@apart-tech/intelligence-mcp 0.2.0 → 0.3.1

package/dist/index.js

@@ -2,19 +2,14 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import { z } from "zod";
-import { loadConfig, getTenantDb, NodeService, EdgeService, SearchService, ContextService, DomainService, WorkspaceService, createEmbeddingProvider, SINGLE_TENANT_ORG_ID, } from "@apart-tech/intelligence-core";
-const config = loadConfig();
-const tenant = {
-    organizationId: config.tenancy.organizationId ?? SINGLE_TENANT_ORG_ID,
-};
-const db = getTenantDb(config.database.url, tenant);
-const embeddings = createEmbeddingProvider(config, { db });
-const nodeService = new NodeService(db, embeddings, tenant);
-const edgeService = new EdgeService(db);
-const searchService = new SearchService(db, embeddings, config, tenant);
-const domainService = new DomainService(db, tenant);
-const workspaceService = new WorkspaceService(db, tenant);
-const contextService = new ContextService(nodeService, edgeService, searchService, config, workspaceService, domainService);
+import { createApiProvider } from "@apart-tech/intelligence-api-client";
+const apiUrl = process.env.APART_API_URL;
+const apiKey = process.env.APART_API_KEY;
+if (!apiUrl || !apiKey) {
+    console.error("APART_API_URL and APART_API_KEY environment variables are required");
+    process.exit(1);
+}
+const api = createApiProvider({ server: apiUrl, apiKey });
 const server = new McpServer({
     name: "apart-intelligence",
     version: "0.1.0",
@@ -41,26 +36,16 @@ server.tool("search_knowledge", "Hybrid semantic + keyword search across all kno
         .describe("Workspace slug — auto-applies domain/type/tag filters"),
 }, async ({ query, limit, types, include_drafts, domain_slugs, workspace }) => {
     let domainIds;
-    let resolvedTypes = types;
-    // Apply workspace filters (explicit params override workspace defaults)
-    if (workspace) {
-        const filter = await workspaceService.resolveFilter(workspace, (slugs) => domainService.resolveSlugs(slugs));
-        if (filter) {
-            if (!domainIds && filter.domainIds)
-                domainIds = filter.domainIds;
-            if (!resolvedTypes && filter.types)
-                resolvedTypes = filter.types;
-        }
-    }
     if (domain_slugs?.length) {
-        domainIds = await domainService.resolveSlugs(domain_slugs);
+        domainIds = await api.domains.resolveSlugs(domain_slugs);
     }
-    const results = await searchService.search({
+    const results = await api.search.search({
         query,
         limit,
-        types: resolvedTypes,
+        types,
         includeDrafts: include_drafts,
         domainIds,
+        workspace,
     });
     return {
         content: [
@@ -73,15 +58,16 @@ server.tool("search_knowledge", "Hybrid semantic + keyword search across all kno
 });
 server.tool("get_node", "Retrieve a specific knowledge node by ID with its edges", {
     id: z.string().describe("Node UUID"),
-}, async ({ id }) => {
-    const node = await nodeService.getById(id);
+    decrypt: z.boolean().optional().describe("Decrypt PII fields if the node contains encrypted PII"),
+}, async ({ id, decrypt: _decrypt }) => {
+    const node = await api.nodes.getById(id);
     if (!node) {
         return {
             content: [{ type: "text", text: "Node not found" }],
             isError: true,
         };
     }
-    const edges = await edgeService.getByNodeId(id);
+    const edges = await api.edges.getByNodeId(id);
     return {
         content: [
             {
@@ -108,9 +94,9 @@ server.tool("get_context", "Assemble a context package for a topic — returns r
 }, async ({ query, max_depth, max_nodes, include_drafts, types, domain_slugs, workspace }) => {
     let domainIds;
     if (domain_slugs?.length) {
-        domainIds = await domainService.resolveSlugs(domain_slugs);
+        domainIds = await api.domains.resolveSlugs(domain_slugs);
     }
-    const ctx = await contextService.assemble({
+    const ctx = await api.search.context({
         query,
         maxDepth: max_depth,
         maxNodes: max_nodes,
@@ -129,26 +115,12 @@ server.tool("get_neighborhood", "Return a node and its N-hop graph neighborhood"
     id: z.string().describe("Node UUID"),
     depth: z.number().optional().describe("Hops to traverse (default 1)"),
 }, async ({ id, depth }) => {
-    const node = await nodeService.getById(id);
-    if (!node) {
-        return {
-            content: [{ type: "text", text: "Node not found" }],
-            isError: true,
-        };
-    }
-    const neighborIds = await edgeService.getNeighborIds(id, depth ?? 1);
-    const neighbors = [];
-    for (const nId of neighborIds) {
-        const n = await nodeService.getById(nId);
-        if (n)
-            neighbors.push(n);
-    }
-    const edges = await edgeService.getByNodeId(id);
+    const result = await api.nodes.getNeighborhood(id, depth);
     return {
         content: [
             {
                 type: "text",
-                text: JSON.stringify({ node, neighbors, edges }, null, 2),
+                text: JSON.stringify(result, null, 2),
             },
         ],
     };
@@ -156,7 +128,7 @@ server.tool("get_neighborhood", "Return a node and its N-hop graph neighborhood"
 server.tool("list_drafts", "List all draft nodes pending curation", {
     limit: z.number().optional().describe("Max results (default 50)"),
 }, async ({ limit }) => {
-    const drafts = await nodeService.listDrafts(limit);
+    const drafts = await api.nodes.listDrafts(limit);
     return {
         content: [
             { type: "text", text: JSON.stringify(drafts, null, 2) },
@@ -165,8 +137,8 @@ server.tool("list_drafts", "List all draft nodes pending curation", {
 });
 server.tool("list_types", "List all node types and relationship types currently in use", {}, async () => {
     const [nodeTypes, edgeTypes] = await Promise.all([
-        nodeService.listTypes(),
-        edgeService.listRelationshipTypes(),
+        api.nodes.listTypes(),
+        api.edges.listRelationshipTypes(),
     ]);
     return {
         content: [
@@ -178,7 +150,7 @@ server.tool("list_types", "List all node types and relationship types currently
     };
 });
 server.tool("list_domains", "List the full domain taxonomy tree", {}, async () => {
-    const tree = await domainService.getTree();
+    const tree = await api.domains.getTree();
     return {
         content: [
             { type: "text", text: JSON.stringify(tree, null, 2) },
@@ -186,7 +158,7 @@ server.tool("list_domains", "List the full domain taxonomy tree", {}, async () =
     };
 });
 server.tool("seed_domains", "Seed the default domain taxonomy", {}, async () => {
-    const result = await domainService.seed();
+    const result = await api.domains.seed();
     return {
         content: [
             {
@@ -198,7 +170,7 @@ server.tool("seed_domains", "Seed the default domain taxonomy", {}, async () =>
 });
 // ── Workspace Tools ───────────────────────────────────────────────────────
 server.tool("list_workspaces", "List all workspaces — each defines a filtered view of the knowledge graph for a specific kind of work", {}, async () => {
-    const list = await workspaceService.list();
+    const list = await api.workspaces.list();
     return {
         content: [
             { type: "text", text: JSON.stringify(list, null, 2) },
@@ -208,7 +180,7 @@ server.tool("list_workspaces", "List all workspaces — each defines a filtered
 server.tool("get_workspace", "Get full workspace definition including filter rules and system prompt", {
     slug: z.string().describe("Workspace slug"),
 }, async ({ slug }) => {
-    const ws = await workspaceService.getBySlug(slug);
+    const ws = await api.workspaces.getBySlug(slug);
     if (!ws) {
         return {
             content: [{ type: "text", text: "Workspace not found" }],
@@ -224,7 +196,7 @@ server.tool("get_workspace", "Get full workspace definition including filter rul
 server.tool("export_workspace", "Export a workspace as a CLAUDE.md-formatted markdown document", {
     slug: z.string().describe("Workspace slug"),
 }, async ({ slug }) => {
-    const md = await workspaceService.exportAsMarkdown(slug);
+    const md = await api.workspaces.exportAsMarkdown(slug);
     if (!md) {
         return {
             content: [{ type: "text", text: "Workspace not found" }],
@@ -257,11 +229,11 @@ server.tool("add_node", "Create a new knowledge node (defaults to draft status)"
 }, async ({ type, title, content, metadata, created_by, domain_slug }) => {
     let domainId;
     if (domain_slug) {
-        const domain = await domainService.getBySlug(domain_slug);
+        const domain = await api.domains.getBySlug(domain_slug);
         if (domain)
             domainId = domain.id;
     }
-    const node = await nodeService.create({
+    const node = await api.nodes.create({
         type,
         title,
         content,
@@ -282,7 +254,7 @@ server.tool("update_node", "Update content or metadata of an existing knowledge
     metadata: z.record(z.unknown()).optional().describe("New metadata"),
     type: z.string().optional().describe("New node type"),
 }, async ({ id, title, content, metadata, type }) => {
-    const node = await nodeService.update(id, { title, content, metadata, type });
+    const node = await api.nodes.update(id, { title, content, metadata, type });
     if (!node) {
         return {
             content: [{ type: "text", text: "Node not found" }],
@@ -304,7 +276,7 @@ server.tool("link_nodes", "Create an edge between two knowledge nodes", {
     weight: z.number().optional().describe("Relevance weight (default 1.0)"),
     created_by: z.string().optional().describe("Creator identifier"),
 }, async ({ source_node_id, target_node_id, relationship_type, weight, created_by }) => {
-    const edge = await edgeService.create({
+    const edge = await api.edges.create({
         sourceNodeId: source_node_id,
         targetNodeId: target_node_id,
         relationshipType: relationship_type,
@@ -323,7 +295,7 @@ server.tool("set_status", "Change node status (draft/reviewed/approved/archived)
         .enum(["draft", "reviewed", "approved", "archived"])
         .describe("New status"),
 }, async ({ id, status }) => {
-    const node = await nodeService.setStatus(id, status);
+    const node = await api.nodes.setStatus(id, status);
     if (!node) {
         return {
             content: [{ type: "text", text: "Node not found" }],
@@ -336,6 +308,152 @@ server.tool("set_status", "Change node status (draft/reviewed/approved/archived)
         ],
     };
 });
+// ── Delete Tools ──────────────────────────────────────────────────────────
+server.tool("delete_node", "Delete a knowledge node and all its edges", {
+    id: z.string().describe("Node UUID"),
+}, async ({ id }) => {
+    const node = await api.nodes.getById(id);
+    if (!node) {
+        return {
+            content: [{ type: "text", text: "Node not found" }],
+            isError: true,
+        };
+    }
+    await api.nodes.delete(node.id);
+    return {
+        content: [{ type: "text", text: `Deleted node "${node.title}" (${node.id})` }],
+    };
+});
+server.tool("delete_edge", "Delete an edge between two nodes", {
+    id: z.string().describe("Edge UUID"),
+}, async ({ id }) => {
+    const deleted = await api.edges.delete(id);
+    if (!deleted) {
+        return {
+            content: [{ type: "text", text: "Edge not found" }],
+            isError: true,
+        };
+    }
+    return {
+        content: [{ type: "text", text: `Deleted edge ${id}` }],
+    };
+});
+// ── Graph Health Tools ────────────────────────────────────────────────────
+server.tool("health_report", "Comprehensive graph health report — node/edge counts, orphans, stale nodes, connected components", {
+    stale_days: z.number().optional().describe("Days before a node is considered stale (default 90)"),
+}, async ({ stale_days }) => {
+    const report = await api.cleaning.getHealthReport(stale_days ?? 90);
+    return {
+        content: [{ type: "text", text: JSON.stringify(report, null, 2) }],
+    };
+});
+server.tool("validate_edges", "Validate edge integrity — detect self-loops, duplicates, low-relevance connections, contradictions, and rare types", {
+    low_relevance_threshold: z.number().optional().describe("Similarity threshold for low-relevance detection (default 0.3)"),
+    rare_type_threshold: z.number().optional().describe("Flag relationship types used this many times or fewer (default 1)"),
+}, async ({ low_relevance_threshold, rare_type_threshold }) => {
+    const report = await api.cleaning.validate({
+        lowRelevanceThreshold: low_relevance_threshold,
+        rareTypeThreshold: rare_type_threshold,
+    });
+    return {
+        content: [{ type: "text", text: JSON.stringify(report, null, 2) }],
+    };
+});
+server.tool("find_orphans", "Find nodes with no connections to other nodes", {}, async () => {
+    const orphans = await api.cleaning.findOrphans();
+    return {
+        content: [{ type: "text", text: JSON.stringify(orphans, null, 2) }],
+    };
+});
+server.tool("find_duplicates", "Find near-duplicate node pairs by embedding cosine similarity", {
+    threshold: z.number().optional().describe("Minimum cosine similarity 0-1 (default 0.95)"),
+    limit: z.number().optional().describe("Max pairs to return (default 50)"),
+}, async ({ threshold, limit }) => {
+    const duplicates = await api.cleaning.findDuplicates(threshold ?? 0.95, limit ?? 50);
+    return {
+        content: [{ type: "text", text: JSON.stringify(duplicates, null, 2) }],
+    };
+});
+server.tool("find_islands", "Detect disconnected clusters (connected components) in the graph, optionally with bridge suggestions", {
+    bridges: z.boolean().optional().describe("Include suggested links to bridge islands"),
+    max_bridges: z.number().optional().describe("Max bridge suggestions (default 10)"),
+}, async ({ bridges, max_bridges }) => {
+    const result = await api.cleaning.findIslands({
+        bridges,
+        maxBridges: max_bridges,
+    });
+    return {
+        content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+    };
+});
+server.tool("suggest_links", "Suggest missing links between semantically similar but unconnected nodes", {
+    node_id: z.string().optional().describe("Node UUID to suggest links for (omit for global scan)"),
+    min_similarity: z.number().optional().describe("Minimum cosine similarity (default 0.8 global, 0.7 per-node)"),
+    limit: z.number().optional().describe("Max suggestions (default 10 per-node, 20 global)"),
+}, async ({ node_id, min_similarity, limit }) => {
+    const suggestions = await api.cleaning.suggestLinks({
+        nodeId: node_id,
+        minSimilarity: min_similarity,
+        limit,
+    });
+    return {
+        content: [{ type: "text", text: JSON.stringify(suggestions, null, 2) }],
+    };
+});
+server.tool("analyze_relationship_types", "Analyze relationship type vocabulary and suggest merges for semantically similar types", {
+    min_similarity: z.number().optional().describe("Minimum similarity to suggest merge (default 0.7)"),
+}, async ({ min_similarity }) => {
+    const report = await api.cleaning.analyzeRelationshipTypes({
+        minSimilarity: min_similarity,
+    });
+    return {
+        content: [{ type: "text", text: JSON.stringify(report, null, 2) }],
+    };
+});
+server.tool("retype_edges", "Rename all edges of one relationship type to another", {
+    from_type: z.string().describe("Current relationship type to rename"),
+    to_type: z.string().describe("New relationship type name"),
+}, async ({ from_type, to_type }) => {
+    const result = await api.cleaning.retypeMany(from_type, to_type);
+    return {
+        content: [{ type: "text", text: JSON.stringify({ renamed: result.count, from: from_type, to: to_type }, null, 2) }],
+    };
+});
+// ── PII Tools ─────────────────────────────────────────────────────────────
+server.tool("get_pii_config", "Get the current PII detection/encryption policy for this organization", {}, async () => {
+    const config = await api.pii.getConfig();
+    if (!config) {
+        return {
+            content: [{ type: "text", text: JSON.stringify({ configured: false }, null, 2) }],
+        };
+    }
+    return {
+        content: [{ type: "text", text: JSON.stringify(config, null, 2) }],
+    };
+});
+server.tool("test_pii", "Test a text string for PII detection — returns matches with types and positions", {
+    text: z.string().describe("Text to scan for PII"),
+}, async ({ text }) => {
+    const result = await api.pii.test(text);
+    return {
+        content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+    };
+});
+// ── Maintenance Tools ─────────────────────────────────────────────────────
+server.tool("re_embed", "Re-generate embeddings for nodes (useful after changing embedding provider/model)", {
+    type: z.string().optional().describe("Only re-embed nodes of this type"),
+    limit: z.number().optional().describe("Limit to N nodes"),
+    dry_run: z.boolean().optional().describe("Show what would be re-embedded without making changes"),
+}, async ({ type, limit, dry_run }) => {
+    const result = await api.reEmbed({
+        type,
+        limit,
+        dryRun: dry_run ?? false,
+    });
+    return {
+        content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+    };
+});
 // ── Start Server ───────────────────────────────────────────────────────────
 async function main() {
     const transport = new StdioServerTransport();

package/dist/index.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,27 +1,27 @@
 {
   "name": "@apart-tech/intelligence-mcp",
-  "version": "0.2.0",
+  "version": "0.3.1",
   "description": "MCP server for Apart Intelligence knowledge graph",
   "type": "module",
   "main": "dist/index.js",
   "bin": {
     "tc-mcp": "dist/index.js"
   },
+  "scripts": {
+    "build": "tsc",
+    "dev": "tsc --watch",
+    "start": "node dist/index.js",
+    "lint": "tsc --noEmit",
+    "test": "vitest run"
+  },
   "dependencies": {
     "@modelcontextprotocol/sdk": "^1.8.0",
-    "zod": "^3.24.0",
-    "@apart-tech/intelligence-core": "1.0.3"
+    "@apart-tech/intelligence-api-client": "^0.1.0",
+    "zod": "^3.24.0"
   },
   "devDependencies": {
     "@types/node": "^25.5.0",
     "typescript": "^5.7.0",
     "vitest": "^3.0.0"
-  },
-  "scripts": {
-    "build": "tsc",
-    "dev": "tsc --watch",
-    "start": "node dist/index.js",
-    "lint": "tsc --noEmit",
-    "test": "vitest run"
   }
-}
+}

package/src/index.ts

@@ -3,39 +3,18 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import { z } from "zod";
-import {
-  loadConfig,
-  getTenantDb,
-  NodeService,
-  EdgeService,
-  SearchService,
-  ContextService,
-  DomainService,
-  WorkspaceService,
-  createEmbeddingProvider,
-  SINGLE_TENANT_ORG_ID,
-} from "@apart-tech/intelligence-core";
-import type { NodeStatus, TenantContext } from "@apart-tech/intelligence-core";
-
-const config = loadConfig();
-const tenant: TenantContext = {
-  organizationId: config.tenancy.organizationId ?? SINGLE_TENANT_ORG_ID,
-};
-const db = getTenantDb(config.database.url, tenant);
-const embeddings = createEmbeddingProvider(config, { db });
-const nodeService = new NodeService(db, embeddings, tenant);
-const edgeService = new EdgeService(db);
-const searchService = new SearchService(db, embeddings, config, tenant);
-const domainService = new DomainService(db, tenant);
-const workspaceService = new WorkspaceService(db, tenant);
-const contextService = new ContextService(
-  nodeService,
-  edgeService,
-  searchService,
-  config,
-  workspaceService,
-  domainService,
-);
+import { createApiProvider } from "@apart-tech/intelligence-api-client";
+import type { ServiceProvider, NodeStatus } from "@apart-tech/intelligence-api-client";
+
+const apiUrl = process.env.APART_API_URL;
+const apiKey = process.env.APART_API_KEY;
+
+if (!apiUrl || !apiKey) {
+  console.error("APART_API_URL and APART_API_KEY environment variables are required");
+  process.exit(1);
+}
+
+const api: ServiceProvider = createApiProvider({ server: apiUrl, apiKey });
 
 const server = new McpServer({
   name: "apart-intelligence",
@@ -69,28 +48,17 @@ server.tool(
   },
   async ({ query, limit, types, include_drafts, domain_slugs, workspace }) => {
     let domainIds: string[] | undefined;
-    let resolvedTypes = types;
-
-    // Apply workspace filters (explicit params override workspace defaults)
-    if (workspace) {
-      const filter = await workspaceService.resolveFilter(workspace, (slugs) =>
-        domainService.resolveSlugs(slugs),
-      );
-      if (filter) {
-        if (!domainIds && filter.domainIds) domainIds = filter.domainIds;
-        if (!resolvedTypes && filter.types) resolvedTypes = filter.types;
-      }
-    }
 
     if (domain_slugs?.length) {
-      domainIds = await domainService.resolveSlugs(domain_slugs);
+      domainIds = await api.domains.resolveSlugs(domain_slugs);
     }
-    const results = await searchService.search({
+    const results = await api.search.search({
       query,
       limit,
-      types: resolvedTypes,
+      types,
       includeDrafts: include_drafts,
       domainIds,
+      workspace,
     });
     return {
       content: [
@@ -108,16 +76,18 @@ server.tool(
   "Retrieve a specific knowledge node by ID with its edges",
   {
     id: z.string().describe("Node UUID"),
+    decrypt: z.boolean().optional().describe("Decrypt PII fields if the node contains encrypted PII"),
   },
-  async ({ id }) => {
-    const node = await nodeService.getById(id);
+  async ({ id, decrypt: _decrypt }) => {
+    const node = await api.nodes.getById(id);
     if (!node) {
       return {
         content: [{ type: "text" as const, text: "Node not found" }],
         isError: true,
       };
     }
-    const edges = await edgeService.getByNodeId(id);
+    const edges = await api.edges.getByNodeId(id);
+
     return {
       content: [
         {
@@ -150,9 +120,9 @@ server.tool(
   async ({ query, max_depth, max_nodes, include_drafts, types, domain_slugs, workspace }) => {
     let domainIds: string[] | undefined;
     if (domain_slugs?.length) {
-      domainIds = await domainService.resolveSlugs(domain_slugs);
+      domainIds = await api.domains.resolveSlugs(domain_slugs);
     }
-    const ctx = await contextService.assemble({
+    const ctx = await api.search.context({
       query,
       maxDepth: max_depth,
       maxNodes: max_nodes,
@@ -177,25 +147,12 @@ server.tool(
     depth: z.number().optional().describe("Hops to traverse (default 1)"),
   },
   async ({ id, depth }) => {
-    const node = await nodeService.getById(id);
-    if (!node) {
-      return {
-        content: [{ type: "text" as const, text: "Node not found" }],
-        isError: true,
-      };
-    }
-    const neighborIds = await edgeService.getNeighborIds(id, depth ?? 1);
-    const neighbors = [];
-    for (const nId of neighborIds) {
-      const n = await nodeService.getById(nId);
-      if (n) neighbors.push(n);
-    }
-    const edges = await edgeService.getByNodeId(id);
+    const result = await api.nodes.getNeighborhood(id, depth);
     return {
       content: [
         {
           type: "text" as const,
-          text: JSON.stringify({ node, neighbors, edges }, null, 2),
+          text: JSON.stringify(result, null, 2),
         },
       ],
     };
@@ -209,7 +166,7 @@ server.tool(
     limit: z.number().optional().describe("Max results (default 50)"),
   },
   async ({ limit }) => {
-    const drafts = await nodeService.listDrafts(limit);
+    const drafts = await api.nodes.listDrafts(limit);
     return {
       content: [
         { type: "text" as const, text: JSON.stringify(drafts, null, 2) },
@@ -224,8 +181,8 @@ server.tool(
   {},
   async () => {
     const [nodeTypes, edgeTypes] = await Promise.all([
-      nodeService.listTypes(),
-      edgeService.listRelationshipTypes(),
+      api.nodes.listTypes(),
+      api.edges.listRelationshipTypes(),
     ]);
     return {
       content: [
@@ -243,7 +200,7 @@ server.tool(
   "List the full domain taxonomy tree",
   {},
   async () => {
-    const tree = await domainService.getTree();
+    const tree = await api.domains.getTree();
     return {
       content: [
         { type: "text" as const, text: JSON.stringify(tree, null, 2) },
@@ -257,7 +214,7 @@ server.tool(
   "Seed the default domain taxonomy",
   {},
   async () => {
-    const result = await domainService.seed();
+    const result = await api.domains.seed();
     return {
       content: [
         {
@@ -276,7 +233,7 @@ server.tool(
   "List all workspaces — each defines a filtered view of the knowledge graph for a specific kind of work",
   {},
   async () => {
-    const list = await workspaceService.list();
+    const list = await api.workspaces.list();
     return {
       content: [
         { type: "text" as const, text: JSON.stringify(list, null, 2) },
@@ -292,7 +249,7 @@ server.tool(
     slug: z.string().describe("Workspace slug"),
   },
   async ({ slug }) => {
-    const ws = await workspaceService.getBySlug(slug);
+    const ws = await api.workspaces.getBySlug(slug);
     if (!ws) {
       return {
         content: [{ type: "text" as const, text: "Workspace not found" }],
@@ -314,7 +271,7 @@ server.tool(
     slug: z.string().describe("Workspace slug"),
   },
   async ({ slug }) => {
-    const md = await workspaceService.exportAsMarkdown(slug);
+    const md = await api.workspaces.exportAsMarkdown(slug);
     if (!md) {
       return {
         content: [{ type: "text" as const, text: "Workspace not found" }],
@@ -354,10 +311,10 @@ server.tool(
   async ({ type, title, content, metadata, created_by, domain_slug }) => {
     let domainId: string | undefined;
     if (domain_slug) {
-      const domain = await domainService.getBySlug(domain_slug);
+      const domain = await api.domains.getBySlug(domain_slug);
       if (domain) domainId = domain.id;
     }
-    const node = await nodeService.create({
+    const node = await api.nodes.create({
       type,
       title,
       content,
@@ -384,7 +341,7 @@ server.tool(
     type: z.string().optional().describe("New node type"),
   },
   async ({ id, title, content, metadata, type }) => {
-    const node = await nodeService.update(id, { title, content, metadata, type });
+    const node = await api.nodes.update(id, { title, content, metadata, type });
     if (!node) {
       return {
         content: [{ type: "text" as const, text: "Node not found" }],
@@ -412,7 +369,7 @@ server.tool(
     created_by: z.string().optional().describe("Creator identifier"),
   },
   async ({ source_node_id, target_node_id, relationship_type, weight, created_by }) => {
-    const edge = await edgeService.create({
+    const edge = await api.edges.create({
       sourceNodeId: source_node_id,
       targetNodeId: target_node_id,
       relationshipType: relationship_type,
@@ -437,7 +394,7 @@ server.tool(
       .describe("New status"),
   },
   async ({ id, status }) => {
-    const node = await nodeService.setStatus(id, status as NodeStatus);
+    const node = await api.nodes.setStatus(id, status as NodeStatus);
     if (!node) {
       return {
         content: [{ type: "text" as const, text: "Node not found" }],
@@ -452,6 +409,234 @@ server.tool(
   }
 );
 
+// ── Delete Tools ──────────────────────────────────────────────────────────
+
+server.tool(
+  "delete_node",
+  "Delete a knowledge node and all its edges",
+  {
+    id: z.string().describe("Node UUID"),
+  },
+  async ({ id }) => {
+    const node = await api.nodes.getById(id);
+    if (!node) {
+      return {
+        content: [{ type: "text" as const, text: "Node not found" }],
+        isError: true,
+      };
+    }
+    await api.nodes.delete(node.id);
+    return {
+      content: [{ type: "text" as const, text: `Deleted node "${node.title}" (${node.id})` }],
+    };
+  }
+);
+
+server.tool(
+  "delete_edge",
+  "Delete an edge between two nodes",
+  {
+    id: z.string().describe("Edge UUID"),
+  },
+  async ({ id }) => {
+    const deleted = await api.edges.delete(id);
+    if (!deleted) {
+      return {
+        content: [{ type: "text" as const, text: "Edge not found" }],
+        isError: true,
+      };
+    }
+    return {
+      content: [{ type: "text" as const, text: `Deleted edge ${id}` }],
+    };
+  }
+);
+
+// ── Graph Health Tools ────────────────────────────────────────────────────
+
+server.tool(
+  "health_report",
+  "Comprehensive graph health report — node/edge counts, orphans, stale nodes, connected components",
+  {
+    stale_days: z.number().optional().describe("Days before a node is considered stale (default 90)"),
+  },
+  async ({ stale_days }) => {
+    const report = await api.cleaning.getHealthReport(stale_days ?? 90);
+    return {
+      content: [{ type: "text" as const, text: JSON.stringify(report, null, 2) }],
+    };
+  }
+);
+
+server.tool(
+  "validate_edges",
+  "Validate edge integrity — detect self-loops, duplicates, low-relevance connections, contradictions, and rare types",
+  {
+    low_relevance_threshold: z.number().optional().describe("Similarity threshold for low-relevance detection (default 0.3)"),
+    rare_type_threshold: z.number().optional().describe("Flag relationship types used this many times or fewer (default 1)"),
+  },
+  async ({ low_relevance_threshold, rare_type_threshold }) => {
+    const report = await api.cleaning.validate({
+      lowRelevanceThreshold: low_relevance_threshold,
+      rareTypeThreshold: rare_type_threshold,
+    });
+    return {
+      content: [{ type: "text" as const, text: JSON.stringify(report, null, 2) }],
+    };
+  }
+);
+
+server.tool(
+  "find_orphans",
+  "Find nodes with no connections to other nodes",
+  {},
+  async () => {
+    const orphans = await api.cleaning.findOrphans();
+    return {
+      content: [{ type: "text" as const, text: JSON.stringify(orphans, null, 2) }],
+    };
+  }
+);
+
+server.tool(
+  "find_duplicates",
+  "Find near-duplicate node pairs by embedding cosine similarity",
+  {
+    threshold: z.number().optional().describe("Minimum cosine similarity 0-1 (default 0.95)"),
+    limit: z.number().optional().describe("Max pairs to return (default 50)"),
+  },
+  async ({ threshold, limit }) => {
+    const duplicates = await api.cleaning.findDuplicates(threshold ?? 0.95, limit ?? 50);
+    return {
+      content: [{ type: "text" as const, text: JSON.stringify(duplicates, null, 2) }],
+    };
+  }
+);
+
+server.tool(
+  "find_islands",
+  "Detect disconnected clusters (connected components) in the graph, optionally with bridge suggestions",
+  {
+    bridges: z.boolean().optional().describe("Include suggested links to bridge islands"),
+    max_bridges: z.number().optional().describe("Max bridge suggestions (default 10)"),
+  },
+  async ({ bridges, max_bridges }) => {
+    const result = await api.cleaning.findIslands({
+      bridges,
+      maxBridges: max_bridges,
+    });
+    return {
+      content: [{ type: "text" as const, text: JSON.stringify(result, null, 2) }],
+    };
+  }
+);
+
+server.tool(
+  "suggest_links",
+  "Suggest missing links between semantically similar but unconnected nodes",
+  {
+    node_id: z.string().optional().describe("Node UUID to suggest links for (omit for global scan)"),
+    min_similarity: z.number().optional().describe("Minimum cosine similarity (default 0.8 global, 0.7 per-node)"),
+    limit: z.number().optional().describe("Max suggestions (default 10 per-node, 20 global)"),
+  },
+  async ({ node_id, min_similarity, limit }) => {
+    const suggestions = await api.cleaning.suggestLinks({
+      nodeId: node_id,
+      minSimilarity: min_similarity,
+      limit,
+    });
+    return {
+      content: [{ type: "text" as const, text: JSON.stringify(suggestions, null, 2) }],
+    };
+  }
+);
+
+server.tool(
+  "analyze_relationship_types",
+  "Analyze relationship type vocabulary and suggest merges for semantically similar types",
+  {
+    min_similarity: z.number().optional().describe("Minimum similarity to suggest merge (default 0.7)"),
+  },
+  async ({ min_similarity }) => {
+    const report = await api.cleaning.analyzeRelationshipTypes({
+      minSimilarity: min_similarity,
+    });
+    return {
+      content: [{ type: "text" as const, text: JSON.stringify(report, null, 2) }],
+    };
+  }
+);
+
+server.tool(
+  "retype_edges",
+  "Rename all edges of one relationship type to another",
+  {
+    from_type: z.string().describe("Current relationship type to rename"),
+    to_type: z.string().describe("New relationship type name"),
+  },
+  async ({ from_type, to_type }) => {
+    const result = await api.cleaning.retypeMany(from_type, to_type);
+    return {
+      content: [{ type: "text" as const, text: JSON.stringify({ renamed: result.count, from: from_type, to: to_type }, null, 2) }],
+    };
+  }
+);
+
+// ── PII Tools ─────────────────────────────────────────────────────────────
+
+server.tool(
+  "get_pii_config",
+  "Get the current PII detection/encryption policy for this organization",
+  {},
+  async () => {
+    const config = await api.pii.getConfig();
+    if (!config) {
+      return {
+        content: [{ type: "text" as const, text: JSON.stringify({ configured: false }, null, 2) }],
+      };
+    }
+    return {
+      content: [{ type: "text" as const, text: JSON.stringify(config, null, 2) }],
+    };
+  }
+);
+
+server.tool(
+  "test_pii",
+  "Test a text string for PII detection — returns matches with types and positions",
+  {
+    text: z.string().describe("Text to scan for PII"),
+  },
+  async ({ text }) => {
+    const result = await api.pii.test(text);
+    return {
+      content: [{ type: "text" as const, text: JSON.stringify(result, null, 2) }],
+    };
+  }
+);
+
+// ── Maintenance Tools ─────────────────────────────────────────────────────
+
+server.tool(
+  "re_embed",
+  "Re-generate embeddings for nodes (useful after changing embedding provider/model)",
+  {
+    type: z.string().optional().describe("Only re-embed nodes of this type"),
+    limit: z.number().optional().describe("Limit to N nodes"),
+    dry_run: z.boolean().optional().describe("Show what would be re-embedded without making changes"),
+  },
+  async ({ type, limit, dry_run }) => {
+    const result = await api.reEmbed({
+      type,
+      limit,
+      dryRun: dry_run ?? false,
+    });
+    return {
+      content: [{ type: "text" as const, text: JSON.stringify(result, null, 2) }],
+    };
+  }
+);
+
 // ── Start Server ───────────────────────────────────────────────────────────
 
 async function main() {