
-				SearchIn: tt.searchIn,
-			}
-
-			result, err := handleSearch(reg, params)
-			if err != nil {
-				t.Fatalf("handleSearch() failed: %v", err)
-			}
-
-			assertSearchResults(t, &result, &tt.expected)
-		})
-	}
-}
-
-func TestHandleSearch_InvalidSearchInCategory(t *testing.T) {
-	reg := setupTestRegistry(t)
-
-	params := SearchParams{
-		Alias:    "test-api",
-		Pattern:  "test",
-		SearchIn: []string{"operations", "invalid-category", "foo"},
-	}
-
-	_, err := handleSearch(reg, params)
-	if err == nil {
-		t.Error("Expected error for invalid searchIn categories")
-	}
-
-	expectedError := "invalid searchIn categories"
-	if !strings.Contains(err.Error(), expectedError) {
-		t.Errorf("Expected error to contain '%s', got: %v", expectedError, err)
-	}
-
-	// Should mention the invalid categories
-	if !strings.Contains(err.Error(), "invalid-category") || !strings.Contains(err.Error(), "foo") {
-		t.Errorf("Expected error to mention invalid categories, got: %v", err)
-	}
-}
diff --git a/tools/mcp-server/internal/tools/slice.go b/tools/mcp-server/internal/tools/slice.go
deleted file mode 100644
index ef336d14ae..0000000000
--- a/tools/mcp-server/internal/tools/slice.go
+++ /dev/null
@@ -1,129 +0,0 @@
-package tools
-
-import (
-	"fmt"
-	"strings"
-
-	"github.com/getkin/kin-openapi/openapi3"
-	"github.com/mongodb/openapi/tools/cli/pkg/openapi"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-)
-
-// SliceParams are the parameters for the slice tool.
-type SliceParams struct {
-	SourceAlias  string   `json:"sourceAlias" jsonschema:"Alias of the source spec to slice"`
-	SaveAs       string   `json:"saveAs" jsonschema:"Alias for the resulting virtual spec (e.g. 'my-api-users')"`
-	Tags         []string `json:"tags,omitempty" jsonschema:"Optional: filter by tags"`
-	OperationIDs []string `json:"operationIds,omitempty" jsonschema:"Optional: filter by operation IDs"`
-	Paths        []string `json:"paths,omitempty" jsonschema:"Optional: filter by path patterns"`
-}
-
-// SliceResult is the response from the slice tool.
-type SliceResult struct {
-	Success bool   `json:"success"`
-	Message string `json:"message,omitempty"`
-	Alias   string `json:"alias,omitempty"`
-	Error   string `json:"error,omitempty"`
-}
-
-func handleSlice(reg *registry.Registry, params *SliceParams) (SliceResult, error) {
-	if params.SaveAs == "" {
-		return SliceResult{
-			Success: false,
-			Error:   "saveAs is required: provide an alias for the resulting virtual spec (e.g. 'my-api-users')",
-		}, nil
-	}
-
-	if !isValidAlias(params.SaveAs) {
-		return SliceResult{
-			Success: false,
-			Error:   fmt.Sprintf("invalid saveAs alias '%s': only lowercase letters, numbers, and hyphens allowed", params.SaveAs),
-		}, nil
-	}
-
-	if len(params.Tags) == 0 && len(params.OperationIDs) == 0 && len(params.Paths) == 0 {
-		return SliceResult{
-			Success: false,
-			Error:   "at least one of tags, operationIds, or paths must be specified",
-		}, nil
-	}
-
-	if _, err := reg.GetByAlias(params.SaveAs); err == nil {
-		return SliceResult{
-			Success: false,
-			Error:   fmt.Sprintf("alias '%s' is already in use, choose a different saveAs alias", params.SaveAs),
-		}, nil
-	}
-
-	entry, err := reg.GetByAlias(params.SourceAlias)
-	if err != nil {
-		return SliceResult{
-			Success: false,
-			Error:   fmt.Sprintf("spec with alias '%s' not found", params.SourceAlias),
-		}, nil
-	}
-
-	specCopy, err := copySpec(entry.Spec)
-	if err != nil {
-		return SliceResult{
-			Success: false,
-			Error:   fmt.Sprintf("failed to copy spec: %v", err),
-		}, nil
-	}
-
-	criteria := &openapi.SliceCriteria{
-		Tags:         params.Tags,
-		OperationIDs: params.OperationIDs,
-		Paths:        params.Paths,
-	}
-
-	if sliceErr := openapi.Slice(specCopy, criteria); sliceErr != nil {
-		return SliceResult{
-			Success: false,
-			Error:   fmt.Sprintf("failed to slice spec: %v", sliceErr),
-		}, nil
-	}
-
-	if addErr := reg.Add(params.SaveAs, "", specCopy, entry.Metadata); addErr != nil {
-		return SliceResult{
-			Success: false,
-			Error:   fmt.Sprintf("failed to save virtual spec: %v", addErr),
-		}, nil
-	}
-
-	return SliceResult{
-		Success: true,
-		Message: "Successfully created sliced spec filtered by " + buildFilterDescription(params),
-		Alias:   params.SaveAs,
-	}, nil
-}
-
-func buildFilterDescription(params *SliceParams) string {
-	filters := []string{}
-	if len(params.Tags) > 0 {
-		filters = append(filters, fmt.Sprintf("tags: %v", params.Tags))
-	}
-	if len(params.OperationIDs) > 0 {
-		filters = append(filters, fmt.Sprintf("operation IDs: %v", params.OperationIDs))
-	}
-	if len(params.Paths) > 0 {
-		filters = append(filters, fmt.Sprintf("paths: %v", params.Paths))
-	}
-
-	return strings.Join(filters, ", ")
-}
-
-// copySpec creates a deep copy of an OpenAPI spec by marshaling and unmarshaling.
-func copySpec(spec *openapi3.T) (*openapi3.T, error) {
-	data, err := spec.MarshalJSON()
-	if err != nil {
-		return nil, fmt.Errorf("failed to marshal spec: %w", err)
-	}
-
-	specCopy, err := openapi3.NewLoader().LoadFromData(data)
-	if err != nil {
-		return nil, fmt.Errorf("failed to unmarshal spec: %w", err)
-	}
-
-	return specCopy, nil
-}
diff --git a/tools/mcp-server/internal/tools/slice_test.go b/tools/mcp-server/internal/tools/slice_test.go
deleted file mode 100644
index 4a8ee4789c..0000000000
--- a/tools/mcp-server/internal/tools/slice_test.go
+++ /dev/null
@@ -1,239 +0,0 @@
-package tools
-
-import (
-	"testing"
-
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-)
-
-func setupSliceRegistry(t *testing.T) *registry.Registry {
-	t.Helper()
-	reg := registry.New()
-	if err := reg.Add("test-api", "/test/api.yaml", createTestSpec(), nil); err != nil {
-		t.Fatalf("failed to set up registry: %v", err)
-	}
-	return reg
-}
-
-func getSlicedEntry(t *testing.T, reg *registry.Registry, alias string) *registry.Entry {
-	t.Helper()
-	entry, err := reg.GetByAlias(alias)
-	if err != nil {
-		t.Fatalf("GetByAlias(%q) failed: %v", alias, err)
-	}
-	if entry.SourceType != registry.SourceTypeVirtual {
-		t.Errorf("entry.SourceType = %q, want %q", entry.SourceType, registry.SourceTypeVirtual)
-	}
-	if entry.FilePath != "" {
-		t.Errorf("entry.FilePath = %q, want empty string", entry.FilePath)
-	}
-	return entry
-}
-
-func collectOperationIDs(t *testing.T, reg *registry.Registry, alias string) map[string]bool {
-	t.Helper()
-	entry := getSlicedEntry(t, reg, alias)
-	ops := make(map[string]bool)
-	for _, pathItem := range entry.Spec.Paths.Map() {
-		for _, op := range pathItem.Operations() {
-			if op != nil {
-				ops[op.OperationID] = true
-			}
-		}
-	}
-	return ops
-}
-
-// TestHandleSlice_ByTags verifies that slicing by tag "Users" keeps only the 3
-// Users operations (getUsers, createUser, getUser) and excludes the 2 Clusters ones.
-func TestHandleSlice_ByTags(t *testing.T) {
-	reg := setupSliceRegistry(t)
-
-	result, err := handleSlice(reg, &SliceParams{
-		SourceAlias: "test-api",
-		SaveAs:      "test-api-users",
-		Tags:        []string{"Users"},
-	})
-	if err != nil {
-		t.Fatalf("handleSlice() returned unexpected error: %v", err)
-	}
-	if !result.Success {
-		t.Fatalf("handleSlice() failed: %s", result.Error)
-	}
-	if result.Alias != "test-api-users" {
-		t.Errorf("result.Alias = %q, want %q", result.Alias, "test-api-users")
-	}
-
-	ops := collectOperationIDs(t, reg, result.Alias)
-	wantOps := map[string]bool{"getUsers": true, "createUser": true, "getUser": true}
-	for opID := range wantOps {
-		if !ops[opID] {
-			t.Errorf("expected operation %q to be present", opID)
-		}
-	}
-	for opID := range ops {
-		if !wantOps[opID] {
-			t.Errorf("unexpected operation %q in sliced spec", opID)
-		}
-	}
-}
-
-// TestHandleSlice_ByOperationIDs verifies that slicing by operationIds keeps
-// exactly the requested operations and no others.
-func TestHandleSlice_ByOperationIDs(t *testing.T) {
-	reg := setupSliceRegistry(t)
-
-	result, err := handleSlice(reg, &SliceParams{
-		SourceAlias:  "test-api",
-		SaveAs:       "test-api-user-ops",
-		OperationIDs: []string{"getUser", "createUser"},
-	})
-	if err != nil {
-		t.Fatalf("handleSlice() returned unexpected error: %v", err)
-	}
-	if !result.Success {
-		t.Fatalf("handleSlice() failed: %s", result.Error)
-	}
-
-	ops := collectOperationIDs(t, reg, result.Alias)
-	wantOps := map[string]bool{"getUser": true, "createUser": true}
-	for opID := range wantOps {
-		if !ops[opID] {
-			t.Errorf("expected operation %q to be present", opID)
-		}
-	}
-	for opID := range ops {
-		if !wantOps[opID] {
-			t.Errorf("unexpected operation %q in sliced spec", opID)
-		}
-	}
-}
-
-// TestHandleSlice_ByPaths verifies that slicing by path "/users" keeps only
-// the operations under that exact path and excludes "/users/{userId}" and "/clusters".
-func TestHandleSlice_ByPaths(t *testing.T) {
-	reg := setupSliceRegistry(t)
-
-	result, err := handleSlice(reg, &SliceParams{
-		SourceAlias: "test-api",
-		SaveAs:      "test-api-users-path",
-		Paths:       []string{"/users"},
-	})
-	if err != nil {
-		t.Fatalf("handleSlice() returned unexpected error: %v", err)
-	}
-	if !result.Success {
-		t.Fatalf("handleSlice() failed: %s", result.Error)
-	}
-
-	ops := collectOperationIDs(t, reg, result.Alias)
-	// /users has GET (getUsers) and POST (createUser); /users/{userId} and /clusters must be excluded
-	wantOps := map[string]bool{"getUsers": true, "createUser": true}
-	for opID := range wantOps {
-		if !ops[opID] {
-			t.Errorf("expected operation %q to be present", opID)
-		}
-	}
-	for opID := range ops {
-		if !wantOps[opID] {
-			t.Errorf("unexpected operation %q in sliced spec", opID)
-		}
-	}
-}
-
-// TestHandleSlice_NoCriteria verifies that omitting all filter criteria is rejected.
-func TestHandleSlice_NoCriteria(t *testing.T) {
-	reg := setupSliceRegistry(t)
-
-	result, err := handleSlice(reg, &SliceParams{
-		SourceAlias: "test-api",
-		SaveAs:      "test-api-sliced",
-	})
-	if err != nil {
-		t.Fatalf("handleSlice() returned unexpected error: %v", err)
-	}
-	wantErr := "at least one of tags, operationIds, or paths must be specified"
-	if result.Success || result.Error != wantErr {
-		t.Errorf("result = {Success: %v, Error: %q}, want {false, %q}", result.Success, result.Error, wantErr)
-	}
-}
-
-// TestHandleSlice_SourceAliasNotFound verifies that referencing a non-existent source alias is rejected.
-func TestHandleSlice_SourceAliasNotFound(t *testing.T) {
-	reg := registry.New()
-
-	result, err := handleSlice(reg, &SliceParams{
-		SourceAlias: "nonexistent",
-		SaveAs:      "nonexistent-sliced",
-		Tags:        []string{"Users"},
-	})
-	if err != nil {
-		t.Fatalf("handleSlice() returned unexpected error: %v", err)
-	}
-	wantErr := "spec with alias 'nonexistent' not found"
-	if result.Success || result.Error != wantErr {
-		t.Errorf("result = {Success: %v, Error: %q}, want {false, %q}", result.Success, result.Error, wantErr)
-	}
-}
-
-// TestHandleSlice_SaveAsAliasAlreadyInUse verifies that reusing an existing alias for saveAs is rejected.
-func TestHandleSlice_SaveAsAliasAlreadyInUse(t *testing.T) {
-	reg := setupSliceRegistry(t)
-
-	_, err := handleSlice(reg, &SliceParams{
-		SourceAlias: "test-api",
-		SaveAs:      "test-api-users",
-		Tags:        []string{"Users"},
-	})
-	if err != nil {
-		t.Fatalf("first handleSlice() returned unexpected error: %v", err)
-	}
-
-	result, err := handleSlice(reg, &SliceParams{
-		SourceAlias: "test-api",
-		SaveAs:      "test-api-users",
-		Tags:        []string{"Clusters"},
-	})
-	if err != nil {
-		t.Fatalf("handleSlice() returned unexpected error: %v", err)
-	}
-	wantErr := "alias 'test-api-users' is already in use, choose a different saveAs alias"
-	if result.Success || result.Error != wantErr {
-		t.Errorf("result = {Success: %v, Error: %q}, want {false, %q}", result.Success, result.Error, wantErr)
-	}
-}
-
-// TestHandleSlice_InvalidSaveAsAlias verifies that a saveAs alias with invalid characters is rejected.
-func TestHandleSlice_InvalidSaveAsAlias(t *testing.T) {
-	reg := setupSliceRegistry(t)
-
-	result, err := handleSlice(reg, &SliceParams{
-		SourceAlias: "test-api",
-		SaveAs:      "Invalid Alias!",
-		Tags:        []string{"Users"},
-	})
-	if err != nil {
-		t.Fatalf("handleSlice() returned unexpected error: %v", err)
-	}
-	wantErr := "invalid saveAs alias 'Invalid Alias!': only lowercase letters, numbers, and hyphens allowed"
-	if result.Success || result.Error != wantErr {
-		t.Errorf("result = {Success: %v, Error: %q}, want {false, %q}", result.Success, result.Error, wantErr)
-	}
-}
-
-// TestHandleSlice_MissingSaveAs verifies that an empty saveAs is rejected.
-func TestHandleSlice_MissingSaveAs(t *testing.T) {
-	reg := setupSliceRegistry(t)
-
-	result, err := handleSlice(reg, &SliceParams{
-		SourceAlias: "test-api",
-		Tags:        []string{"Users"},
-	})
-	if err != nil {
-		t.Fatalf("handleSlice() returned unexpected error: %v", err)
-	}
-	wantErr := "saveAs is required: provide an alias for the resulting virtual spec (e.g. 'my-api-users')"
-	if result.Success || result.Error != wantErr {
-		t.Errorf("result = {Success: %v, Error: %q}, want {false, %q}", result.Success, result.Error, wantErr)
-	}
-}
diff --git a/tools/mcp-server/internal/tools/testhelper_test.go b/tools/mcp-server/internal/tools/testhelper_test.go
deleted file mode 100644
index 8e2e7ad7a7..0000000000
--- a/tools/mcp-server/internal/tools/testhelper_test.go
+++ /dev/null
@@ -1,137 +0,0 @@
-package tools
-
-import (
-	"github.com/getkin/kin-openapi/openapi3"
-)
-
-// createTestSpec creates a comprehensive test OpenAPI spec shared across test files.
-func createTestSpec() *openapi3.T {
-	spec := &openapi3.T{
-		OpenAPI: "3.0.0",
-		Info: &openapi3.Info{
-			Title:   "Test API",
-			Version: "1.0.0",
-		},
-		Paths:      &openapi3.Paths{},
-		Components: &openapi3.Components{},
-		Tags: []*openapi3.Tag{
-			{Name: "Users", Description: "User management endpoints"},
-			{Name: "Clusters", Description: "Cluster operations"},
-		},
-	}
-
-	spec.Paths.Set("/users", &openapi3.PathItem{
-		Get: &openapi3.Operation{
-			OperationID: "getUsers",
-			Summary:     "Get all users",
-			Description: "Retrieve a list of all users in the system",
-			Tags:        []string{"Users"},
-		},
-		Post: &openapi3.Operation{
-			OperationID: "createUser",
-			Summary:     "Create a user",
-			Description: "Create a new user account",
-			Tags:        []string{"Users"},
-		},
-	})
-
-	spec.Paths.Set("/users/{userId}", &openapi3.PathItem{
-		Get: &openapi3.Operation{
-			OperationID: "getUser",
-			Summary:     "Get user by ID",
-			Description: "Retrieve a specific user by their ID",
-			Tags:        []string{"Users"},
-		},
-	})
-
-	spec.Paths.Set("/clusters", &openapi3.PathItem{
-		Post: &openapi3.Operation{
-			OperationID: "createCluster",
-			Summary:     "Create a new cluster",
-			Description: "Creates a new cluster in the project",
-			Tags:        []string{"Clusters"},
-		},
-		Get: &openapi3.Operation{
-			OperationID: "listClusters",
-			Summary:     "List clusters",
-			Description: "Get all clusters in the project",
-			Tags:        []string{"Clusters"},
-		},
-	})
-
-	spec.Paths.Set("/clusters/{clusterId}", &openapi3.PathItem{
-		Get: &openapi3.Operation{
-			OperationID: "getCluster",
-			Summary:     "Get cluster details",
-			Description: "Retrieve details for a specific cluster",
-			Tags:        []string{"Clusters"},
-		},
-	})
-
-	spec.Components.Schemas = make(map[string]*openapi3.SchemaRef)
-	spec.Components.Schemas["User"] = &openapi3.SchemaRef{
-		Value: &openapi3.Schema{
-			Type:        &openapi3.Types{"object"},
-			Description: "User account information",
-			Properties: map[string]*openapi3.SchemaRef{
-				"userId":   {Value: &openapi3.Schema{Type: &openapi3.Types{"string"}}},
-				"username": {Value: &openapi3.Schema{Type: &openapi3.Types{"string"}}},
-				"email":    {Value: &openapi3.Schema{Type: &openapi3.Types{"string"}}},
-			},
-		},
-	}
-
-	spec.Components.Schemas["Cluster"] = &openapi3.SchemaRef{
-		Value: &openapi3.Schema{
-			Type:        &openapi3.Types{"object"},
-			Description: "Cluster configuration",
-			Properties: map[string]*openapi3.SchemaRef{
-				"clusterId": {Value: &openapi3.Schema{Type: &openapi3.Types{"string"}}},
-				"name":      {Value: &openapi3.Schema{Type: &openapi3.Types{"string"}}},
-				"region":    {Value: &openapi3.Schema{Type: &openapi3.Types{"string"}}},
-			},
-		},
-	}
-
-	spec.Components.Schemas["Database"] = &openapi3.SchemaRef{
-		Value: &openapi3.Schema{
-			Type:        &openapi3.Types{"object"},
-			Description: "Database information",
-			Properties: map[string]*openapi3.SchemaRef{
-				"databaseName": {Value: &openapi3.Schema{Type: &openapi3.Types{"string"}}},
-			},
-		},
-	}
-
-	spec.Components.Parameters = make(map[string]*openapi3.ParameterRef)
-	spec.Components.Parameters["userId"] = &openapi3.ParameterRef{
-		Value: &openapi3.Parameter{
-			Name:        "userId",
-			In:          "path",
-			Description: "Unique identifier for the user",
-			Required:    true,
-		},
-	}
-
-	spec.Components.Parameters["clusterId"] = &openapi3.ParameterRef{
-		Value: &openapi3.Parameter{
-			Name:        "clusterId",
-			In:          "path",
-			Description: "Unique identifier for the cluster",
-			Required:    true,
-		},
-	}
-
-	spec.Components.Responses = make(map[string]*openapi3.ResponseRef)
-	notFound := "Not Found"
-	spec.Components.Responses["NotFound"] = &openapi3.ResponseRef{
-		Value: &openapi3.Response{Description: &notFound},
-	}
-
-	unauthorized := "Unauthorized"
-	spec.Components.Responses["Unauthorized"] = &openapi3.ResponseRef{
-		Value: &openapi3.Response{Description: &unauthorized},
-	}
-
-	return spec
-}
diff --git a/tools/mcp-server/internal/tools/tools.go b/tools/mcp-server/internal/tools/tools.go
deleted file mode 100644
index fa52171455..0000000000
--- a/tools/mcp-server/internal/tools/tools.go
+++ /dev/null
@@ -1,104 +0,0 @@
-package tools
-
-import (
-	"context"
-
-	"github.com/modelcontextprotocol/go-sdk/mcp"
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-)
-
-// Register registers all tool handlers with the server.
-func Register(server *mcp.Server, reg *registry.Registry) {
-	// Register load tool
-	loadTool := &mcp.Tool{
-		Name: "load",
-		Description: "Load an OpenAPI specification file (JSON or YAML) into memory. " +
-			"Assigns an alias for easy reference in other commands. " +
-			"Validates the spec and makes it available for searching, exporting, and inspection. " +
-			"Required before using search or export tools on a spec.",
-	}
-	mcp.AddTool(server, loadTool, makeLoadHandler(reg))
-
-	// Register unload tool
-	unloadTool := &mcp.Tool{
-		Name: "unload",
-		Description: "Remove a previously loaded OpenAPI specification from memory by its alias. " +
-			"Frees up resources and removes the spec from the available list. " +
-			"Use this to clean up specs you no longer need to search or reference.",
-	}
-	mcp.AddTool(server, unloadTool, makeUnloadHandler(reg))
-
-	// Register export tool
-	exportTool := &mcp.Tool{
-		Name: "export",
-		Description: "Export a loaded OpenAPI specification to a file in JSON or YAML format. " +
-			"Useful for converting between formats, saving modified specs, or creating copies. " +
-			"Specify the output path and desired format (json/yaml).",
-	}
-	mcp.AddTool(server, exportTool, makeExportHandler(reg))
-
-	// Register search tool
-	searchTool := &mcp.Tool{
-		Name: "search",
-		Description: "Search across OpenAPI specifications using regex patterns. " +
-			"Searches operations, schemas, parameters, responses, tags, and paths. " +
-			"Returns matches grouped by category with details on what matched (operationId, schema name, property names, etc.). " +
-			"Supports case-sensitive/insensitive search, category filtering, and per-category result limits. " +
-			"Use this to find specific endpoints, data structures, or API components by name or pattern.",
-	}
-	mcp.AddTool(server, searchTool, makeSearchHandler(reg))
-
-	// Register slice tool
-	sliceTool := &mcp.Tool{
-		Name: "slice",
-		Description: "Create a filtered subset of an OpenAPI specification by selecting specific operations. " +
-			"Filter by tags, operation IDs, or path patterns. " +
-			"Uses OR logic: operations matching ANY of the specified criteria are included. " +
-			"Automatically includes all schemas, parameters, and components referenced by the selected operations. " +
-			"Requires a 'saveAs' alias chosen by the agent to name the resulting virtual spec (e.g. 'atlas-api-users'). " +
-			"The same source spec can be sliced multiple times with different aliases for different subsets. " +
-			"Returns the alias and updated list of available specs. " +
-			"Useful for creating API subsets, generating client SDKs for specific features, or analyzing specific API areas.",
-	}
-	mcp.AddTool(server, sliceTool, makeSliceHandler(reg))
-}
-
-// makeLoadHandler creates the handler for the load tool.
-func makeLoadHandler(reg *registry.Registry) mcp.ToolHandlerFor[LoadParams, LoadResult] {
-	return func(_ context.Context, _ *mcp.CallToolRequest, params LoadParams) (*mcp.CallToolResult, LoadResult, error) {
-		result, err := handleLoad(reg, params)
-		return nil, result, err
-	}
-}
-
-// makeUnloadHandler creates the handler for the unload tool.
-func makeUnloadHandler(reg *registry.Registry) mcp.ToolHandlerFor[UnloadParams, UnloadResult] {
-	return func(_ context.Context, _ *mcp.CallToolRequest, params UnloadParams) (*mcp.CallToolResult, UnloadResult, error) {
-		result, err := handleUnload(reg, params)
-		return nil, result, err
-	}
-}
-
-// makeExportHandler creates the handler for the export tool.
-func makeExportHandler(reg *registry.Registry) mcp.ToolHandlerFor[ExportParams, ExportResult] {
-	return func(_ context.Context, _ *mcp.CallToolRequest, params ExportParams) (*mcp.CallToolResult, ExportResult, error) {
-		result, err := handleExport(reg, params)
-		return nil, result, err
-	}
-}
-
-// makeSearchHandler creates the handler for the search tool.
-func makeSearchHandler(reg *registry.Registry) mcp.ToolHandlerFor[SearchParams, SearchResult] {
-	return func(_ context.Context, _ *mcp.CallToolRequest, params SearchParams) (*mcp.CallToolResult, SearchResult, error) {
-		result, err := handleSearch(reg, params)
-		return nil, result, err
-	}
-}
-
-// makeSliceHandler creates the handler for the slice tool.
-func makeSliceHandler(reg *registry.Registry) mcp.ToolHandlerFor[SliceParams, SliceResult] {
-	return func(_ context.Context, _ *mcp.CallToolRequest, params SliceParams) (*mcp.CallToolResult, SliceResult, error) {
-		result, err := handleSlice(reg, &params)
-		return nil, result, err
-	}
-}
diff --git a/tools/mcp-server/internal/tools/unload.go b/tools/mcp-server/internal/tools/unload.go
deleted file mode 100644
index 7f7cd10eab..0000000000
--- a/tools/mcp-server/internal/tools/unload.go
+++ /dev/null
@@ -1,33 +0,0 @@
-package tools
-
-import (
-	"fmt"
-
-	"github.com/mongodb/openapi/tools/mcp-server/internal/registry"
-)
-
-// UnloadParams are the parameters for the unload tool.
-type UnloadParams struct {
-	Alias string `json:"alias" jsonschema:"Alias of the spec to unload"`
-}
-
-// UnloadResult is the result of an unload operation.
-type UnloadResult struct {
-	Success bool   `json:"success"`
-	Alias   string `json:"alias"`
-	Message string `json:"message"`
-}
-
-// handleUnload removes a spec from the registry.
-// The SDK handles parameter unmarshaling and validation automatically.
-func handleUnload(reg *registry.Registry, params UnloadParams) (UnloadResult, error) {
-	if err := reg.Remove(params.Alias); err != nil {
-		return UnloadResult{Success: false}, err
-	}
-
-	return UnloadResult{
-		Success: true,
-		Alias:   params.Alias,
-		Message: fmt.Sprintf("Unloaded '%s' successfully", params.Alias),
-	}, nil
-}