mcp-ai-agent-guidelines 0.16.0 → 0.17.0

package/CHANGELOG.md

@@ -8,6 +8,22 @@ and [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
+## [0.17.0] - 2026-05-05
+### Added
+- implement workspace root anchoring for state storage and enhance ToonMemoryInterface
+- **mcp**: implement startup onboarding memory handling and enhance tool result summarization
+- **mcp**: allow workspace writes when uninitialized
+
+### Documentation
+- **mcp**: document local write behavior for .mcp-ai-agent-guidelines
+
+### Fixed
+- **pr**: address PR #1467 review feedback
+- **mcp**: make all state artifact writes atomic
+- **mcp**: use atomic writes for memory artifacts and snapshots
+
+### Changed
+- **mcp**: improve workspace directory handling and cleanup in tests
 ## [0.16.0] - 2026-04-28
 ### Fixed
 - update tool references and enhance memory tool tests for better context handling

package/README.md

@@ -116,12 +116,19 @@ Add the server to your MCP host config. The entry-point is `dist/index.js` and c
 
 ### Claude Desktop (`~/Library/Application Support/Claude/claude_desktop_config.json`)
 
+> [!IMPORTANT]
+> Claude Desktop spawns the server with a different working directory than your project.
+> Set `MCP_WORKSPACE_ROOT` to the absolute path of the project you want the server to write state into.
+
 ```json
 {
   "mcpServers": {
     "ai-agent-guidelines": {
       "command": "npx",
-      "args": ["mcp-ai-agent-guidelines"]
+      "args": ["-y", "mcp-ai-agent-guidelines@latest"],
+      "env": {
+        "MCP_WORKSPACE_ROOT": "/absolute/path/to/your/project"
+      }
     }
   }
 }
@@ -135,7 +142,10 @@ Add the server to your MCP host config. The entry-point is `dist/index.js` and c
     "ai-agent-guidelines": {
       "type": "stdio",
       "command": "npx",
-      "args": ["mcp-ai-agent-guidelines"]
+      "args": ["-y", "mcp-ai-agent-guidelines@latest"],
+      "env": {
+        "MCP_WORKSPACE_ROOT": "${workspaceFolder}"
+      }
     }
   }
 }
@@ -359,6 +369,7 @@ Published package note: the npm package ships `dist/`, `README.md`, and `LICENSE
 | `DISABLE_ADAPTIVE_ROUTING` | unset / `"false"` | Set to `true` to hide `routing-adapt` and block `adapt-*` skills; enabled by default (opt-out model) |
 | `ALLOW_INTENSIVE_SKILLS` | unset / `"false"` | Must be `true` to allow resource-intensive skills such as `bench-eval-suite`, `eval-prompt-bench`, `qm-path-integral-historian`, and `gr-spacetime-debt-metric` |
 | `ENABLE_PHYSICS_SKILLS` | unset / `"false"` | Required by input validation when physics skills are not otherwise authorized; physics skills also require conventional-evidence schema validation |
+| `MCP_WORKSPACE_ROOT` | unset | Absolute path to the project directory the server should write state into (`.mcp-ai-agent-guidelines/`). Required when using `npx` via Claude Desktop, Cursor, or Windsurf — these clients do not preserve the terminal's working directory. VS Code supports `${workspaceFolder}`. |
 | `MCP_SLIM_MODE` | unset / `"false"` | Set to `true` to expose only the minimal surface: `task-bootstrap`, `meta-routing`, and `project-onboard` (useful for low-context agents) |
 
 ### Skill gates

package/dist/index.d.ts

@@ -197,6 +197,24 @@ export declare function createServer(sharedRuntime?: ServerRuntime): {
     }>;
     runtime: ServerRuntime;
 };
+/**
+ * Phase C: Anchor state storage to the MCP client's workspace root.
+ *
+ * When launched via `npx`, `process.cwd()` is typically the user's home
+ * directory (~) or the filesystem root.  The MCP `roots/list` call returns the
+ * actual project directories the client has open, so we redirect all
+ * memory/session/snapshot writes there before bootstrap fires.
+ *
+ * Exported for testability — the function is side-effect-free with respect to
+ * the transport and can be exercised with a mocked Server instance.
+ *
+ * @returns The resolved workspace root path, or `undefined` if no roots were
+ *          available (client doesn't expose roots capability, empty roots list,
+ *          or any error during the roots query).
+ */
+export declare function anchorStateToClientRoots(server: Server, runtime: WorkflowExecutionRuntime, memoryInterface?: {
+    setBaseDir(dir: string): void;
+}): Promise<string | undefined>;
 export declare function main(): Promise<void>;
 export declare function isDirectExecutionEntry(entryPath?: string, moduleUrl?: string): boolean;
 //# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

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package/dist/index.js

@@ -1,9 +1,11 @@
 #!/usr/bin/env node
 import { realpathSync } from "node:fs";
+import { join } from "node:path";
 import { fileURLToPath, pathToFileURL } from "node:url";
 import { Server } from "@modelcontextprotocol/sdk/server/index.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import { CallToolRequestSchema, GetPromptRequestSchema, ListPromptsRequestSchema, ListResourcesRequestSchema, ListToolsRequestSchema, ReadResourceRequestSchema, } from "@modelcontextprotocol/sdk/types.js";
+import { loadOrchestrationConfig, resetConfigCache, resolveOrchestrationConfigPath, } from "./config/orchestration-config.js";
 import { toErrorMessage } from "./infrastructure/object-utilities.js";
 import { packageMetadata } from "./infrastructure/package-metadata.js";
 import { InstructionRegistry } from "./instructions/instruction-registry.js";
@@ -14,6 +16,7 @@ import { buildPublicResources, readPublicResource, } from "./resources/resource-
 import { createIntegratedRuntime } from "./runtime/integration.js";
 import { createSessionId, isValidSessionId, SecureFileSessionStore, } from "./runtime/secure-session-store.js";
 import { SessionBootstrap } from "./runtime/session-bootstrap.js";
+import { DEFAULT_SESSION_STATE_DIR, resolveWorkspaceRoot, } from "./runtime/session-store-utils.js";
 import { SkillRegistry } from "./skills/skill-registry.js";
 import { dispatchMemoryToolCall, MEMORY_TOOL_DEFINITIONS, resolveMemoryToolName, } from "./tools/memory-tools.js";
 import { dispatchModelDiscoveryToolCall, MODEL_DISCOVERY_TOOL_DEFINITIONS, MODEL_DISCOVERY_TOOL_NAME, } from "./tools/model-discovery.js";
@@ -28,6 +31,7 @@ import { buildVisualizationToolSurface, dispatchVisualizationToolCall, } from ".
 import { buildWorkspaceToolSurface, dispatchWorkspaceToolCall, resolveWorkspaceToolName, } from "./tools/workspace-tools.js";
 import { createErrorContext, ValidationService } from "./validation/index.js";
 import { WorkflowEngine } from "./workflows/workflow-engine.js";
+const STARTUP_ONBOARDING_MEMORY_ID = "system-bootstrap-onboarding";
 function getValidationService() {
     try {
         return ValidationService.getInstance();
@@ -54,6 +58,53 @@ function formatAuxToolError(toolName, runtime, error) {
         ],
     };
 }
+function summarizeToolResult(result) {
+    return result.content
+        .map((item) => ("text" in item ? item.text : ""))
+        .filter((text) => text.length > 0)
+        .join(" ")
+        .trim();
+}
+async function runStartupToolCall(label, operation) {
+    try {
+        const result = await operation();
+        if (!result.isError) {
+            return;
+        }
+        const detail = summarizeToolResult(result);
+        process.stderr.write(`[warn] Startup ${label} failed${detail ? `: ${detail}` : ""}\n`);
+    }
+    catch (error) {
+        process.stderr.write(`[warn] Startup ${label} failed: ${toErrorMessage(error)}\n`);
+    }
+}
+async function ensureStartupOnboardingMemory(runtime) {
+    const existingArtifact = await sharedToonMemoryInterface.loadMemoryArtifact(STARTUP_ONBOARDING_MEMORY_ID);
+    if (existingArtifact) {
+        return;
+    }
+    const now = new Date().toISOString();
+    await sharedToonMemoryInterface.saveMemoryArtifact({
+        meta: {
+            id: STARTUP_ONBOARDING_MEMORY_ID,
+            created: now,
+            updated: now,
+            tags: ["bootstrap", "onboarding", "system"],
+            relevance: 0.2,
+        },
+        content: {
+            summary: "Workspace bootstrap initialized",
+            details: "This onboarding artifact is created automatically on first startup. It records that local TOON state is active before interactive onboarding and that snapshots, sessions, and memory can persist under .mcp-ai-agent-guidelines.",
+            context: `Workspace root: ${runtime.workspaceRoot}`,
+            actionable: false,
+        },
+        links: {
+            relatedSessions: [],
+            relatedMemories: [],
+            sources: ["startup-bootstrap"],
+        },
+    });
+}
 export function createRuntime() {
     const instructionRegistry = new InstructionRegistry();
     const skillRegistry = new SkillRegistry();
@@ -65,7 +116,7 @@ export function createRuntime() {
     });
     return {
         sessionId: createSessionId(),
-        workspaceRoot: process.cwd(),
+        workspaceRoot: resolveWorkspaceRoot(),
         executionState: {
             instructionStack: [],
             progressRecords: [],
@@ -193,6 +244,51 @@ export function createServer(sharedRuntime = createRuntime()) {
     server.setRequestHandler(GetPromptRequestSchema, handlers.getPrompt);
     return { server, runtime: sharedRuntime };
 }
+/**
+ * Phase C: Anchor state storage to the MCP client's workspace root.
+ *
+ * When launched via `npx`, `process.cwd()` is typically the user's home
+ * directory (~) or the filesystem root.  The MCP `roots/list` call returns the
+ * actual project directories the client has open, so we redirect all
+ * memory/session/snapshot writes there before bootstrap fires.
+ *
+ * Exported for testability — the function is side-effect-free with respect to
+ * the transport and can be exercised with a mocked Server instance.
+ *
+ * @returns The resolved workspace root path, or `undefined` if no roots were
+ *          available (client doesn't expose roots capability, empty roots list,
+ *          or any error during the roots query).
+ */
+export async function anchorStateToClientRoots(server, runtime, memoryInterface = sharedToonMemoryInterface) {
+    try {
+        const clientCaps = server.getClientCapabilities();
+        if (!clientCaps?.roots) {
+            return undefined;
+        }
+        const { roots } = await server.listRoots();
+        if (roots.length === 0) {
+            return undefined;
+        }
+        const firstRootUri = roots[0].uri;
+        const firstRoot = firstRootUri.startsWith("file://")
+            ? fileURLToPath(firstRootUri)
+            : firstRootUri;
+        const stateDir = join(firstRoot, DEFAULT_SESSION_STATE_DIR);
+        memoryInterface.setBaseDir(stateDir);
+        runtime.workspaceRoot = firstRoot;
+        // Reset the orchestration config cache so it reloads from the correct
+        // project path (it may have cached a stale home-dir path during
+        // modelRouter.initialize() before roots were known).
+        resetConfigCache();
+        loadOrchestrationConfig(resolveOrchestrationConfigPath(firstRoot));
+        process.stderr.write(`[info] Workspace root resolved from client roots: ${firstRoot}\n`);
+        return firstRoot;
+    }
+    catch (err) {
+        process.stderr.write(`[warn] Could not resolve workspace root from client roots: ${toErrorMessage(err)}\n`);
+        return undefined;
+    }
+}
 export async function main() {
     const { server, runtime } = createServer();
     ValidationService.initialize();
@@ -217,17 +313,35 @@ export async function main() {
     });
     const transport = new StdioServerTransport();
     await server.connect(transport);
+    // Phase C: Anchor state storage to the MCP client's workspace root.
+    await anchorStateToClientRoots(server, runtime);
     void (async () => {
         await Promise.all([
-            dispatchSnapshotToolCall("agent-snapshot-write", {}).catch(() => { }),
-            dispatchSessionToolCall("agent-session-fetch", {}, runtime).catch(() => { }),
-            dispatchSessionToolCall("agent-session-write", {
+            runStartupToolCall("snapshot bootstrap", () => dispatchSnapshotToolCall("agent-snapshot-write", {})),
+            runStartupToolCall("session listing bootstrap", () => dispatchSessionToolCall("agent-session-fetch", {}, runtime)),
+            runStartupToolCall("session scan-results bootstrap", () => dispatchSessionToolCall("agent-session-write", {
                 target: "scan-results",
                 data: {
                     scannedAt: new Date().toISOString(),
                     sessionId: runtime.sessionId,
                 },
-            }, runtime).catch(() => { }),
+            }, runtime)),
+            runStartupToolCall("session context bootstrap", () => dispatchSessionToolCall("agent-session-write", {
+                target: "session-context",
+                data: {
+                    context: {
+                        requestScope: "Startup bootstrap",
+                        constraints: ["Pre-onboarding local state"],
+                        phase: "bootstrap",
+                    },
+                    progress: {
+                        next: ["Run onboarding or continue with MCP tools"],
+                    },
+                },
+            }, runtime)),
+            ensureStartupOnboardingMemory(runtime).catch((error) => {
+                process.stderr.write(`[warn] Startup onboarding memory bootstrap failed: ${toErrorMessage(error)}\n`);
+            }),
         ]);
         resolveContextReady();
         // Emit a codebase-specific orientation message after context is ready so

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/memory/toon-interface.d.ts

@@ -74,6 +74,12 @@ export declare class ToonMemoryInterface {
     private instructionNameSource?;
     /** Resolves once the workspace-root–aware base directory has been determined. */
     private baseDirReadyPromise;
+    /**
+     * Incremented each time the base directory is overridden so that any
+     * in-flight async resolution callbacks can detect they are stale and skip
+     * the update.
+     */
+    private baseDirGeneration;
     /**
      * Wire live registry data into the scanner so skillIds / instructionNames
      * are populated even when .github/ skill/instruction source files have been
@@ -81,6 +87,18 @@ export declare class ToonMemoryInterface {
      * Call this from main() after the runtime is fully initialised.
      */
     setRegistrySources(skillIdSource: () => string[], instructionNameSource: () => string[]): void;
+    /**
+     * Override the base storage directory after construction.
+     *
+     * Call this once the MCP transport has connected and the client's workspace
+     * roots are known (e.g. via `server.listRoots()`).  This redirects all
+     * state writes — memory, sessions, snapshots — to the correct project
+     * directory instead of the `npx` launch directory (typically `~`).
+     *
+     * The pending async resolution promise is cancelled so it can never
+     * overwrite the explicitly-provided directory.
+     */
+    setBaseDir(newBaseDir: string): void;
     constructor(customDir?: string, options?: {
         enableEncryption?: boolean;
         encryptionKey?: string;
@@ -122,6 +140,7 @@ export declare class ToonMemoryInterface {
     private ensureSnapshotHistoryInitialized;
     private persistFingerprintSnapshot;
     listFingerprintSnapshots(): Promise<FingerprintSnapshotIndexEntry[]>;
+    private awaitBaseDirReady;
     private ensureSessionDir;
     /** Save an explicit workspace map artifact for the current session. */
     saveWorkspaceMap(sessionId: string, map: PersistedWorkspaceMap | Record<string, PersistedWorkspaceModuleEntry>): Promise<void>;

package/dist/memory/toon-interface.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"toon-interface.d.ts","sourceRoot":"","sources":["../../src/memory/toon-interface.ts"],"names":[],"mappings":"AAAA;;GAEG;AAMH,OAAO,KAAK,EACX,uBAAuB,EACvB,iBAAiB,EACjB,MAAM,yBAAyB,CAAC;AAqBjC,OAAO,KAAK,EACX,mBAAmB,EACnB,cAAc,EACd,mBAAmB,EAEnB,6BAA6B,EAC7B,MAAM,sBAAsB,CAAC;AAC9B,OAAO,EACN,KAAK,qBAAqB,EAC1B,KAAK,oBAAoB,EAiBzB,KAAK,mBAAmB,EACxB,KAAK,YAAY,EAMjB,MAAM,0BAA0B,CAAC;AAElC,MAAM,WAAW,kBAAkB;IAClC,IAAI,EAAE;QACL,OAAO,EAAE,MAAM,CAAC;QAChB,OAAO,EAAE,MAAM,CAAC;QAChB,OAAO,EAAE,MAAM,CAAC;QAChB,SAAS,EAAE,MAAM,CAAC;KAClB,CAAC;IACF,OAAO,EAAE;QACR,YAAY,EAAE,MAAM,CAAC;QACrB,WAAW,EAAE,MAAM,EAAE,CAAC;QACtB,eAAe,CAAC,EAAE,MAAM,CAAC;QACzB,KAAK,EAAE,MAAM,CAAC;KACd,CAAC;IACF,QAAQ,EAAE;QACT,SAAS,EAAE,MAAM,EAAE,CAAC;QACpB,UAAU,EAAE,MAAM,EAAE,CAAC;QACrB,OAAO,EAAE,MAAM,EAAE,CAAC;QAClB,IAAI,EAAE,MAAM,EAAE,CAAC;KACf,CAAC;IACF,MAAM,EAAE;QACP,WAAW,EAAE,MAAM,EAAE,CAAC;QACtB,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QAClC,QAAQ,EAAE,MAAM,EAAE,CAAC;QACnB,QAAQ,EAAE,MAAM,EAAE,CAAC;KACnB,CAAC;CACF;AAED,MAAM,WAAW,kBAAkB;IAClC,IAAI,EAAE;QACL,EAAE,EAAE,MAAM,CAAC;QACX,OAAO,EAAE,MAAM,CAAC;QAChB,OAAO,EAAE,MAAM,CAAC;QAChB,IAAI,EAAE,MAAM,EAAE,CAAC;QACf,SAAS,EAAE,MAAM,CAAC;KAClB,CAAC;IACF,OAAO,EAAE;QACR,OAAO,EAAE,MAAM,CAAC;QAChB,OAAO,EAAE,MAAM,CAAC;QAChB,OAAO,EAAE,MAAM,CAAC;QAChB,UAAU,EAAE,OAAO,CAAC;QACpB,cAAc,CAAC,EAAE,MAAM,CAAC;KACxB,CAAC;IACF,KAAK,EAAE;QACN,eAAe,EAAE,MAAM,EAAE,CAAC;QAC1B,eAAe,EAAE,MAAM,EAAE,CAAC;QAC1B,OAAO,EAAE,MAAM,EAAE,CAAC;KAClB,CAAC;CACF;AAED,KAAK,6BAA6B,GAAG;IACpC,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,YAAY,EAAE,MAAM,EAAE,CAAC;CACvB,CAAC;AAEF,KAAK,qBAAqB,GAAG;IAC5B,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,6BAA6B,CAAC,CAAC;CACvD,CAAC;AAEF,KAAK,gBAAgB,GAAG,QAAQ,GAAG,UAAU,GAAG,QAAQ,GAAG,MAAM,CAAC;AAElE,qBAAa,mBAAmB;IAG/B,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,mBAAmB,CAAM;IACjD,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAW;IACnC,OAAO,CAAC,OAAO,CAAS;IACxB,OAAO,CAAC,UAAU,CAAS;IAC3B,OAAO,CAAC,SAAS,CAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAoC;IACjE,OAAO,CAAC,QAAQ,CAAC,eAAe,CAG9B;IACF,OAAO,CAAC,oBAAoB,CAAgC;IAC5D,OAAO,CAAC,aAAa,CAAC,CAAiB;IACvC,OAAO,CAAC,qBAAqB,CAAC,CAAiB;IAC/C,iFAAiF;IACjF,OAAO,CAAC,mBAAmB,CAA4B;IACvD;;;;OAIG;IACH,OAAO,CAAC,iBAAiB,CAAK;IAE9B;;;;;OAKG;IACH,kBAAkB,CACjB,aAAa,EAAE,MAAM,MAAM,EAAE,EAC7B,qBAAqB,EAAE,MAAM,MAAM,EAAE,GACnC,IAAI;IAKP;;;;;;;;;;OAUG;IACH,UAAU,CAAC,UAAU,EAAE,MAAM,GAAG,IAAI;gBAWnC,SAAS,CAAC,EAAE,MAAM,EAClB,OAAO,GAAE;QACR,gBAAgB,CAAC,EAAE,OAAO,CAAC;QAC3B,aAAa,CAAC,EAAE,MAAM,CAAC;KAClB;IA8BP,8EAA8E;IAC9E,OAAO,CAAC,wBAAwB,CAA4B;IAS5D,OAAO,CAAC,WAAW;IAInB,OAAO,CAAC,kBAAkB;IAI1B,OAAO,CAAC,mBAAmB;IAI3B,OAAO,CAAC,mBAAmB;IAI3B,OAAO,CAAC,SAAS;IAIjB,mEAAmE;IACnE,OAAO,CAAC,aAAa;IAmBrB,mEAAmE;IACnE,OAAO,CAAC,kBAAkB;IAI1B,2FAA2F;IAC3F,OAAO,CAAC,gBAAgB;IAIxB,4EAA4E;IAC5E,OAAO,CAAC,eAAe;IAIvB,OAAO,CAAC,kBAAkB;YAUZ,2BAA2B;YAc3B,iBAAiB;IAU/B;;;OAGG;IACH,OAAO,CAAC,0BAA0B;IAmBlC;;;;OAIG;IACG,sBAAsB,IAAI,OAAO,CAAC,OAAO,CAAC;IAWhD,OAAO,CAAC,eAAe;IAKvB,OAAO,CAAC,4BAA4B;YA0BtB,gBAAgB;YAahB,8BAA8B;YAoB9B,8BAA8B;YAS9B,gCAAgC;YA6ChC,0BAA0B;IA0DlC,wBAAwB,IAAI,OAAO,CAAC,6BAA6B,EAAE,CAAC;YAK5D,iBAAiB;YAOjB,gBAAgB;IAU9B,uEAAuE;IACjE,gBAAgB,CACrB,SAAS,EAAE,MAAM,EACjB,GAAG,EAAE,qBAAqB,GAAG,MAAM,CAAC,MAAM,EAAE,6BAA6B,CAAC,GACxE,OAAO,CAAC,IAAI,CAAC;IAgBhB,mEAAmE;IAC7D,eAAe,CAAC,SAAS,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC;IAQnE,cAAc,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;IAWnC,OAAO,CACZ,UAAU,CAAC,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,KAAK,IAAI,GACnE,OAAO,CAAC,mBAAmB,CAAC;IAyBzB,OAAO,CACZ,QAAQ,GAAE,gBAA2B,GACnC,OAAO,CAAC;QAAE,KAAK,EAAE,cAAc,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC;IAc7C,gBAAgB,CACrB,SAAS,EAAE,MAAM,GACf,OAAO,CAAC,qBAAqB,GAAG,IAAI,CAAC;IASlC,eAAe,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,GAAG,IAAI,CAAC;IAS3D,uBAAuB,CAC5B,QAAQ,GAAE,gBAA2B,GACnC,OAAO,CAAC,mBAAmB,GAAG,IAAI,CAAC;IA4BhC,kBAAkB,CACvB,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,OAAO,CAAC,kBAAkB,CAAC,GAClC,OAAO,CAAC,IAAI,CAAC;YAUF,qBAAqB;IA+B7B,kBAAkB,CACvB,SAAS,EAAE,MAAM,GACf,OAAO,CAAC,kBAAkB,GAAG,IAAI,CAAC;IA+B/B,kBAAkB,CAAC,QAAQ,EAAE,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC;IAW/D,kBAAkB,CACvB,QAAQ,EAAE,MAAM,GACd,OAAO,CAAC,kBAAkB,GAAG,IAAI,CAAC;IA+B/B,mBAAmB,CAAC,MAAM,CAAC,EAAE;QAClC,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;QAChB,YAAY,CAAC,EAAE,MAAM,CAAC;QACtB,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,QAAQ,CAAC,EAAE,MAAM,CAAC;KAClB,GAAG,OAAO,CAAC,kBAAkB,EAAE,CAAC;IAmC3B,qBAAqB,CAC1B,SAAS,EAAE,MAAM,EACjB,MAAM,EAAE;QACP,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;QACrB,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;QACtB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;QACnB,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;KAChB,GACC,OAAO,CAAC,IAAI,CAAC;IAkBV,iBAAiB,CACtB,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM,EACf,IAAI,GAAE,SAAS,GAAG,UAAU,GAAG,SAAS,GAAG,SAAqB,GAC9D,OAAO,CAAC,IAAI,CAAC;IAoBhB;;;OAGG;IACG,wBAAwB,CAC7B,UAAU,EAAE,MAAM,EAAE,GAClB,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,kBAAkB,GAAG,IAAI,CAAC,CAAC;IAiBlD;;;OAGG;IACG,wBAAwB,CAC7B,OAAO,EAAE,KAAK,CAAC;QAAE,SAAS,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,OAAO,CAAC,kBAAkB,CAAC,CAAA;KAAE,CAAC,GACzE,OAAO,CAAC,IAAI,CAAC;IAYhB;;OAEG;IACG,wBAAwB,CAC7B,SAAS,EAAE,kBAAkB,EAAE,GAC7B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package/dist/memory/toon-interface.js

@@ -2,7 +2,7 @@
  * TOON (Token-Oriented Object Notation) memory interface for session storage.
  */
 import { randomUUID } from "node:crypto";
-import { access, mkdir, readdir, readFile, writeFile } from "node:fs/promises";
+import { access, mkdir, readdir, readFile } from "node:fs/promises";
 import { isAbsolute, join, relative, resolve, sep } from "node:path";
 import { decode as toonDecode, encode as toonEncode } from "@toon-format/toon";
 import { assertValidSessionId, isValidSessionId, } from "../runtime/secure-session-store.js";
@@ -25,6 +25,12 @@ export class ToonMemoryInterface {
     instructionNameSource;
     /** Resolves once the workspace-root–aware base directory has been determined. */
     baseDirReadyPromise;
+    /**
+     * Incremented each time the base directory is overridden so that any
+     * in-flight async resolution callbacks can detect they are stale and skip
+     * the update.
+     */
+    baseDirGeneration = 0;
     /**
      * Wire live registry data into the scanner so skillIds / instructionNames
      * are populated even when .github/ skill/instruction source files have been
@@ -35,6 +41,27 @@ export class ToonMemoryInterface {
         this.skillIdSource = skillIdSource;
         this.instructionNameSource = instructionNameSource;
     }
+    /**
+     * Override the base storage directory after construction.
+     *
+     * Call this once the MCP transport has connected and the client's workspace
+     * roots are known (e.g. via `server.listRoots()`).  This redirects all
+     * state writes — memory, sessions, snapshots — to the correct project
+     * directory instead of the `npx` launch directory (typically `~`).
+     *
+     * The pending async resolution promise is cancelled so it can never
+     * overwrite the explicitly-provided directory.
+     */
+    setBaseDir(newBaseDir) {
+        if (newBaseDir === this.baseDir)
+            return;
+        this.baseDirGeneration++;
+        this.baseDir = newBaseDir;
+        this.sessionDir = join(newBaseDir, "sessions");
+        this.memoryDir = join(newBaseDir, "memory");
+        // Cancel any in-flight async resolution — the explicit root wins.
+        this.baseDirReadyPromise = undefined;
+    }
     constructor(customDir, options = {}) {
         // Sync best-effort resolution — will be refined by resolveBaseDir() on
         // first async operation if no explicit dir was provided.
@@ -48,8 +75,10 @@ export class ToonMemoryInterface {
         // If no explicit dir was provided, kick off async workspace-root detection
         // immediately so it is ready before any IO call.
         if (!customDir && !process.env["MCP_AI_AGENT_GUIDELINES_STATE_DIR"]) {
+            const generation = ++this.baseDirGeneration;
             this.baseDirReadyPromise = resolveSessionStateDirAsync().then((resolvedDir) => {
-                if (resolvedDir !== this.baseDir) {
+                if (this.baseDirGeneration === generation &&
+                    resolvedDir !== this.baseDir) {
                     this.baseDir = resolvedDir;
                     this.sessionDir = join(resolvedDir, "sessions");
                     this.memoryDir = join(resolvedDir, "memory");
@@ -125,12 +154,7 @@ export class ToonMemoryInterface {
         return await this.encryptionKeyPromise;
     }
     async ensureDirectories() {
-        // Await workspace-root resolution before any filesystem access so the
-        // correct baseDir (workspace vs. $HOME) is used for all paths.
-        if (this.baseDirReadyPromise) {
-            await this.baseDirReadyPromise;
-            this.baseDirReadyPromise = undefined;
-        }
+        await this.awaitBaseDirReady();
         await ensureSessionStateGitignore(this.baseDir);
         await mkdir(this.memoryDir, { recursive: true });
         await mkdir(this.snapshotDir(), { recursive: true });
@@ -166,10 +190,7 @@ export class ToonMemoryInterface {
      * write-path tool guards.
      */
     async isWorkspaceInitialized() {
-        if (this.baseDirReadyPromise) {
-            await this.baseDirReadyPromise;
-            this.baseDirReadyPromise = undefined;
-        }
+        await this.awaitBaseDirReady();
         const configPath = join(this.configDir(), "orchestration.toml");
         try {
             await access(configPath);
@@ -230,7 +251,7 @@ export class ToonMemoryInterface {
         }
     }
     async saveFingerprintSnapshotHistory(history) {
-        await writeFile(this.snapshotHistoryPath(), JSON.stringify(history, null, 2), "utf8");
+        await writeTextFileAtomic(this.snapshotHistoryPath(), JSON.stringify(history, null, 2));
     }
     async ensureSnapshotHistoryInitialized() {
         const history = await this.loadFingerprintSnapshotHistory();
@@ -247,8 +268,8 @@ export class ToonMemoryInterface {
             return history;
         }
         const fileName = `fingerprint-${snapshotId}.json`;
-        await writeFile(this.snapshotArchivePath(snapshotId), JSON.stringify(migratedSnapshot, null, 2), "utf8");
-        await writeFile(this.snapshotLatestPath(), JSON.stringify(migratedSnapshot, null, 2), "utf8");
+        await writeTextFileAtomic(this.snapshotArchivePath(snapshotId), JSON.stringify(migratedSnapshot, null, 2));
+        await writeTextFileAtomic(this.snapshotLatestPath(), JSON.stringify(migratedSnapshot, null, 2));
         const migratedHistory = {
             version: "1",
             latestSnapshotId: snapshotId,
@@ -271,8 +292,8 @@ export class ToonMemoryInterface {
         }
         const normalizedSnapshot = this.normalizeFingerprintSnapshot(snapshot);
         const fileName = `fingerprint-${snapshotId}.json`;
-        await writeFile(this.snapshotArchivePath(snapshotId), JSON.stringify(normalizedSnapshot, null, 2), "utf8");
-        await writeFile(this.snapshotLatestPath(), JSON.stringify(normalizedSnapshot, null, 2), "utf8");
+        await writeTextFileAtomic(this.snapshotArchivePath(snapshotId), JSON.stringify(normalizedSnapshot, null, 2));
+        await writeTextFileAtomic(this.snapshotLatestPath(), JSON.stringify(normalizedSnapshot, null, 2));
         const existingHistory = await this.ensureSnapshotHistoryInitialized();
         const filteredSnapshots = existingHistory.snapshots.filter((entry) => entry.snapshotId !== snapshotId);
         const updatedHistory = {
@@ -302,7 +323,17 @@ export class ToonMemoryInterface {
         await this.ensureDirectories();
         return (await this.ensureSnapshotHistoryInitialized()).snapshots;
     }
+    async awaitBaseDirReady() {
+        if (this.baseDirReadyPromise) {
+            await this.baseDirReadyPromise;
+            this.baseDirReadyPromise = undefined;
+        }
+    }
     async ensureSessionDir(sessionId) {
+        // Session writes need the same workspace-root correction as snapshot and
+        // memory writes, otherwise an npx-launched server can leak state into the
+        // launch directory before MCP_WORKSPACE_ROOT takes effect.
+        await this.awaitBaseDirReady();
         await ensureSessionStateGitignore(this.baseDir);
         await mkdir(this.sessionSubDir(sessionId), { recursive: true });
         await mkdir(this.memoryDir, { recursive: true });
@@ -316,12 +347,12 @@ export class ToonMemoryInterface {
                 modules: map,
             };
         await this.ensureSessionDir(sessionId);
-        await writeFile(this.workspaceMapPath(sessionId), JSON.stringify(workspaceMap, null, 2), "utf8");
+        await writeTextFileAtomic(this.workspaceMapPath(sessionId), JSON.stringify(workspaceMap, null, 2));
     }
     /** Save per-session scan results (code scanning / AST outputs). */
     async saveScanResults(sessionId, results) {
         await this.ensureSessionDir(sessionId);
-        await writeFile(this.scanResultsPath(sessionId), JSON.stringify(results, null, 2), "utf8");
+        await writeTextFileAtomic(this.scanResultsPath(sessionId), JSON.stringify(results, null, 2));
     }
     async listSessionIds() {
         await this.ensureDirectories();
@@ -449,7 +480,7 @@ export class ToonMemoryInterface {
         await this.ensureDirectories();
         const now = new Date().toISOString();
         const enhancedArtifact = enhanceMemoryArtifact(artifact, now);
-        await writeFile(this.memoryArtifactPath(enhancedArtifact.meta.id), toonEncode(enhancedArtifact, { delimiter: "\t", keyFolding: "safe" }), "utf8");
+        await writeTextFileAtomic(this.memoryArtifactPath(enhancedArtifact.meta.id), toonEncode(enhancedArtifact, { delimiter: "\t", keyFolding: "safe" }));
     }
     async loadMemoryArtifact(memoryId) {
         try {