@mcp-graph-workflow/mcp-graph 5.0.4 → 5.1.0

package/README.md

@@ -77,7 +77,8 @@ npm run dev        # HTTP + dashboard at localhost:3000
 - **Semantic Search + RAG** — Full-text BM25 search + TF-IDF embeddings, 100% local
 - **Sprint Planning** — Velocity metrics, capacity-based planning, risk assessment
 - **Web Dashboard** — Interactive graph visualization, backlog tracking, code intelligence, insights
-- **Multi-Agent Mesh** — Serena + GitNexus + Context7 + Playwright coordinated via event bus
+- **Multi-Agent Mesh** — Serena + GitNexus + Context7 + Playwright coordinated via event bus, with phase-aware MCP suggestions
+- **Environment Doctor** — `mcp-graph doctor` validates Node.js, SQLite, permissions, integrations, and suggests fixes
 - **Local-First** — SQLite persistence, zero external dependencies, cross-platform
 
 ## Who is this for?
@@ -115,7 +116,7 @@ mcp-graph serve --port 3000    # or: npm run dev
 |---|---|---|
 | **MCP Tools** | 26 | [MCP-TOOLS-REFERENCE.md](docs/MCP-TOOLS-REFERENCE.md) |
 | **REST Endpoints** | 44 (17 routers) | [REST-API-REFERENCE.md](docs/REST-API-REFERENCE.md) |
-| **CLI Commands** | 5 | `init`, `import`, `index`, `stats`, `serve` |
+| **CLI Commands** | 6 | `init`, `import`, `index`, `stats`, `serve`, `doctor` |
 
 ## Integrations
 
@@ -149,6 +150,7 @@ npm run test:all    # Everything
 | [Knowledge Pipeline](docs/KNOWLEDGE-PIPELINE.md) | RAG, embeddings, context assembly |
 | [Integrations](docs/INTEGRATIONS-GUIDE.md) | Serena, GitNexus, Context7, Playwright |
 | [Test Guide](docs/TEST-GUIDE.md) | Test pyramid and best practices |
+| [PRD Writing Guide](docs/PRD-WRITING-GUIDE.md) | How to write PRDs that import correctly |
 | [Lifecycle](docs/LIFECYCLE.md) | 8-phase dev methodology |
 
 ## Support the Project

package/dist/api/routes/benchmark.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"benchmark.d.ts","sourceRoot":"","sources":["../../../src/api/routes/benchmark.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,SAAS,CAAC;AACjC,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,mCAAmC,CAAC;AAIlE,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,QAAQ,GAAG,MAAM,CA+FhE"}

package/dist/api/routes/benchmark.js

@@ -1,6 +1,5 @@
 import { Router } from "express";
 import { buildTaskContext } from "../../core/context/compact-context.js";
-import { estimateTokens } from "../../core/context/token-estimator.js";
 import { detectCycles } from "../../core/planner/dependency-chain.js";
 export function createBenchmarkRouter(storeRef) {
     const router = Router();
@@ -19,7 +18,7 @@ export function createBenchmarkRouter(storeRef) {
                 const ctx = buildTaskContext(store, node.id);
                 if (!ctx)
                     continue;
-                const rawTokens = estimateTokens(String(ctx.metrics.originalChars));
+                const rawTokens = Math.ceil(ctx.metrics.originalChars / 4);
                 perTaskMetrics.push({
                     id: node.id,
                     title: node.title,

package/dist/api/routes/benchmark.js.map

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package/dist/cli/commands/doctor.d.ts

@@ -0,0 +1,3 @@
+import { Command } from "commander";
+export declare function doctorCommand(): Command;
+//# sourceMappingURL=doctor.d.ts.map

package/dist/cli/commands/doctor.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/commands/doctor.js

@@ -0,0 +1,55 @@
+import { Command } from "commander";
+import { runDoctor } from "../../core/doctor/doctor-runner.js";
+import { logger } from "../../core/utils/logger.js";
+function output(msg) {
+    process.stdout.write(msg + "\n");
+}
+const LEVEL_ICON = {
+    ok: "\u2713",
+    warning: "\u26A0",
+    error: "\u2717",
+};
+function formatCheck(check) {
+    const icon = LEVEL_ICON[check.level] ?? "?";
+    let line = `  ${icon} ${check.message}`;
+    if (check.suggestion) {
+        line += `\n      ${check.suggestion}`;
+    }
+    return line;
+}
+export function doctorCommand() {
+    return new Command("doctor")
+        .description("Validate the execution environment")
+        .option("-d, --dir <dir>", "Project directory", process.cwd())
+        .option("--json", "Output as JSON")
+        .action(async (opts) => {
+        try {
+            const report = await runDoctor(opts.dir);
+            if (opts.json) {
+                output(JSON.stringify(report, null, 2));
+            }
+            else {
+                output("mcp-graph doctor\n");
+                for (const check of report.checks) {
+                    output(formatCheck(check));
+                }
+                output("");
+                output(`Summary: ${report.summary.ok} ok, ${report.summary.warning} warnings, ${report.summary.error} errors`);
+                if (report.passed) {
+                    output("\nAll critical checks passed.");
+                }
+                else {
+                    output("\nSome critical checks failed. Fix errors above.");
+                }
+            }
+            if (!report.passed) {
+                process.exit(1);
+            }
+        }
+        catch (err) {
+            logger.error(`Doctor failed: ${err instanceof Error ? err.message : String(err)}`);
+            process.exit(1);
+        }
+    });
+}
+//# sourceMappingURL=doctor.js.map

package/dist/cli/commands/doctor.js.map

@@ -0,0 +1 @@
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package/dist/cli/index.js

@@ -20,6 +20,7 @@ else {
     const { statsCommand } = await import("./commands/stats.js");
     const { initCommand } = await import("./commands/init.js");
     const { indexCommand } = await import("./commands/index-cmd.js");
+    const { doctorCommand } = await import("./commands/doctor.js");
     const program = new Command();
     program
         .name("mcp-graph")
@@ -30,6 +31,7 @@ else {
     program.addCommand(statsCommand());
     program.addCommand(initCommand());
     program.addCommand(indexCommand());
+    program.addCommand(doctorCommand());
     program.parse();
 }
 //# sourceMappingURL=index.js.map

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package/dist/core/doctor/doctor-checks.d.ts

@@ -0,0 +1,43 @@
+import type { SqliteStore } from "../store/sqlite-store.js";
+import type { CheckResult } from "./doctor-types.js";
+/**
+ * Check Node.js version >= 20 using the current runtime.
+ */
+export declare function checkNodeVersion(): CheckResult;
+/**
+ * Check Node.js version >= 20 with an explicit version string (testable).
+ */
+export declare function checkNodeVersionWith(version: string): CheckResult;
+/**
+ * Check write permissions on the store directory.
+ */
+export declare function checkWritePermissions(basePath: string): Promise<CheckResult>;
+/**
+ * Check that the SQLite database exists and can be opened.
+ */
+export declare function checkSqliteDatabase(basePath: string): Promise<CheckResult>;
+/**
+ * Check database integrity via PRAGMA integrity_check.
+ */
+export declare function checkDbIntegrity(basePath: string): Promise<CheckResult>;
+/**
+ * Check if the graph project is initialized.
+ */
+export declare function checkGraphInitialized(store: SqliteStore): CheckResult;
+/**
+ * Check if the config file exists and is valid.
+ */
+export declare function checkConfigFile(basePath: string): CheckResult;
+/**
+ * Check if the dashboard build artifacts exist.
+ */
+export declare function checkDashboardBuild(basePath: string): Promise<CheckResult>;
+/**
+ * Check if .mcp.json exists and is valid.
+ */
+export declare function checkMcpJson(basePath: string): CheckResult;
+/**
+ * Check integration tools (GitNexus, Serena, Playwright).
+ */
+export declare function checkIntegrations(basePath: string): Promise<CheckResult[]>;
+//# sourceMappingURL=doctor-checks.d.ts.map

package/dist/core/doctor/doctor-checks.d.ts.map

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package/dist/core/doctor/doctor-checks.js

@@ -0,0 +1,313 @@
+import { existsSync, readFileSync } from "node:fs";
+import { access, constants } from "node:fs/promises";
+import path from "node:path";
+import Database from "better-sqlite3";
+import { STORE_DIR, DB_FILE } from "../utils/constants.js";
+import { fileExists } from "../utils/fs.js";
+import { getIntegrationsStatus } from "../integrations/tool-status.js";
+import { logger } from "../utils/logger.js";
+const MIN_NODE_VERSION = 20;
+/**
+ * Check Node.js version >= 20 using the current runtime.
+ */
+export function checkNodeVersion() {
+    return checkNodeVersionWith(process.versions.node);
+}
+/**
+ * Check Node.js version >= 20 with an explicit version string (testable).
+ */
+export function checkNodeVersionWith(version) {
+    const major = parseInt(version.split(".")[0], 10);
+    if (major >= MIN_NODE_VERSION) {
+        return {
+            name: "node-version",
+            level: "ok",
+            message: `Node.js v${version} (>= ${MIN_NODE_VERSION})`,
+        };
+    }
+    return {
+        name: "node-version",
+        level: "error",
+        message: `Node.js v${version} is below minimum v${MIN_NODE_VERSION}`,
+        suggestion: `Upgrade Node.js to v${MIN_NODE_VERSION} or later: https://nodejs.org`,
+    };
+}
+/**
+ * Check write permissions on the store directory.
+ */
+export async function checkWritePermissions(basePath) {
+    const storeDir = path.join(basePath, STORE_DIR);
+    try {
+        await access(storeDir, constants.W_OK);
+        return {
+            name: "write-permissions",
+            level: "ok",
+            message: `Write access to ${STORE_DIR}/`,
+        };
+    }
+    catch {
+        // If store dir doesn't exist, check parent
+        try {
+            await access(basePath, constants.W_OK);
+            return {
+                name: "write-permissions",
+                level: "ok",
+                message: `Write access to project directory (${STORE_DIR}/ will be created)`,
+            };
+        }
+        catch {
+            return {
+                name: "write-permissions",
+                level: "error",
+                message: `No write access to ${basePath}`,
+                suggestion: `Check directory permissions: chmod u+w "${basePath}"`,
+            };
+        }
+    }
+}
+/**
+ * Check that the SQLite database exists and can be opened.
+ */
+export async function checkSqliteDatabase(basePath) {
+    const dbPath = path.join(basePath, STORE_DIR, DB_FILE);
+    if (!existsSync(dbPath)) {
+        return {
+            name: "sqlite-database",
+            level: "error",
+            message: `Database not found at ${STORE_DIR}/${DB_FILE}`,
+            suggestion: "Run 'mcp-graph init' to create the database",
+        };
+    }
+    try {
+        const db = new Database(dbPath, { readonly: true });
+        db.close();
+        return {
+            name: "sqlite-database",
+            level: "ok",
+            message: `Database exists at ${STORE_DIR}/${DB_FILE}`,
+        };
+    }
+    catch (err) {
+        return {
+            name: "sqlite-database",
+            level: "error",
+            message: `Database corrupt or unreadable: ${err instanceof Error ? err.message : String(err)}`,
+            suggestion: "Try restoring from a snapshot or re-running 'mcp-graph init'",
+        };
+    }
+}
+/**
+ * Check database integrity via PRAGMA integrity_check.
+ */
+export async function checkDbIntegrity(basePath) {
+    const dbPath = path.join(basePath, STORE_DIR, DB_FILE);
+    if (!existsSync(dbPath)) {
+        return {
+            name: "db-integrity",
+            level: "error",
+            message: "Cannot check integrity — database not found",
+        };
+    }
+    try {
+        const db = new Database(dbPath, { readonly: true });
+        const result = db.pragma("integrity_check");
+        db.close();
+        const isOk = result.length === 1 && result[0].integrity_check === "ok";
+        if (isOk) {
+            return {
+                name: "db-integrity",
+                level: "ok",
+                message: "Database integrity check passed",
+            };
+        }
+        return {
+            name: "db-integrity",
+            level: "error",
+            message: `Database integrity issues: ${result.map((r) => r.integrity_check).join(", ")}`,
+            suggestion: "Restore from a snapshot: mcp-graph snapshot --restore <id>",
+        };
+    }
+    catch (err) {
+        return {
+            name: "db-integrity",
+            level: "error",
+            message: `Integrity check failed: ${err instanceof Error ? err.message : String(err)}`,
+        };
+    }
+}
+/**
+ * Check if the graph project is initialized.
+ */
+export function checkGraphInitialized(store) {
+    try {
+        const project = store.getProject();
+        if (project) {
+            return {
+                name: "graph-initialized",
+                level: "ok",
+                message: `Project "${project.name}" initialized`,
+            };
+        }
+        return {
+            name: "graph-initialized",
+            level: "warning",
+            message: "No project initialized",
+            suggestion: "Run 'mcp-graph init' to initialize a project",
+        };
+    }
+    catch {
+        return {
+            name: "graph-initialized",
+            level: "warning",
+            message: "Could not check project initialization",
+            suggestion: "Run 'mcp-graph init' to initialize a project",
+        };
+    }
+}
+/**
+ * Check if the config file exists and is valid.
+ */
+export function checkConfigFile(basePath) {
+    const configPath = path.join(basePath, "mcp-graph.config.json");
+    if (!existsSync(configPath)) {
+        return {
+            name: "config-file",
+            level: "ok",
+            message: "No config file — using defaults",
+        };
+    }
+    try {
+        const raw = readFileSync(configPath, "utf-8");
+        JSON.parse(raw);
+        return {
+            name: "config-file",
+            level: "ok",
+            message: "Config file is valid JSON",
+        };
+    }
+    catch (err) {
+        return {
+            name: "config-file",
+            level: "warning",
+            message: `Config file has invalid JSON: ${err instanceof Error ? err.message : String(err)}`,
+            suggestion: "Fix the JSON syntax in mcp-graph.config.json",
+        };
+    }
+}
+/**
+ * Check if the dashboard build artifacts exist.
+ */
+export async function checkDashboardBuild(basePath) {
+    const dashboardIndex = path.join(basePath, "dist", "web", "dashboard", "index.html");
+    const exists = await fileExists(dashboardIndex);
+    if (exists) {
+        return {
+            name: "dashboard-build",
+            level: "ok",
+            message: "Dashboard build found",
+        };
+    }
+    return {
+        name: "dashboard-build",
+        level: "warning",
+        message: "Dashboard build not found",
+        suggestion: "Run 'npm run build' to build the dashboard",
+    };
+}
+/**
+ * Check if .mcp.json exists and is valid.
+ */
+export function checkMcpJson(basePath) {
+    const mcpPath = path.join(basePath, ".mcp.json");
+    if (!existsSync(mcpPath)) {
+        return {
+            name: "mcp-json",
+            level: "warning",
+            message: ".mcp.json not found",
+            suggestion: "Create .mcp.json with MCP server configuration",
+        };
+    }
+    try {
+        const raw = readFileSync(mcpPath, "utf-8");
+        JSON.parse(raw);
+        return {
+            name: "mcp-json",
+            level: "ok",
+            message: ".mcp.json is valid",
+        };
+    }
+    catch {
+        return {
+            name: "mcp-json",
+            level: "warning",
+            message: ".mcp.json has invalid JSON",
+            suggestion: "Fix the JSON syntax in .mcp.json",
+        };
+    }
+}
+/**
+ * Check integration tools (GitNexus, Serena, Playwright).
+ */
+export async function checkIntegrations(basePath) {
+    try {
+        const status = await getIntegrationsStatus(basePath);
+        const results = [];
+        // GitNexus
+        results.push({
+            name: "integration-gitnexus",
+            level: status.gitnexus.installed ? "ok" : "warning",
+            message: status.gitnexus.installed
+                ? `GitNexus installed${status.gitnexus.running ? " and running" : ""}`
+                : "GitNexus not installed",
+            ...(!status.gitnexus.installed && {
+                suggestion: "Install GitNexus: npm install -g gitnexus",
+            }),
+        });
+        // Serena
+        results.push({
+            name: "integration-serena",
+            level: status.serena.installed ? "ok" : "warning",
+            message: status.serena.installed
+                ? `Serena configured (${status.serena.memories.length} memories)`
+                : "Serena not configured",
+            ...(!status.serena.installed && {
+                suggestion: "Configure Serena: create .serena/ directory with project config",
+            }),
+        });
+        // Playwright
+        results.push({
+            name: "integration-playwright",
+            level: status.playwright.installed ? "ok" : "warning",
+            message: status.playwright.installed
+                ? "Playwright available"
+                : "Playwright not available",
+            ...(!status.playwright.installed && {
+                suggestion: "Install Playwright: npx playwright install",
+            }),
+        });
+        return results;
+    }
+    catch (err) {
+        logger.debug("doctor:integrations:fail", {
+            error: err instanceof Error ? err.message : String(err),
+        });
+        return [
+            {
+                name: "integration-gitnexus",
+                level: "warning",
+                message: "Could not check GitNexus status",
+            },
+            {
+                name: "integration-serena",
+                level: "warning",
+                message: "Could not check Serena status",
+            },
+            {
+                name: "integration-playwright",
+                level: "warning",
+                message: "Could not check Playwright status",
+            },
+        ];
+    }
+}
+//# sourceMappingURL=doctor-checks.js.map

package/dist/core/doctor/doctor-checks.js.map

@@ -0,0 +1 @@
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package/dist/core/doctor/doctor-runner.d.ts

@@ -0,0 +1,6 @@
+import type { DoctorReport } from "./doctor-types.js";
+/**
+ * Run all doctor checks and return a structured report.
+ */
+export declare function runDoctor(basePath: string): Promise<DoctorReport>;
+//# sourceMappingURL=doctor-runner.d.ts.map

package/dist/core/doctor/doctor-runner.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"doctor-runner.d.ts","sourceRoot":"","sources":["../../../src/core/doctor/doctor-runner.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAe,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAyBnE;;GAEG;AACH,wBAAsB,SAAS,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,CAAC,CAqDvE"}

package/dist/core/doctor/doctor-runner.js

@@ -0,0 +1,72 @@
+import { existsSync } from "node:fs";
+import path from "node:path";
+import { SqliteStore } from "../store/sqlite-store.js";
+import { STORE_DIR, DB_FILE } from "../utils/constants.js";
+import { logger } from "../utils/logger.js";
+import { checkNodeVersion, checkWritePermissions, checkSqliteDatabase, checkDbIntegrity, checkGraphInitialized, checkConfigFile, checkDashboardBuild, checkMcpJson, checkIntegrations, } from "./doctor-checks.js";
+function buildSummary(checks) {
+    let ok = 0;
+    let warning = 0;
+    let error = 0;
+    for (const c of checks) {
+        if (c.level === "ok")
+            ok++;
+        else if (c.level === "warning")
+            warning++;
+        else
+            error++;
+    }
+    return { ok, warning, error };
+}
+/**
+ * Run all doctor checks and return a structured report.
+ */
+export async function runDoctor(basePath) {
+    logger.info("Running doctor checks", { basePath });
+    const checks = [];
+    // 1. Sync checks
+    checks.push(checkNodeVersion());
+    checks.push(checkConfigFile(basePath));
+    checks.push(checkMcpJson(basePath));
+    // 2. Async checks (parallel where possible)
+    const [writeResult, sqliteResult, dbIntegrityResult, dashboardResult, integrationResults] = await Promise.all([
+        checkWritePermissions(basePath),
+        checkSqliteDatabase(basePath),
+        checkDbIntegrity(basePath),
+        checkDashboardBuild(basePath),
+        checkIntegrations(basePath),
+    ]);
+    checks.push(writeResult);
+    checks.push(sqliteResult);
+    checks.push(dbIntegrityResult);
+    checks.push(dashboardResult);
+    checks.push(...integrationResults);
+    // 3. Store-dependent checks (only if DB exists)
+    const dbPath = path.join(basePath, STORE_DIR, DB_FILE);
+    if (existsSync(dbPath)) {
+        try {
+            const store = SqliteStore.open(basePath);
+            try {
+                checks.push(checkGraphInitialized(store));
+            }
+            finally {
+                store.close();
+            }
+        }
+        catch (err) {
+            checks.push({
+                name: "graph-initialized",
+                level: "warning",
+                message: `Could not open store: ${err instanceof Error ? err.message : String(err)}`,
+                suggestion: "Run 'mcp-graph init' to initialize the project",
+            });
+        }
+    }
+    const summary = buildSummary(checks);
+    return {
+        checks,
+        summary,
+        passed: summary.error === 0,
+    };
+}
+//# sourceMappingURL=doctor-runner.js.map

package/dist/core/doctor/doctor-runner.js.map

@@ -0,0 +1 @@
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package/dist/core/doctor/doctor-types.d.ts

@@ -0,0 +1,20 @@
+/**
+ * Types for the `mcp-graph doctor` diagnostic command.
+ */
+export type CheckLevel = "ok" | "warning" | "error";
+export interface CheckResult {
+    name: string;
+    level: CheckLevel;
+    message: string;
+    suggestion?: string;
+}
+export interface DoctorReport {
+    checks: CheckResult[];
+    summary: {
+        ok: number;
+        warning: number;
+        error: number;
+    };
+    passed: boolean;
+}
+//# sourceMappingURL=doctor-types.d.ts.map

package/dist/core/doctor/doctor-types.d.ts.map

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