@cortexkit/opencode-magic-context 0.45.0 → 0.46.1

package/dist/v2/store-reader.d.ts

@@ -1,4 +1,6 @@
+import type { Statement } from "better-sqlite3";
 import type { RawMessageOrdinalAnchor } from "../hooks/magic-context/read-session-raw";
+import { Database } from "../shared/sqlite";
 /** Compatibility export; shared/opencode-db-path.ts is the single filename authority. */
 export declare function sourceDatabaseFilename(channel: string, env?: NodeJS.ProcessEnv): string;
 /** GA data root resolved by the shared host-generation-aware resolver. */
@@ -99,11 +101,35 @@ export declare function getV2StoreReaderDebugCounters(): V2StoreReaderDebugCount
 export declare function resetV2StoreReaderDebugCounters(options?: {
     captureQueries?: boolean;
 }): void;
+interface ReaderConnection {
+    db: Database;
+    statements: Map<string, Statement>;
+    identity: string;
+    leases: number;
+    retired: boolean;
+}
+/** Boot-scoped read-only handles. Each lease still closes in the caller's finally block.
+ * Statements, not results, are cached: WAL updates are visible on the next query.
+ * A replaced/missing file cannot reuse the old inode, and disposal releases all handles. */
+export declare class V2StoreReaderPool {
+    private readonly capacity;
+    private readonly connections;
+    private closed;
+    constructor(capacity?: number);
+    open(path: string): V2StoreReader;
+    acquire(path: string): ReaderConnection;
+    release(connection: ReaderConnection): void;
+    private retire;
+    close(): void;
+}
 /** Opens an existing store read-only; missing/corrupt stores propagate errors, never an empty history. */
 export declare class V2StoreReader {
+    private readonly pool?;
     private readonly db;
+    private readonly connection;
     private closed;
-    constructor(path: string);
+    constructor(path: string, pool?: V2StoreReaderPool | undefined);
+    private prepare;
     close(): void;
     /** Exclusive cursor, ascending seq. IDs are not chronological in the v2 store. */
     page(sessionID: string, options?: {
@@ -134,6 +160,15 @@ export declare class V2StoreReader {
     latestMessageTime(sessionID: string): number | undefined;
     /** Parent links are recorded by the host before a child's first context pass. */
     isSubagent(sessionID: string): boolean | null;
+    /**
+     * The most recently updated top-level user session the host created in
+     * `directory`, or undefined when there is none. Children, Magic Context's
+     * own hidden runs and archived sessions are never returned. The directory
+     * must match exactly: OpenCode 2 puts a child session in its parent's
+     * location, and only the plugin context of that location recognises the
+     * child, so a parent from a sibling checkout would strand the run.
+     */
+    latestRootSessionInDirectory(directory: string): string | undefined;
     /** Native user activity on root sessions; internal children must never become
      * retrospective input. Activity is read from the source, not project-binding
      * times or optional activity keys in Magic Context's store. */
@@ -170,6 +205,8 @@ export declare class V2StoreReader {
     /** Conversational rows at or before `throughSeq`, newest first. */
     rawRowsThrough(sessionID: string, throughSeq: number, limit: number): StoreRow[];
     sequenceForId(sessionID: string, id: string | null | undefined): number | undefined;
+    /** Native synthetics are user-shaped on the wire; their store kind is unambiguous. */
+    syntheticMessageIDs(sessionID: string): Set<string>;
     /**
      * The session this one was forked from and where the fork was cut, as the
      * host recorded them (`session_v2.fork_session_id` and `fork_boundary`).
@@ -204,4 +241,5 @@ export declare class V2StoreReader {
     history(sessionID: string): StoreRow[];
     private all;
 }
+export {};
 //# sourceMappingURL=store-reader.d.ts.map

package/dist/v2/store-reader.d.ts.map

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package/dist/v2/tool-result.d.ts

@@ -0,0 +1,8 @@
+type Part = Record<string, unknown>;
+/** The context hook sees normalized results; checkpoint replay sees raw error envelopes. */
+export declare function isToolError(part: Part): boolean;
+/** Match the host's error wire text, including the content and the structured error. */
+export declare function toolErrorText(result: Part): string;
+export declare function toolStateContent(state: Part): string;
+export {};
+//# sourceMappingURL=tool-result.d.ts.map

package/dist/v2/tool-result.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"tool-result.d.ts","sourceRoot":"","sources":["../../src/v2/tool-result.ts"],"names":[],"mappings":"AAAA,KAAK,IAAI,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;AAEpC,4FAA4F;AAC5F,wBAAgB,WAAW,CAAC,IAAI,EAAE,IAAI,GAAG,OAAO,CAO/C;AAED,wFAAwF;AACxF,wBAAgB,aAAa,CAAC,MAAM,EAAE,IAAI,GAAG,MAAM,CAGlD;AAED,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,IAAI,GAAG,MAAM,CAiBpD"}

package/dist/v2/tui/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/v2/tui/index.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,eAAe,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAI5E,OAAO,EAYH,KAAK,kBAAkB,EAC1B,MAAM,2BAA2B,CAAC;AAUnC,OAAO,KAAK,EAAiC,YAAY,EAAE,MAAM,SAAS,CAAC;AAY3E;;;;;;;;;;GAUG;AACH,wBAAgB,WAAW,CAAC,QAAQ,EAAE,eAAe,GAAG,SAAS,GAAG,MAAM,CAyBzE;AAED;;;;;;;;GAQG;AACH,wBAAgB,UAAU,CACtB,MAAM,EAAE,IAAI,CACR,YAAY,EACV,cAAc,GACd,iBAAiB,GACjB,aAAa,GACb,oBAAoB,GACpB,kBAAkB,GAClB,kBAAkB,GAClB,kBAAkB,GAClB,aAAa,GACb,iBAAiB,GACjB,kBAAkB,GAClB,iBAAiB,GACjB,qBAAqB,GACrB,oBAAoB,CACzB,GACF,MAAM,CA6BR;AAED;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,MAAM,EAAE,kBAAkB,GAAG,MAAM,CAoBhE;AAOD,KAAK,UAAU,GAAG,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,KAAK,OAAO,CAAC;AAE5E,wBAAsB,YAAY,CAAC,OAAO,EAAE,YAAY,EAAE,GAAG,EAAE,UAAU,GAAG,OAAO,CAAC,MAAM,IAAI,CAAC,CAgZ9F;AAED,wBAAsB,KAAK,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,MAAM,IAAI,CAAC,CAEtE;;;;;AAED,wBAAuD"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/v2/tui/index.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,eAAe,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAI5E,OAAO,EAYH,KAAK,kBAAkB,EAC1B,MAAM,2BAA2B,CAAC;AAUnC,OAAO,KAAK,EAAiC,YAAY,EAAE,MAAM,SAAS,CAAC;AAY3E;;;;;;;;;;GAUG;AACH,wBAAgB,WAAW,CAAC,QAAQ,EAAE,eAAe,GAAG,SAAS,GAAG,MAAM,CAyBzE;AAED;;;;;;;;GAQG;AACH,wBAAgB,UAAU,CACtB,MAAM,EAAE,IAAI,CACR,YAAY,EACV,cAAc,GACd,iBAAiB,GACjB,aAAa,GACb,oBAAoB,GACpB,kBAAkB,GAClB,kBAAkB,GAClB,kBAAkB,GAClB,aAAa,GACb,iBAAiB,GACjB,kBAAkB,GAClB,iBAAiB,GACjB,qBAAqB,GACrB,oBAAoB,CACzB,GACF,MAAM,CA6BR;AAED;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,MAAM,EAAE,kBAAkB,GAAG,MAAM,CAoBhE;AAOD,KAAK,UAAU,GAAG,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,KAAK,OAAO,CAAC;AAE5E,wBAAsB,YAAY,CAAC,OAAO,EAAE,YAAY,EAAE,GAAG,EAAE,UAAU,GAAG,OAAO,CAAC,MAAM,IAAI,CAAC,CAgZ9F;AAED,wBAAsB,KAAK,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,MAAM,IAAI,CAAC,CAStE;;;;;AAED,wBAAuD"}

package/dist/v2/{wrapup-orchestrator-tbyx78dz.js → wrapup-orchestrator-0snhvwcv.js}

@@ -1,7 +1,7 @@
 import {
   sessionLog
-} from "./server-ckpc8pxy.js";
-import"./server-e36nf2p1.js";
+} from "./server-1qbnzc80.js";
+import"./server-frbm99q5.js";
 import {
   COMPARTMENT_LEASE_RENEWAL_MS,
   acquireCompartmentLease,
@@ -24,25 +24,28 @@ import {
   registerActiveCompartmentRun,
   setRecompStarting2,
   setRecompTerminal2
-} from "./server-c4g2y1z8.js";
-import"./server-rhdgxp1t.js";
-import"./server-v5xgft5v.js";
-import"./server-a4m2b1yv.js";
-import"./server-hfjfbg59.js";
-import"./server-remp7e2g.js";
-import"./server-qpg6wf72.js";
-import"./server-w99cyt6a.js";
-import"./server-r7cmye3k.js";
-import"./server-n96ag4rk.js";
+} from "./server-jc7y02q0.js";
+import"./server-51dv1pr5.js";
+import"./server-xa4xe3rv.js";
+import"./server-fg34g6a5.js";
+import"./server-vs5gpnd4.js";
+import"./server-1zx87sdm.js";
+import"./server-qp5hx1ad.js";
+import"./server-g0fjrkta.js";
+import"./server-ajzeteqw.js";
+import"./server-wvjvfhck.js";
+import"./server-e29d7p7c.js";
 import {
   pushNotification2
 } from "./server-x8a7jmkh.js";
 import {
   sendStatusNotification2
-} from "./server-z19x7eqz.js";
-import"./server-0jqw05sa.js";
-import"./server-5317ykaf.js";
-import"./server-fgmxwrgy.js";
+} from "./server-mcfawjgc.js";
+import"./server-c5gz8wph.js";
+import"./server-y8maxeft.js";
+import"./server-3n4q9xme.js";
+import"./server-6r257mf5.js";
+import"./server-14vq4kpm.js";
 
 // src/hooks/magic-context/wrapup-orchestrator.ts
 import * as crypto from "node:crypto";
@@ -178,6 +181,7 @@ async function runOneWrapupIteration(args) {
   const runnerPromise = runCompartmentAgentForWrapup({
     client: ctx.client,
     hiddenCompletionExecutor: ctx.hiddenCompletionExecutor,
+    compactionMarkerStrategy: ctx.compactionMarkerStrategy,
     db: ctx.db,
     sessionId,
     historianChunkTokens: ctx.historianChunkTokens,

package/dist/wrapup-orchestrator-39amhv9s.js

@@ -0,0 +1,26 @@
+import {
+  runManagedWrapup2
+} from "./index-5p8jdswx.js";
+import"./index-sgthv3f7.js";
+import"./index-sjthx78w.js";
+import"./index-sd3egckz.js";
+import"./index-7qw742ev.js";
+import"./index-0d3g3461.js";
+import"./index-8x2v7gg9.js";
+import"./index-r5hmbx3t.js";
+import"./index-3h0ybwah.js";
+import"./index-majxda46.js";
+import"./index-1zx87sdm.js";
+import"./index-q4yp4b52.js";
+import"./index-5gq3b2ya.js";
+import"./index-b35pxds2.js";
+import"./index-5eqk6z3s.js";
+import"./index-sj29b3z2.js";
+import"./index-fg34g6a5.js";
+import"./index-x8a7jmkh.js";
+import"./index-fzbvakh0.js";
+import"./index-hybnrwq0.js";
+import"./index-q6hef7fh.js";
+export {
+  runManagedWrapup2 as runManagedWrapup
+};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cortexkit/opencode-magic-context",
-  "version": "0.45.0",
+  "version": "0.46.1",
   "type": "module",
   "description": "OpenCode plugin for Magic Context — cross-session memory and context management",
   "main": "dist/index.js",
@@ -38,34 +38,33 @@
   ],
   "scripts": {
     "build": "bun ../../scripts/check-bun.mjs && tsc -p ../retina-local-fs/tsconfig.build.json && bun run build:tui && bun ../../scripts/clean-dist-chunks.mjs dist index.js transformers-web.js transformers-node-wasm.js && bun build src/features/magic-context/memory/transformers-web-entry.ts --outfile dist/transformers-web.js --target browser --format esm --external onnxruntime-web && bun scripts/build-transformers-node-wasm.ts dist && bun build src/index.ts src/features/magic-context/memory/embedding-worker.ts src/features/magic-context/migration-worker.ts --outdir dist --entry-naming '[name].[ext]' --target node --format esm --splitting --external @opencode-ai/plugin --external onnxruntime-node --external onnxruntime-web --external sharp --external bun:sqlite --external node:sqlite && bun run build:v2 && tsc --emitDeclarationOnly",
-    "build:v2": "bun ../../scripts/clean-dist-chunks.mjs dist/v2 server.js embedding-worker.js migration-worker.js && bun build src/features/magic-context/memory/transformers-web-entry.ts --outfile dist/v2/transformers-web.js --target browser --format esm --external onnxruntime-web && bun scripts/build-transformers-node-wasm.ts dist/v2 && bun build src/v2/server.ts src/features/magic-context/memory/embedding-worker.ts src/features/magic-context/migration-worker.ts --outdir dist/v2 --entry-naming '[name].[ext]' --target node --format esm --splitting --external @opencode/plugin --external onnxruntime-node --external onnxruntime-web --external sharp --external bun:sqlite --external node:sqlite && bun test src/v2/server.test.ts",
+    "build:v2": "bun ../../scripts/clean-dist-chunks.mjs dist/v2 server.js embedding-worker.js migration-worker.js && bun build src/features/magic-context/memory/transformers-web-entry.ts --outfile dist/v2/transformers-web.js --target browser --format esm --external onnxruntime-web && bun scripts/build-transformers-node-wasm.ts dist/v2 && bun build src/v2/server.ts src/features/magic-context/memory/embedding-worker.ts src/features/magic-context/migration-worker.ts --outdir dist/v2 --entry-naming '[name].[ext]' --target node --format esm --splitting --external @opencode/plugin --external onnxruntime-node --external onnxruntime-web --external sharp --external bun:sqlite --external node:sqlite",
     "build:tui": "bun scripts/build-tui.ts",
-    "check:tui-compiled": "bun run build:tui && git diff --exit-code -- src/tui-compiled && test -z \"$(git status --porcelain -- src/tui-compiled)\"",
+    "check:tui-compiled": "git diff --exit-code -- src/tui-compiled && test -z \"$(git status --porcelain -- src/tui-compiled)\"",
     "check:transformers-node-wasm": "bun scripts/verify-transformers-node-wasm.ts",
     "typecheck": "tsc -p ../retina-local-fs/tsconfig.build.json && tsc --noEmit && tsc -p tsconfig.scripts.json",
-    "test": "bun ../../scripts/check-bun.mjs && bun install --frozen-lockfile && bun test --parallel=4 --timeout 30000",
-    "test:serial": "bun install --frozen-lockfile && bun test --timeout 30000",
+    "test": "bun ../../scripts/check-bun.mjs && bun install --frozen-lockfile && BUN_JSC_useOMGJIT=0 bun test --parallel=4 --timeout 30000",
+    "test:serial": "bun install --frozen-lockfile && BUN_JSC_useOMGJIT=0 bun test --timeout 30000",
     "test:parallel:probe": "bun scripts/verify-parallel-db-isolation.ts",
     "lint": "bun ../../scripts/check-bun.mjs && biome check .",
     "lint:fix": "biome check --write .",
     "format": "biome format --write .",
     "format:check": "biome format .",
     "clean": "bun ../../scripts/clean-dist-chunks.mjs dist index.js embedding-worker.js migration-worker.js transformers-web.js transformers-node-wasm.js && bun ../../scripts/clean-dist-chunks.mjs dist/v2 server.js embedding-worker.js migration-worker.js transformers-web.js transformers-node-wasm.js",
-    "prepublishOnly": "bun run build && bun run build:tui"
+    "prepublishOnly": "bun run build && bun run check:tui-compiled"
   },
+  "//check:tui-compiled": "Check drift on output already generated by build or build:tui; this check never regenerates files. CI and prepublishOnly build first.",
+  "//test": "Only test runs disable JSC's optimizing WebAssembly tier so per-file isolation does not pay its compilation cost on every file. This is not a production setting and does not change host process engine options.",
   "dependencies": {
     "@cortexkit/subc-client": "0.11.1",
     "@jitl/quickjs-singlefile-cjs-release-asyncify": "0.32.0",
     "@opencode-ai/plugin": "^1.17.11",
     "@opencode-ai/sdk": "^1.17.11",
-    "@opentui/core": "^0.4.2",
-    "@opentui/solid": "^0.4.2",
     "ai-tokenizer": "^1.0.6",
     "comment-json": "^5.0.0",
     "jsonc-parser": "^3.3.1",
     "onnxruntime-web": "1.26.0-dev.20260416-b7804b056c",
     "quickjs-emscripten": "^0.32.0",
-    "solid-js": "1.9.12",
     "zod": "^4.1.8"
   },
   "optionalDependencies": {
@@ -73,6 +72,9 @@
     "sharp": "^0.35.0"
   },
   "devDependencies": {
+    "@opentui/core": "^0.4.2",
+    "@opentui/solid": "^0.4.2",
+    "solid-js": "1.9.12",
     "@opencode/plugin": "2.0.22",
     "@opencode/ai": "2.0.22",
     "@opencode/cli": "2.0.22",
@@ -103,6 +105,20 @@
     "tui"
   ],
   "peerDependencies": {
-    "@opencode-ai/plugin": ">=1.15.0"
+    "@opencode-ai/plugin": ">=1.15.0",
+    "@opentui/core": ">=0.4.2",
+    "@opentui/solid": ">=0.4.2",
+    "solid-js": "^1.9.12"
+  },
+  "peerDependenciesMeta": {
+    "@opentui/core": {
+      "optional": true
+    },
+    "@opentui/solid": {
+      "optional": true
+    },
+    "solid-js": {
+      "optional": true
+    }
   }
 }

package/src/config/index.ts

@@ -284,10 +284,22 @@ function deepMergeRawConfig(
             typeof overrideVal === "object" &&
             !Array.isArray(overrideVal)
         ) {
-            mergedValue = deepMergeRawConfig(
-                baseVal as Record<string, unknown>,
-                overrideVal as Record<string, unknown>,
-            );
+            mergedValue =
+                key === "protected_tools"
+                    ? Object.fromEntries(
+                          [baseVal, overrideVal].flatMap((value) =>
+                              Object.entries(value as Record<string, unknown>).map(
+                                  ([name, count]) => [
+                                      name.toLowerCase().replace(/^mcp_/, ""),
+                                      count,
+                                  ],
+                              ),
+                          ),
+                      )
+                    : deepMergeRawConfig(
+                          baseVal as Record<string, unknown>,
+                          overrideVal as Record<string, unknown>,
+                      );
         } else if (
             key === "disabled_hooks" &&
             Array.isArray(baseVal) &&
@@ -409,6 +421,11 @@ export function parsePluginConfig(
             "protected_tags is deprecated and ignored; use protected_tokens instead.",
         );
     }
+    if (Object.hasOwn(rawConfig, "smart_drops")) {
+        preMigrationWarnings.push(
+            "smart_drops is deprecated and ignored; supersession reclaim is always on. This key no longer does anything; remove it.",
+        );
+    }
     preMigrationWarnings.push(...misplacedAgentModelWarnings(rawConfig));
     const migratedExperimental = migrateLegacyExperimental(
         configWithoutRemovedAgent,

package/src/config/latch-permanence-guard.test.ts

@@ -83,8 +83,13 @@ const KNOWN_SLOTS: Record<string, KnownSlot> = {
         },
     "packages/plugin/src/features/magic-context/smart-notes/sandbox-runner.ts:asyncModulePromise": {
         classification: "VERDICT",
-        reason: "DEFECT: a rejected dynamic-import/WASM-init promise is retained for every later smart-note check.",
+        reason: "Saved: the shared load has a ten-second deadline; timeout or rejection evicts the same cached attempt so a later check retries, and late native results cannot publish over a replacement.",
     },
+    "packages/plugin/src/features/magic-context/smart-notes/sandbox-runner.ts:asyncModuleLoadAttempted":
+        {
+            classification: "DIAGNOSTIC",
+            reason: "Memory-stat history only: records that loading was attempted even after cache eviction; it never gates loading, retry or guest execution.",
+        },
     "packages/plugin/src/features/magic-context/storage-meta-session.ts:sessionMetaSelectColumnsCache":
         {
             classification: "VERDICT",

package/src/config/live-run-config.ts

@@ -6,6 +6,7 @@ import { LIVE_RELOAD_CONFIG_PATHS, type MagicContextConfig } from "./schema/magi
 /** Copy only schema-marked live paths from fresh config; other settings retain boot values. */
 export function sampleLiveConfig<T extends MagicContextConfig>(boot: T, fresh: T): T {
     const result = { ...boot } as Record<string, unknown>;
+    result.cacheTtlConfigured = fresh.cacheTtlConfigured;
     for (const path of LIVE_RELOAD_CONFIG_PATHS) {
         const parts = path.split(".");
         let value: unknown = fresh;

package/src/config/migrate-config-location.test.ts

@@ -1,5 +1,13 @@
 import { describe, expect, it } from "bun:test";
-import { existsSync, mkdirSync, readFileSync, rmSync, utimesSync, writeFileSync } from "node:fs";
+import {
+    existsSync,
+    mkdirSync,
+    readFileSync,
+    rmSync,
+    statSync,
+    utimesSync,
+    writeFileSync,
+} from "node:fs";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { createTestTempDirFromPath } from "../shared/test-temp-dir";
@@ -18,6 +26,28 @@ function src(path: string, label = "legacy"): LegacyConfigSource {
 }
 
 describe("migrateConfigFile (location migration)", () => {
+    it("writes a user config migration with owner-only permissions", () => {
+        if (process.platform === "win32") return;
+        const dir = tmp();
+        try {
+            const target = join(dir, "config", "cortexkit", "magic-context.jsonc");
+            const legacy = join(dir, "legacy.jsonc");
+            writeFileSync(legacy, '{ "api_key": "secret" }\n');
+
+            const result = migrateConfigFile({
+                scope: "user",
+                targetPath: target,
+                legacySources: [src(legacy)],
+            });
+
+            expect(result.migrated).toBe(true);
+            expect(statSync(target).mode & 0o777).toBe(0o600);
+            expect(statSync(join(dir, "config", "cortexkit")).mode & 0o777).toBe(0o700);
+        } finally {
+            rmSync(dir, { recursive: true, force: true });
+        }
+    });
+
     it("no-ops when no legacy source exists", () => {
         const dir = tmp();
         try {

package/src/config/migrate-config-location.ts

@@ -1,18 +1,11 @@
-import {
-    closeSync,
-    existsSync,
-    mkdirSync,
-    openSync,
-    readFileSync,
-    renameSync,
-    rmSync,
-    statSync,
-    unlinkSync,
-    writeFileSync,
-} from "node:fs";
+import { existsSync, readFileSync, rmSync, statSync, unlinkSync } from "node:fs";
 import { homedir } from "node:os";
 import { basename, dirname, isAbsolute, join } from "node:path";
 import { removeJsoncValue } from "../shared/jsonc-edit";
+import {
+    ensureStorageDirectorySync,
+    writeStorageFileAtomicSync,
+} from "../shared/storage-permissions";
 
 /**
  * Config-LOCATION migration: move Magic Context config from the per-harness
@@ -328,7 +321,7 @@ const CONFIG_LOCK_STALE_MS = 4_000;
 function acquireConfigMigrationLock(lockDir: string): (() => void) | null {
     for (let attempt = 0; attempt < 2; attempt++) {
         try {
-            mkdirSync(lockDir, { recursive: false });
+            ensureStorageDirectorySync(lockDir, true, false);
             return () => {
                 try {
                     rmSync(lockDir, { recursive: true, force: true });
@@ -361,33 +354,7 @@ function acquireConfigMigrationLock(lockDir: string): (() => void) | null {
 // ── Atomic writes ────────────────────────────────────────────
 
 function atomicWriteConfigFile(targetPath: string, content: string): void {
-    mkdirSync(dirname(targetPath), { recursive: true });
-    const tmpPath = join(
-        dirname(targetPath),
-        `.${basename(targetPath)}.${process.pid}.${Date.now()}.${Math.random().toString(16).slice(2)}.tmp`,
-    );
-    let fd: number | null = null;
-    try {
-        fd = openSync(tmpPath, "wx", 0o600);
-        writeFileSync(fd, content);
-        closeSync(fd);
-        fd = null;
-        renameSync(tmpPath, targetPath);
-    } catch (err) {
-        if (fd !== null) {
-            try {
-                closeSync(fd);
-            } catch {
-                // best-effort close before cleanup
-            }
-        }
-        try {
-            unlinkSync(tmpPath);
-        } catch {
-            // best-effort temp cleanup
-        }
-        throw err;
-    }
+    writeStorageFileAtomicSync(targetPath, content, true);
 }
 
 // ── Marker ───────────────────────────────────────────────────
@@ -483,7 +450,7 @@ export function migrateConfigFile(opts: ConfigFileMigrationOptions): ConfigFileM
         return { migrated: false, conflict: false, targetPath: opts.targetPath, warnings };
     }
 
-    mkdirSync(dirname(opts.targetPath), { recursive: true });
+    ensureStorageDirectorySync(dirname(opts.targetPath), true);
     const release = acquireConfigMigrationLock(`${opts.targetPath}.lock`);
     if (!release) {
         // Another instance holds the lock past our short budget. Skip rather than

package/src/config/protected-tools.test.ts

@@ -0,0 +1,70 @@
+import { expect, it } from "bun:test";
+import { mkdirSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { protectedToolTagNumbers } from "../features/magic-context/reclaim-protection";
+import { createTestTempDirFromPath } from "../shared/test-temp-dir";
+import { loadPluginConfigDetailed, parsePluginConfig } from ".";
+import { MagicContextConfigSchema } from "./schema/magic-context";
+
+it("protected_tools defaults, validation, active-only ordinals and zero override", () => {
+    expect(MagicContextConfigSchema.parse({}).protected_tools).toEqual({
+        todowrite: 1,
+        ctx_reduce: 3,
+    });
+    for (const value of [-1, 1.5, "2", null])
+        expect(
+            MagicContextConfigSchema.safeParse({ protected_tools: { custom: value } }).success,
+        ).toBe(false);
+    const tags = [1, 2, 3, 4, 5].map((tagNumber) => ({
+        tagNumber,
+        toolName: tagNumber % 2 ? "MCP_CUSTOM" : "custom",
+        type: "tool",
+        status: tagNumber === 5 ? "compacted" : tagNumber === 4 ? "dropped" : "active",
+    }));
+    expect([...protectedToolTagNumbers(tags, { custom: 2 })]).toEqual([3, 2]);
+    expect([...protectedToolTagNumbers(tags, { custom: 0 })]).toEqual([]);
+    expect(parsePluginConfig({ smart_drops: false }).configWarnings).toContain(
+        "smart_drops is deprecated and ignored; supersession reclaim is always on. This key no longer does anything; remove it.",
+    );
+    expect(MagicContextConfigSchema.safeParse({ smart_drops: "ignored" }).success).toBe(true);
+});
+
+it("protected_tools does not treat inherited object keys as configured tools", () => {
+    const tags = ["constructor", "__proto__"].map((toolName, i) => ({
+        tagNumber: i + 1,
+        toolName,
+        type: "tool",
+        status: "active",
+    }));
+    expect([...protectedToolTagNumbers(tags)]).toEqual([]);
+    expect([...protectedToolTagNumbers(tags, { constructor: 1 })]).toEqual([1]);
+});
+
+it("protected_tools merges normalized project keys over user and shipped defaults", () => {
+    const dir = createTestTempDirFromPath(join(tmpdir(), "protected-tools-config-"));
+    const old = process.env.XDG_CONFIG_HOME;
+    try {
+        const project = join(dir, "project");
+        mkdirSync(join(dir, "cortexkit"), { recursive: true });
+        mkdirSync(join(project, ".cortexkit"), { recursive: true });
+        writeFileSync(
+            join(dir, "cortexkit/magic-context.jsonc"),
+            JSON.stringify({ protected_tools: { MCP_CUSTOM: 3, todowrite: 0 } }),
+        );
+        writeFileSync(
+            join(project, ".cortexkit/magic-context.jsonc"),
+            JSON.stringify({ protected_tools: { custom: 2, CTX_REDUCE: 1 } }),
+        );
+        process.env.XDG_CONFIG_HOME = dir;
+        expect(loadPluginConfigDetailed(project).config.protected_tools).toEqual({
+            custom: 2,
+            todowrite: 0,
+            ctx_reduce: 1,
+        });
+    } finally {
+        if (old === undefined) delete process.env.XDG_CONFIG_HOME;
+        else process.env.XDG_CONFIG_HOME = old;
+        rmSync(dir, { recursive: true, force: true });
+    }
+});

package/src/config/raw-loader.test.ts

@@ -375,6 +375,21 @@ describe("per-harness raw config migration", () => {
         expect(statSync(backupPath).ino).toBe(backupInode);
     });
 
+    it("creates user migration backups and replacement configs owner-only", () => {
+        if (process.platform === "win32") return;
+        const directory = temporaryDirectory();
+        const configPath = join(directory, "magic-context.jsonc");
+        const original = Buffer.from('{ "historian": { "model": "provider/model" } }\n');
+        writeFileSync(configPath, original);
+        chmodSync(configPath, 0o644);
+
+        const loaded = loadRawConfigFile({ configPath, tier: "user" });
+
+        expect(loaded?.migrated).toBe(true);
+        expect(statSync(configPath).mode & 0o777).toBe(0o600);
+        expect(statSync(`${configPath}.pre-per-harness.bak`).mode & 0o777).toBe(0o600);
+    });
+
     // stow, chezmoi and home-manager link the user config into a dotfiles repo.
     // Replacing the link with a regular file would silently stop later edits
     // from reaching that repo, so the migration writes through to the target.

package/src/config/raw-loader.ts

@@ -439,7 +439,7 @@ export function loadRawConfigFile(options: RawConfigLoadOptions): RawConfigLoadR
             // it in a dotfiles repo): the temporary file is created next to the
             // real file and renamed onto it, so the link itself stays a link.
             const writePath = realpathSync(options.configPath);
-            const mode = statSync(writePath).mode & 0o777;
+            const mode = options.tier === "user" ? 0o600 : statSync(writePath).mode & 0o777;
             writeExclusiveBackup(backupPath, observedBytes, mode);
             temporaryPath = writeTemporaryCandidate(writePath, migration.bytes, mode);
             options.afterTemporaryWrite?.();

package/src/config/removed-agent-source-fence.test.ts

@@ -23,6 +23,13 @@ const SOURCE_ROOTS = [
     join(REPO_ROOT, "packages", "dashboard", "src-tauri", "src"),
 ];
 const SOURCE_EXTENSIONS = new Set([".ts", ".tsx", ".js", ".jsx", ".mjs", ".cjs", ".rs", ".json"]);
+// The dashboard labels sessions from other CortexKit agents, and one of their run
+// kinds shares this name. These files name that external run kind, not the retired
+// Magic Context agent, so they are allowed to mention it.
+const EXTERNAL_RUN_KIND_FILES = new Set([
+    join(REPO_ROOT, "packages", "dashboard", "src", "lib", "session-label.ts"),
+    join(REPO_ROOT, "packages", "dashboard", "src", "lib", "session-label.test.ts"),
+]);
 
 function sourceFiles(directory: string, files: string[] = []): string[] {
     for (const entry of readdirSync(directory)) {
@@ -44,7 +51,9 @@ describe("retired agent source fence", () => {
         const offenses: string[] = [];
         for (const file of SOURCE_ROOTS.flatMap((root) => sourceFiles(root))) {
             const matches = readFileSync(file, "utf8").match(RETIRED_AGENT_PATTERN) ?? [];
-            const allowed = file === WARNING_SOURCE && matches.length === 1;
+            const allowed =
+                (file === WARNING_SOURCE && matches.length === 1) ||
+                EXTERNAL_RUN_KIND_FILES.has(file);
             if (!allowed && matches.length > 0) {
                 offenses.push(`${relative(REPO_ROOT, file)} (${matches.length})`);
             }