@mcp-graph-workflow/mcp-graph 5.4.0 → 5.5.1

package/dist/mcp/init-project.js

@@ -2,12 +2,14 @@ import { writeFileSync, existsSync, readFileSync, mkdirSync } from "node:fs";
 import path from "node:path";
 import { SqliteStore } from "../core/store/sqlite-store.js";
 import { logger } from "../core/utils/logger.js";
+import { GraphNotInitializedError } from "../core/utils/errors.js";
 import { buildMcpServersConfig } from "../core/integrations/mcp-servers-config.js";
 import { installAllMcpDeps } from "../core/integrations/mcp-deps-installer.js";
 import { generateClaudeMdSection, generateCopilotInstructions, applySection } from "../core/config/ai-memory-generator.js";
 import { STORE_DIR } from "../core/utils/constants.js";
 const MCP_CONFIG_FILE = ".mcp.json";
 const GITIGNORE_ENTRY = "workflow-graph/";
+// --- Internal helpers ---
 function _resolveCommand() {
     // Check if running via npx/global — use package name
     // Check if running from node_modules — use relative path
@@ -24,10 +26,11 @@ function _resolveArgs() {
     }
     return ["-y", "mcp-graph"];
 }
-function writeMcpJson(projectDir) {
+function writeMcpJson(projectDir, dryRun) {
     const mcpConfigPath = path.join(projectDir, MCP_CONFIG_FILE);
     let existing = {};
-    if (existsSync(mcpConfigPath)) {
+    const fileExists = existsSync(mcpConfigPath);
+    if (fileExists) {
         try {
             existing = JSON.parse(readFileSync(mcpConfigPath, "utf-8"));
         }
@@ -36,15 +39,29 @@ function writeMcpJson(projectDir) {
         }
     }
     const config = buildMcpServersConfig(existing);
-    writeFileSync(mcpConfigPath, JSON.stringify(config, null, 2) + "\n", "utf-8");
-    logger.info(`${MCP_CONFIG_FILE} configured with all MCP servers`, { path: mcpConfigPath });
+    const newContent = JSON.stringify(config, null, 2) + "\n";
+    if (fileExists) {
+        const currentContent = readFileSync(mcpConfigPath, "utf-8");
+        if (currentContent === newContent) {
+            return { step: "mcp-json", status: "up-to-date", message: ".mcp.json up-to-date" };
+        }
+    }
+    if (!dryRun) {
+        writeFileSync(mcpConfigPath, newContent, "utf-8");
+        logger.info(`${MCP_CONFIG_FILE} configured with all MCP servers`, { path: mcpConfigPath });
+    }
+    return {
+        step: "mcp-json",
+        status: fileExists ? "updated" : "created",
+        message: fileExists ? ".mcp.json updated" : ".mcp.json created",
+    };
 }
-function writeVscodeMcpJson(projectDir) {
+function writeVscodeMcpJson(projectDir, dryRun) {
     const vscodeDir = path.join(projectDir, ".vscode");
-    mkdirSync(vscodeDir, { recursive: true });
     const vscodeMcpPath = path.join(vscodeDir, "mcp.json");
     let existing = {};
-    if (existsSync(vscodeMcpPath)) {
+    const fileExists = existsSync(vscodeMcpPath);
+    if (fileExists) {
         try {
             existing = JSON.parse(readFileSync(vscodeMcpPath, "utf-8"));
         }
@@ -59,59 +76,146 @@ function writeVscodeMcpJson(projectDir) {
         servers[name] = { type: "stdio", command: entry.command, args: entry.args };
     }
     const config = { ...existing, servers };
-    writeFileSync(vscodeMcpPath, JSON.stringify(config, null, 2) + "\n", "utf-8");
-    logger.info(".vscode/mcp.json configured with all MCP servers", { path: vscodeMcpPath });
+    const newContent = JSON.stringify(config, null, 2) + "\n";
+    if (fileExists) {
+        const currentContent = readFileSync(vscodeMcpPath, "utf-8");
+        if (currentContent === newContent) {
+            return { step: "vscode-mcp", status: "up-to-date", message: ".vscode/mcp.json up-to-date" };
+        }
+    }
+    if (!dryRun) {
+        mkdirSync(vscodeDir, { recursive: true });
+        writeFileSync(vscodeMcpPath, newContent, "utf-8");
+        logger.info(".vscode/mcp.json configured with all MCP servers", { path: vscodeMcpPath });
+    }
+    return {
+        step: "vscode-mcp",
+        status: fileExists ? "updated" : "created",
+        message: fileExists ? ".vscode/mcp.json updated" : ".vscode/mcp.json created",
+    };
 }
-function ensureGitignore(projectDir) {
+function ensureGitignore(projectDir, dryRun) {
     const gitignorePath = path.join(projectDir, ".gitignore");
     if (!existsSync(gitignorePath)) {
-        writeFileSync(gitignorePath, GITIGNORE_ENTRY + "\n", "utf-8");
-        logger.info(".gitignore created", { entry: GITIGNORE_ENTRY });
-        return;
+        if (!dryRun) {
+            writeFileSync(gitignorePath, GITIGNORE_ENTRY + "\n", "utf-8");
+            logger.info(".gitignore created", { entry: GITIGNORE_ENTRY });
+        }
+        return { step: "gitignore", status: "created", message: ".gitignore created with workflow-graph/" };
     }
     const content = readFileSync(gitignorePath, "utf-8");
     if (content.includes(GITIGNORE_ENTRY)) {
-        logger.debug(".gitignore already has entry", { entry: GITIGNORE_ENTRY });
-        return;
+        return { step: "gitignore", status: "up-to-date", message: ".gitignore up-to-date" };
     }
-    const separator = content.endsWith("\n") ? "" : "\n";
-    writeFileSync(gitignorePath, content + separator + GITIGNORE_ENTRY + "\n", "utf-8");
-    logger.info(".gitignore updated", { entry: GITIGNORE_ENTRY });
-}
-function initStore(projectDir) {
-    const storeDir = path.join(projectDir, STORE_DIR);
-    mkdirSync(storeDir, { recursive: true });
-    const store = SqliteStore.open(projectDir);
-    const projectName = path.basename(projectDir);
-    store.initProject(projectName);
-    store.close();
-    logger.info("Database initialized", { dir: STORE_DIR });
+    if (!dryRun) {
+        const separator = content.endsWith("\n") ? "" : "\n";
+        writeFileSync(gitignorePath, content + separator + GITIGNORE_ENTRY + "\n", "utf-8");
+        logger.info(".gitignore updated", { entry: GITIGNORE_ENTRY });
+    }
+    return { step: "gitignore", status: "updated", message: ".gitignore updated with workflow-graph/" };
 }
-function generateAndWriteClaudeMd(projectDir) {
+function generateAndWriteClaudeMd(projectDir, dryRun) {
     const projectName = path.basename(projectDir);
     const claudeMdPath = path.join(projectDir, "CLAUDE.md");
     const section = generateClaudeMdSection(projectName);
+    const fileExists = existsSync(claudeMdPath);
     let existing = "";
-    if (existsSync(claudeMdPath)) {
+    if (fileExists) {
         existing = readFileSync(claudeMdPath, "utf-8");
     }
     const result = applySection(existing, section);
-    writeFileSync(claudeMdPath, result, "utf-8");
-    logger.info("CLAUDE.md updated with mcp-graph instructions", { path: claudeMdPath });
+    if (fileExists && existing === result) {
+        return { step: "claude-md", status: "up-to-date", message: "CLAUDE.md up-to-date" };
+    }
+    if (!dryRun) {
+        writeFileSync(claudeMdPath, result, "utf-8");
+        logger.info("CLAUDE.md updated with mcp-graph instructions", { path: claudeMdPath });
+    }
+    return {
+        step: "claude-md",
+        status: fileExists ? "updated" : "created",
+        message: fileExists ? "CLAUDE.md updated" : "CLAUDE.md created",
+    };
 }
-function generateAndWriteCopilotInstructions(projectDir) {
+function generateAndWriteCopilotInstructions(projectDir, dryRun) {
     const projectName = path.basename(projectDir);
     const githubDir = path.join(projectDir, ".github");
-    mkdirSync(githubDir, { recursive: true });
     const copilotPath = path.join(githubDir, "copilot-instructions.md");
     const section = generateCopilotInstructions(projectName);
+    const fileExists = existsSync(copilotPath);
     let existing = "";
-    if (existsSync(copilotPath)) {
+    if (fileExists) {
         existing = readFileSync(copilotPath, "utf-8");
     }
     const result = applySection(existing, section);
-    writeFileSync(copilotPath, result, "utf-8");
-    logger.info("copilot-instructions.md updated", { path: copilotPath });
+    if (fileExists && existing === result) {
+        return { step: "copilot-md", status: "up-to-date", message: "copilot-instructions.md up-to-date" };
+    }
+    if (!dryRun) {
+        mkdirSync(githubDir, { recursive: true });
+        writeFileSync(copilotPath, result, "utf-8");
+        logger.info("copilot-instructions.md updated", { path: copilotPath });
+    }
+    return {
+        step: "copilot-md",
+        status: fileExists ? "updated" : "created",
+        message: fileExists ? "copilot-instructions.md updated" : "copilot-instructions.md created",
+    };
+}
+function initStore(projectDir) {
+    const storeDir = path.join(projectDir, STORE_DIR);
+    mkdirSync(storeDir, { recursive: true });
+    const store = SqliteStore.open(projectDir);
+    const projectName = path.basename(projectDir);
+    store.initProject(projectName);
+    store.close();
+    logger.info("Database initialized", { dir: STORE_DIR });
+}
+// --- Public API ---
+export async function runUpdate(projectDir, options = {}) {
+    const dbPath = path.join(projectDir, STORE_DIR, "graph.db");
+    if (!existsSync(dbPath)) {
+        throw new GraphNotInitializedError();
+    }
+    const steps = [];
+    const shouldRun = (step) => !options.only || options.only.includes(step);
+    // 1. DB migrations
+    if (shouldRun("db")) {
+        const store = SqliteStore.open(projectDir);
+        store.close();
+        steps.push({ step: "db", status: "up-to-date", message: "Database migrations applied" });
+    }
+    // 2. Config files
+    if (shouldRun("mcp-json"))
+        steps.push(writeMcpJson(projectDir, options.dryRun));
+    if (shouldRun("vscode-mcp"))
+        steps.push(writeVscodeMcpJson(projectDir, options.dryRun));
+    if (shouldRun("gitignore"))
+        steps.push(ensureGitignore(projectDir, options.dryRun));
+    // 3. MCP dependencies
+    if (shouldRun("deps")) {
+        const depResults = await installAllMcpDeps(projectDir);
+        const ready = depResults.filter((r) => r.status === "installed" || r.status === "already_available");
+        steps.push({
+            step: "deps",
+            status: "up-to-date",
+            message: `MCP dependencies: ${ready.length}/${depResults.length} ready`,
+        });
+    }
+    // 4. AI instruction files
+    if (shouldRun("claude-md"))
+        steps.push(generateAndWriteClaudeMd(projectDir, options.dryRun));
+    if (shouldRun("copilot-md"))
+        steps.push(generateAndWriteCopilotInstructions(projectDir, options.dryRun));
+    const report = {
+        steps,
+        hasChanges: steps.some((s) => s.status === "updated" || s.status === "created"),
+    };
+    logger.info("mcp-graph update complete", {
+        updated: steps.filter((s) => s.status === "updated").length,
+        upToDate: steps.filter((s) => s.status === "up-to-date").length,
+    });
+    return report;
 }
 export async function runInit(projectDir) {
     logger.info("mcp-graph init", { dir: projectDir });

package/dist/mcp/init-project.js.map

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package/dist/mcp/server.js

@@ -28,24 +28,26 @@ const app = createApp({
 // ── Code Graph auto-index ────────────────────────────────
 if (config.integrations.codeGraphAutoIndex) {
     const basePath = storeManager.basePath;
-    try {
-        const project = storeManager.store.getProject();
-        if (project) {
-            const codeStore = new CodeStore(storeManager.store.getDb());
-            const indexer = new CodeIndexer(codeStore, project.id);
-            const result = indexer.indexDirectory(basePath, basePath);
-            logger.info("Code graph auto-indexed", {
-                files: result.fileCount,
-                symbols: result.symbolCount,
-                relations: result.relationCount,
+    (async () => {
+        try {
+            const project = storeManager.store.getProject();
+            if (project) {
+                const codeStore = new CodeStore(storeManager.store.getDb());
+                const indexer = new CodeIndexer(codeStore, project.id);
+                const result = await indexer.indexDirectory(basePath, basePath);
+                logger.info("Code graph auto-indexed", {
+                    files: result.fileCount,
+                    symbols: result.symbolCount,
+                    relations: result.relationCount,
+                });
+            }
+        }
+        catch (err) {
+            logger.warn("Code graph auto-index failed (non-blocking)", {
+                error: err instanceof Error ? err.message : String(err),
             });
         }
-    }
-    catch (err) {
-        logger.warn("Code graph auto-index failed (non-blocking)", {
-            error: err instanceof Error ? err.message : String(err),
-        });
-    }
+    })();
 }
 // ── Cleanup on shutdown ──────────────────────────────────
 function cleanup(signal) {

package/dist/mcp/server.js.map

@@ -1 +1 @@
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+{"version":3,"file":"server.js","sourceRoot":"","sources":["../../src/mcp/server.ts"],"names":[],"mappings":";AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACpE,OAAO,EAAE,gBAAgB,EAAE,MAAM,kBAAkB,CAAC;AACpD,OAAO,EAAE,aAAa,EAAE,MAAM,6BAA6B,CAAC;AAC5D,OAAO,EAAE,MAAM,EAAE,MAAM,yBAAyB,CAAC;AACjD,OAAO,EAAE,UAAU,EAAE,MAAM,iCAAiC,CAAC;AAC7D,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,YAAY,EAAE,MAAM,gCAAgC,CAAC;AAC9D,OAAO,EAAE,SAAS,EAAE,MAAM,4BAA4B,CAAC;AACvD,OAAO,EAAE,WAAW,EAAE,MAAM,8BAA8B,CAAC;AAE3D,MAAM,MAAM,GAAG,UAAU,EAAE,CAAC;AAC5B,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC;AAEzB,4DAA4D;AAC5D,MAAM,YAAY,GAAG,YAAY,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC;AACxD,MAAM,QAAQ,GAAG,IAAI,aAAa,EAAE,CAAC;AACrC,YAAY,CAAC,KAAK,CAAC,QAAQ,GAAG,QAAQ,CAAC;AAEvC,4DAA4D;AAC5D,MAAM,GAAG,GAAG,IAAI,SAAS,CACvB,EAAE,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,OAAO,EAAE,EACvC,EAAE,YAAY,EAAE,EAAE,KAAK,EAAE,EAAE,EAAE,EAAE,CAChC,CAAC;AAEF,gBAAgB,CAAC,GAAG,EAAE,YAAY,CAAC,KAAK,CAAC,CAAC;AAE1C,4DAA4D;AAC5D,MAAM,GAAG,GAAG,SAAS,CAAC;IACpB,KAAK,EAAE,YAAY,CAAC,KAAK;IACzB,QAAQ,EAAE,YAAY,CAAC,QAAQ;IAC/B,QAAQ;IACR,GAAG;IACH,YAAY;CACb,CAAC,CAAC;AAEH,4DAA4D;AAC5D,IAAI,MAAM,CAAC,YAAY,CAAC,kBAAkB,EAAE,CAAC;IAC3C,MAAM,QAAQ,GAAG,YAAY,CAAC,QAAQ,CAAC;IACvC,CAAC,KAAK,IAAI,EAAE;QACV,IAAI,CAAC;YACH,MAAM,OAAO,GAAG,YAAY,CAAC,KAAK,CAAC,UAAU,EAAE,CAAC;YAChD,IAAI,OAAO,EAAE,CAAC;gBACZ,MAAM,SAAS,GAAG,IAAI,SAAS,CAAC,YAAY,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;gBAC5D,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,SAAS,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC;gBACvD,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,cAAc,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;gBAChE,MAAM,CAAC,IAAI,CAAC,yBAAyB,EAAE;oBACrC,KAAK,EAAE,MAAM,CAAC,SAAS;oBACvB,OAAO,EAAE,MAAM,CAAC,WAAW;oBAC3B,SAAS,EAAE,MAAM,CAAC,aAAa;iBAChC,CAAC,CAAC;YACL,CAAC;QACH,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,MAAM,CAAC,IAAI,CAAC,6CAA6C,EAAE;gBACzD,KAAK,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;aACxD,CAAC,CAAC;QACL,CAAC;IACH,CAAC,CAAC,EAAE,CAAC;AACP,CAAC;AAED,4DAA4D;AAC5D,SAAS,OAAO,CAAC,MAAc;IAC7B,MAAM,CAAC,IAAI,CAAC,iBAAiB,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;IAC3C,YAAY,CAAC,KAAK,EAAE,CAAC;IACrB,MAAM,CAAC,IAAI,CAAC,oBAAoB,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;IAC9C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC;AACD,OAAO,CAAC,EAAE,CAAC,SAAS,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC;AAChD,OAAO,CAAC,EAAE,CAAC,QAAQ,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC;AAC9C,OAAO,CAAC,EAAE,CAAC,QAAQ,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC;AAE9C,GAAG,CAAC,MAAM,CAAC,IAAI,EAAE,GAAG,EAAE;IACpB,MAAM,CAAC,IAAI,CAAC,kDAAkD,IAAI,MAAM,CAAC,CAAC;AAC5E,CAAC,CAAC,CAAC"}

package/dist/mcp/tools/add-node.d.ts

@@ -1,3 +1,6 @@
+/**
+ * @deprecated Use `node` tool with action:"add" instead. Will be removed in v7.0.
+ */
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import type { SqliteStore } from "../../core/store/sqlite-store.js";
 export declare function registerAddNode(server: McpServer, store: SqliteStore): void;

package/dist/mcp/tools/add-node.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"add-node.d.ts","sourceRoot":"","sources":["../../../src/mcp/tools/add-node.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACzE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kCAAkC,CAAC;AAQpE,wBAAgB,eAAe,CAAC,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,WAAW,GAAG,IAAI,CAoF3E"}
+{"version":3,"file":"add-node.d.ts","sourceRoot":"","sources":["../../../src/mcp/tools/add-node.ts"],"names":[],"mappings":"AAAA;;GAEG;AAGH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACzE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kCAAkC,CAAC;AAQpE,wBAAgB,eAAe,CAAC,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,WAAW,GAAG,IAAI,CAqF3E"}

package/dist/mcp/tools/add-node.js

@@ -1,3 +1,6 @@
+/**
+ * @deprecated Use `node` tool with action:"add" instead. Will be removed in v7.0.
+ */
 import { z } from "zod/v4";
 import { NodeTypeSchema, NodeStatusSchema, XpSizeSchema, PrioritySchema } from "../../schemas/node.schema.js";
 import { NodeNotFoundError } from "../../core/utils/errors.js";
@@ -5,7 +8,7 @@ import { generateId } from "../../core/utils/id.js";
 import { now } from "../../core/utils/time.js";
 import { logger } from "../../core/utils/logger.js";
 export function registerAddNode(server, store) {
-    server.tool("add_node", "Create a single node in the graph", {
+    server.tool("add_node", "Create a single node in the graph (DEPRECATED — use `node` with action:\"add\")", {
         type: NodeTypeSchema.describe("Node type (epic, task, subtask, etc.)"),
         title: z.string().describe("Node title"),
         description: z.string().optional().describe("Node description"),
@@ -20,6 +23,7 @@ export function registerAddNode(server, store) {
         blocked: z.boolean().optional().describe("Whether the node is blocked"),
         metadata: z.record(z.string(), z.unknown()).optional().describe("Custom metadata"),
     }, async (args) => {
+        logger.warn("tool:add_node:deprecated", { message: "Use 'node' tool with action:'add' instead" });
         logger.debug("tool:add_node", { type: args.type, title: args.title, parentId: args.parentId });
         if (args.parentId) {
             const parent = store.getNodeById(args.parentId);
@@ -27,7 +31,7 @@ export function registerAddNode(server, store) {
                 const err = new NodeNotFoundError(args.parentId);
                 return {
                     content: [
-                        { type: "text", text: JSON.stringify({ error: `Parent not found: ${err.message}` }) },
+                        { type: "text", text: JSON.stringify({ error: `Parent not found: ${err.message}`, _deprecated: "Use 'node' tool with action:'add'" }) },
                     ],
                     isError: true,
                 };
@@ -74,7 +78,7 @@ export function registerAddNode(server, store) {
             content: [
                 {
                     type: "text",
-                    text: JSON.stringify({ ok: true, node }, null, 2),
+                    text: JSON.stringify({ ok: true, node, _deprecated: "Use 'node' tool with action:'add'" }, null, 2),
                 },
             ],
         };

package/dist/mcp/tools/add-node.js.map

@@ -1 +1 @@
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+{"version":3,"file":"add-node.js","sourceRoot":"","sources":["../../../src/mcp/tools/add-node.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,QAAQ,CAAC;AAI3B,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAC9G,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EAAE,UAAU,EAAE,MAAM,wBAAwB,CAAC;AACpD,OAAO,EAAE,GAAG,EAAE,MAAM,0BAA0B,CAAC;AAC/C,OAAO,EAAE,MAAM,EAAE,MAAM,4BAA4B,CAAC;AAEpD,MAAM,UAAU,eAAe,CAAC,MAAiB,EAAE,KAAkB;IACnE,MAAM,CAAC,IAAI,CACT,UAAU,EACV,iFAAiF,EACjF;QACE,IAAI,EAAE,cAAc,CAAC,QAAQ,CAAC,uCAAuC,CAAC;QACtE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC;QACxC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QAC/D,MAAM,EAAE,gBAAgB,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;QAC9E,QAAQ,EAAE,cAAc,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;QACzE,MAAM,EAAE,YAAY,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QACjE,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;QAC3E,IAAI,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;QACxE,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;QACrE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;QACtE,kBAAkB,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qBAAqB,CAAC;QAClF,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;QACvE,QAAQ,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;KACnF,EACD,KAAK,EAAE,IAAI,EAAE,EAAE;QACb,MAAM,CAAC,IAAI,CAAC,0BAA0B,EAAE,EAAE,OAAO,EAAE,2CAA2C,EAAE,CAAC,CAAC;QAClG,MAAM,CAAC,KAAK,CAAC,eAAe,EAAE,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;QAC/F,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,MAAM,MAAM,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;YAChD,IAAI,CAAC,MAAM,EAAE,CAAC;gBACZ,MAAM,GAAG,GAAG,IAAI,iBAAiB,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;gBACjD,OAAO;oBACL,OAAO,EAAE;wBACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,qBAAqB,GAAG,CAAC,OAAO,EAAE,EAAE,WAAW,EAAE,mCAAmC,EAAE,CAAC,EAAE;qBACjJ;oBACD,OAAO,EAAE,IAAI;iBACd,CAAC;YACJ,CAAC;QACH,CAAC;QAED,MAAM,SAAS,GAAG,GAAG,EAAE,CAAC;QACxB,MAAM,IAAI,GAAG;YACX,EAAE,EAAE,UAAU,CAAC,MAAM,CAAC;YACtB,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,KAAK,EAAE,IAAI,CAAC,KAAK;YACjB,WAAW,EAAE,IAAI,CAAC,WAAW;YAC7B,MAAM,EAAE,IAAI,CAAC,MAAM,IAAI,SAAkB;YACzC,QAAQ,EAAE,IAAI,CAAC,QAAQ,IAAK,CAAW;YACvC,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,eAAe,EAAE,IAAI,CAAC,eAAe;YACrC,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,QAAQ,EAAE,IAAI,CAAC,QAAQ;YACvB,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,kBAAkB,EAAE,IAAI,CAAC,kBAAkB;YAC3C,OAAO,EAAE,IAAI,CAAC,OAAO;YACrB,QAAQ,EAAE,IAAI,CAAC,QAAQ;YACvB,SAAS,EAAE,SAAS;YACpB,SAAS,EAAE,SAAS;SACrB,CAAC;QAEF,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC;QAEvB,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,KAAK,CAAC,UAAU,CAAC;gBACf,EAAE,EAAE,UAAU,CAAC,MAAM,CAAC;gBACtB,IAAI,EAAE,IAAI,CAAC,QAAQ;gBACnB,EAAE,EAAE,IAAI,CAAC,EAAE;gBACX,YAAY,EAAE,WAA2B;gBACzC,SAAS,EAAE,SAAS;aACrB,CAAC,CAAC;YACH,KAAK,CAAC,UAAU,CAAC;gBACf,EAAE,EAAE,UAAU,CAAC,MAAM,CAAC;gBACtB,IAAI,EAAE,IAAI,CAAC,EAAE;gBACb,EAAE,EAAE,IAAI,CAAC,QAAQ;gBACjB,YAAY,EAAE,UAA0B;gBACxC,SAAS,EAAE,SAAS;aACrB,CAAC,CAAC;QACL,CAAC;QAED,MAAM,CAAC,IAAI,CAAC,kBAAkB,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC;QACtE,OAAO;YACL,OAAO,EAAE;gBACP;oBACE,IAAI,EAAE,MAAe;oBACrB,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,mCAAmC,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC;iBACpG;aACF;SACF,CAAC;IACJ,CAAC,CACF,CAAC;AACJ,CAAC"}

package/dist/mcp/tools/delete-node.d.ts

@@ -1,3 +1,6 @@
+/**
+ * @deprecated Use `node` tool with action:"delete" instead. Will be removed in v7.0.
+ */
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import type { SqliteStore } from "../../core/store/sqlite-store.js";
 export declare function registerDeleteNode(server: McpServer, store: SqliteStore): void;

package/dist/mcp/tools/delete-node.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"delete-node.d.ts","sourceRoot":"","sources":["../../../src/mcp/tools/delete-node.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACzE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kCAAkC,CAAC;AAIpE,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,WAAW,GAAG,IAAI,CA+B9E"}
+{"version":3,"file":"delete-node.d.ts","sourceRoot":"","sources":["../../../src/mcp/tools/delete-node.ts"],"names":[],"mappings":"AAAA;;GAEG;AAGH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACzE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kCAAkC,CAAC;AAIpE,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,WAAW,GAAG,IAAI,CAgC9E"}

package/dist/mcp/tools/delete-node.js

@@ -1,8 +1,12 @@
+/**
+ * @deprecated Use `node` tool with action:"delete" instead. Will be removed in v7.0.
+ */
 import { z } from "zod/v4";
 import { NodeNotFoundError } from "../../core/utils/errors.js";
 import { logger } from "../../core/utils/logger.js";
 export function registerDeleteNode(server, store) {
-    server.tool("delete_node", "Delete a node and all its associated edges from the graph", { id: z.string().describe("The node ID to delete") }, async ({ id }) => {
+    server.tool("delete_node", "Delete a node and all its associated edges (DEPRECATED — use `node` with action:\"delete\")", { id: z.string().describe("The node ID to delete") }, async ({ id }) => {
+        logger.warn("tool:delete_node:deprecated", { message: "Use 'node' tool with action:'delete' instead" });
         logger.debug("tool:delete_node", { id });
         const deleted = store.deleteNode(id);
         if (!deleted) {
@@ -10,7 +14,7 @@ export function registerDeleteNode(server, store) {
             logger.warn("tool:delete_node:fail", { error: err.message });
             return {
                 content: [
-                    { type: "text", text: JSON.stringify({ error: err.message }) },
+                    { type: "text", text: JSON.stringify({ error: err.message, _deprecated: "Use 'node' tool with action:'delete'" }) },
                 ],
                 isError: true,
             };
@@ -20,7 +24,7 @@ export function registerDeleteNode(server, store) {
             content: [
                 {
                     type: "text",
-                    text: JSON.stringify({ ok: true, deletedId: id }, null, 2),
+                    text: JSON.stringify({ ok: true, deletedId: id, _deprecated: "Use 'node' tool with action:'delete'" }, null, 2),
                 },
             ],
         };

package/dist/mcp/tools/delete-node.js.map

@@ -1 +1 @@
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package/dist/mcp/tools/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/mcp/tools/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACzE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kCAAkC,CAAC;AA+BpE,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,WAAW,GAAG,IAAI,CAgC5E"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/mcp/tools/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACzE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kCAAkC,CAAC;AAmCpE,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,WAAW,GAAG,IAAI,CAuC5E"}

package/dist/mcp/tools/index.js

@@ -6,28 +6,33 @@ import { registerNext } from "./next.js";
 import { registerUpdateStatus } from "./update-status.js";
 import { registerMetrics } from "./metrics.js";
 import { registerContext } from "./context.js";
-import { registerUpdateNode } from "./update-node.js";
-import { registerDeleteNode } from "./delete-node.js";
 import { registerSearch } from "./search.js";
 import { registerRagContext } from "./rag-context.js";
 import { registerAnalyze } from "./analyze.js";
 import { registerEdge } from "./edge.js";
 import { registerSnapshot } from "./snapshot.js";
-import { registerAddNode } from "./add-node.js";
 import { registerExport } from "./export.js";
 import { registerMoveNode } from "./move-node.js";
 import { registerCloneNode } from "./clone-node.js";
 import { registerReindexKnowledge } from "./reindex-knowledge.js";
 import { registerSyncStackDocs } from "./sync-stack-docs.js";
-import { registerValidateTask } from "./validate-task.js";
-import { registerValidateAc } from "./validate-ac.js";
 import { registerPlanSprint } from "./plan-sprint.js";
 import { registerSetPhase } from "./set-phase.js";
 import { registerMemory } from "./memory.js";
-import { registerListSkills } from "./list-skills.js";
 import { registerManageSkill } from "./manage-skill.js";
+// Consolidated tools
+import { registerNode } from "./node.js";
+import { registerValidate } from "./validate.js";
+// Deprecated tools (backward compat — will be removed in v7.0)
+import { registerAddNode } from "./add-node.js";
+import { registerUpdateNode } from "./update-node.js";
+import { registerDeleteNode } from "./delete-node.js";
+import { registerValidateTask } from "./validate-task.js";
+import { registerValidateAc } from "./validate-ac.js";
+import { registerListSkills } from "./list-skills.js";
 import { wrapToolsWithLifecycle } from "../lifecycle-wrapper.js";
 export function registerAllTools(server, store) {
+    // Core tools
     registerInit(server, store);
     registerImportPrd(server, store);
     registerList(server, store);
@@ -36,26 +41,30 @@ export function registerAllTools(server, store) {
     registerUpdateStatus(server, store);
     registerMetrics(server, store);
     registerContext(server, store);
-    registerUpdateNode(server, store);
-    registerDeleteNode(server, store);
     registerSearch(server, store);
     registerRagContext(server, store);
     registerAnalyze(server, store);
     registerEdge(server, store);
     registerSnapshot(server, store);
-    registerAddNode(server, store);
     registerExport(server, store);
     registerMoveNode(server, store);
     registerCloneNode(server, store);
     registerReindexKnowledge(server, store);
     registerSyncStackDocs(server, store);
-    registerValidateTask(server, store);
-    registerValidateAc(server, store);
     registerPlanSprint(server, store);
     registerSetPhase(server, store);
     registerMemory(server, store);
-    registerListSkills(server);
     registerManageSkill(server, store);
+    // Consolidated tools
+    registerNode(server, store);
+    registerValidate(server, store);
+    // Deprecated tools (backward compat — will be removed in v7.0)
+    registerAddNode(server, store);
+    registerUpdateNode(server, store);
+    registerDeleteNode(server, store);
+    registerValidateTask(server, store);
+    registerValidateAc(server, store);
+    registerListSkills(server);
     // Wrap all registered tool responses with lifecycle context
     wrapToolsWithLifecycle(server, store);
 }

package/dist/mcp/tools/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/mcp/tools/index.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,YAAY,EAAE,MAAM,WAAW,CAAC;AACzC,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAAE,YAAY,EAAE,MAAM,WAAW,CAAC;AACzC,OAAO,EAAE,YAAY,EAAE,MAAM,WAAW,CAAC;AACzC,OAAO,EAAE,YAAY,EAAE,MAAM,WAAW,CAAC;AACzC,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAC;AAC1D,OAAO,EAAE,eAAe,EAAE,MAAM,cAAc,CAAC;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,cAAc,CAAC;AAC/C,OAAO,EAAE,cAAc,EAAE,MAAM,aAAa,CAAC;AAC7C,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AACtD,OAAO,EAAE,eAAe,EAAE,MAAM,cAAc,CAAC;AAC/C,OAAO,EAAE,YAAY,EAAE,MAAM,WAAW,CAAC;AACzC,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,aAAa,CAAC;AAC7C,OAAO,EAAE,gBAAgB,EAAE,MAAM,gBAAgB,CAAC;AAClD,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAAE,wBAAwB,EAAE,MAAM,wBAAwB,CAAC;AAClE,OAAO,EAAE,qBAAqB,EAAE,MAAM,sBAAsB,CAAC;AAC7D,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AACtD,OAAO,EAAE,gBAAgB,EAAE,MAAM,gBAAgB,CAAC;AAClD,OAAO,EAAE,cAAc,EAAE,MAAM,aAAa,CAAC;AAC7C,OAAO,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AACxD,qBAAqB;AACrB,OAAO,EAAE,YAAY,EAAE,MAAM,WAAW,CAAC;AACzC,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AACjD,+DAA+D;AAC/D,OAAO,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAChD,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AACtD,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AACtD,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAC;AAC1D,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AACtD,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAC;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,yBAAyB,CAAC;AAEjE,MAAM,UAAU,gBAAgB,CAAC,MAAiB,EAAE,KAAkB;IACpE,aAAa;IACb,YAAY,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC5B,iBAAiB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IACjC,YAAY,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC5B,YAAY,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC5B,YAAY,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC5B,oBAAoB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IACpC,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC/B,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC/B,cAAc,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC9B,kBAAkB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAClC,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC/B,YAAY,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC5B,gBAAgB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAChC,cAAc,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC9B,gBAAgB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAChC,iBAAiB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IACjC,wBAAwB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IACxC,qBAAqB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IACrC,kBAAkB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAClC,gBAAgB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAChC,cAAc,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC9B,mBAAmB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAEnC,qBAAqB;IACrB,YAAY,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC5B,gBAAgB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAEhC,+DAA+D;IAC/D,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAC/B,kBAAkB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAClC,kBAAkB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAClC,oBAAoB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IACpC,kBAAkB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAClC,kBAAkB,CAAC,MAAM,CAAC,CAAC;IAE3B,4DAA4D;IAC5D,sBAAsB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;AACxC,CAAC"}

package/dist/mcp/tools/list-skills.d.ts

@@ -1,6 +1,5 @@
 /**
- * MCP Tool — list_skills
- * Lists built-in skills with optional phase filter.
+ * @deprecated Use `manage_skill` tool with action:"list" instead. Will be removed in v7.0.
  */
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 export declare function registerListSkills(server: McpServer): void;

package/dist/mcp/tools/list-skills.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"list-skills.d.ts","sourceRoot":"","sources":["../../../src/mcp/tools/list-skills.ts"],"names":[],"mappings":"AAAA;;GAEG;AAGH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAKzE,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAwE1D"}