claude-flow 3.57.1 → 3.57.2

package/.claude/helpers/intelligence.cjs

@@ -277,11 +277,9 @@ function sessionGet(key) {
 
 function sessionSet(key, value) {
   try {
-    if (!fs.existsSync(SESSION_DIR)) fs.mkdirSync(SESSION_DIR, { recursive: true });
-    let session = {};
-    if (fs.existsSync(SESSION_FILE)) {
-      session = JSON.parse(fs.readFileSync(SESSION_FILE, 'utf-8'));
-    }
+    // Session creation belongs to session.cjs; recall may run before SessionStart.
+    if (!fs.existsSync(SESSION_FILE)) return;
+    const session = JSON.parse(fs.readFileSync(SESSION_FILE, 'utf-8'));
     if (!session.context) session.context = {};
     session.context[key] = value;
     session.updatedAt = new Date().toISOString();

package/.claude/proven-config.json

@@ -1,5 +1,5 @@
 {
-  "adoptedAt": 1792428331158,
+  "adoptedAt": 1792452783501,
   "championId": "sha256:6141a8ea990c5063b77e090ae8f37f9c539d8aa8f58dcceb30f3a82f97e57319",
   "manifest": {
     "schema": "ruflo.proven-config/v1",

package/node_modules/@claude-flow/codex/README.md

@@ -639,19 +639,19 @@ The `@claude-flow/codex` package now includes built-in dual-mode orchestration:
 
 ```bash
 # List available collaboration templates
-npx claude-flow-codex dual templates
+npx @claude-flow/codex dual templates
 
 # Run a feature development swarm
-npx claude-flow-codex dual run --template feature --task "Add user authentication"
+npx @claude-flow/codex dual run --template feature --task "Add user authentication"
 
 # Run a security audit swarm
-npx claude-flow-codex dual run --template security --task "src/auth/"
+npx @claude-flow/codex dual run --template security --task "src/auth/"
 
 # Run a refactoring swarm
-npx claude-flow-codex dual run --template refactor --task "src/legacy/"
+npx @claude-flow/codex dual run --template refactor --task "src/legacy/"
 
 # Check collaboration status
-npx claude-flow-codex dual status
+npx @claude-flow/codex dual status
 ```
 
 ### Codex Loop Runner
@@ -660,15 +660,15 @@ Codex does not expose Claude Code's `ScheduleWakeup`, so `@claude-flow/codex` pr
 
 ```bash
 # Run Codex repeatedly until it creates .codex/loop/default.complete or reaches 10 iterations
-npx claude-flow-codex loop run "Fix failing tests and create the completion marker when done"
+npx @claude-flow/codex loop run "Fix failing tests and create the completion marker when done"
 
 # Use command mode for recurring Ruflo workers or custom scripts
-npx claude-flow-codex loop run --name testgaps --interval 270 --max-iterations 0 \
+npx @claude-flow/codex loop run --name testgaps --interval 270 --max-iterations 0 \
   --command "npx claude-flow hooks worker dispatch --trigger testgaps"
 
 # Inspect or stop a loop from another terminal
-npx claude-flow-codex loop status --name testgaps
-npx claude-flow-codex loop stop --name testgaps
+npx @claude-flow/codex loop status --name testgaps
+npx @claude-flow/codex loop stop --name testgaps
 ```
 
 Loop state is stored in `.codex/loop/<name>.json`; `loop stop` writes `.codex/loop/<name>.stop`, which the runner observes between iterations.

package/node_modules/@claude-flow/codex/dist/dual-mode/cli.js

@@ -174,17 +174,17 @@ function createTemplateCommand() {
         console.log(chalk.cyan('feature') + ' - Feature Development Swarm');
         console.log('  Pipeline: architect → coder → tester → reviewer');
         console.log('  Platforms: Claude (architect, reviewer) + Codex (coder, tester)');
-        console.log('  Usage: npx claude-flow-codex dual run --template feature --task "Add user auth"');
+        console.log('  Usage: npx @claude-flow/codex dual run --template feature --task "Add user auth"');
         console.log();
         console.log(chalk.cyan('security') + ' - Security Audit Swarm');
         console.log('  Pipeline: scanner → analyzer → fixer');
         console.log('  Platforms: Codex (scanner, fixer) + Claude (analyzer)');
-        console.log('  Usage: npx claude-flow-codex dual run --template security --task "src/auth/"');
+        console.log('  Usage: npx @claude-flow/codex dual run --template security --task "src/auth/"');
         console.log();
         console.log(chalk.cyan('refactor') + ' - Refactoring Swarm');
         console.log('  Pipeline: analyzer → planner → refactorer → validator');
         console.log('  Platforms: Claude (analyzer, planner) + Codex (refactorer, validator)');
-        console.log('  Usage: npx claude-flow-codex dual run --template refactor --task "src/legacy/"');
+        console.log('  Usage: npx @claude-flow/codex dual run --template refactor --task "src/legacy/"');
         console.log();
         console.log(chalk.gray('Custom configurations can be provided via --config <path.json>'));
     });

package/node_modules/@claude-flow/codex/dist/dual-mode/cli.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "claude-flow",
-  "version": "3.57.1",
+  "version": "3.57.2",
   "workspaces": [
     "v3/@claude-flow/codex",
     "v3/@claude-flow/mcp",
@@ -68,7 +68,7 @@
     "v3:security": "npm run security:audit && npm run security:test"
   },
   "dependencies": {
-    "@claude-flow/cli-core": "3.7.4",
+    "@claude-flow/cli-core": "3.7.5",
     "@claude-flow/codex": "3.0.5",
     "@claude-flow/mcp": "3.1.1",
     "@claude-flow/neural": "3.0.0",
@@ -113,6 +113,7 @@
     "js-yaml": ">=4.3.0",
     "hono": ">=4.13.2",
     "@ruvector/rvf-wasm": "0.1.5",
+    "@ruvector/rvf": "0.3.4",
     "@hono/node-server": ">=2.1.1",
     "flatted": ">=3.4.0",
     "tar": ">=7.5.11",

package/v3/@claude-flow/cli/catalog-manifest.json

@@ -1,8 +1,8 @@
 {
   "schemaVersion": 1,
   "generation": 7,
-  "generatedAt": "2026-10-19T16:47:16.220Z",
-  "gitSha": "aedd3d53",
+  "generatedAt": "2026-10-19T23:34:04.095Z",
+  "gitSha": "7be330bc",
   "catalog": {
     "agents": 176,
     "tools": 423,

package/v3/@claude-flow/cli/dist/src/commands/hooks.js

@@ -2333,6 +2333,19 @@ const workerListCommand = {
         }
     }
 };
+// Render the status hooks_worker-dispatch actually returned. Only a status that
+// means work finished may read as "completed" (#4196).
+function dispatchStatusLabel(status) {
+    switch (status) {
+        case 'dispatched': return output.highlight('dispatched (background)');
+        case 'queued': return output.highlight('queued (daemon)');
+        case 'no-daemon': return output.warning('no-daemon (not run)');
+        case 'mcp-only': return output.warning('mcp-only (not queued)');
+        case 'synthetic-completed': return output.warning('recorded (no work executed)');
+        case 'completed': return output.success('completed');
+        default: return output.dim(String(status));
+    }
+}
 const workerDispatchCommand = {
     name: 'dispatch',
     description: 'Dispatch a background worker for analysis/optimization',
@@ -2386,9 +2399,15 @@ const workerDispatchCommand = {
                     { field: 'Description', value: result.config.description },
                     { field: 'Est. Duration', value: result.config.estimatedDuration },
                     { field: 'Capabilities', value: result.config.capabilities.join(', ') },
-                    { field: 'Status', value: result.status === 'dispatched' ? output.highlight('dispatched (background)') : output.success('completed') },
+                    { field: 'Status', value: dispatchStatusLabel(result.status) },
                 ],
             });
+            // The tool says why it could not run the worker (e.g. no daemon); show it
+            // rather than letting a recorded-only dispatch read as finished work (#4196).
+            if (result.note) {
+                output.writeln();
+                output.printWarning(result.note);
+            }
             if (background) {
                 output.writeln();
                 output.writeln(output.dim(`Check status: claude-flow hooks worker status --id ${result.workerId}`));

package/v3/@claude-flow/cli/dist/src/commands/memory.js

@@ -659,7 +659,9 @@ const searchCommand = {
                     });
                     return {
                         results: r.results.map(e => ({
-                            id: e.id,
+                            // #2271: searchEntries() ids are truncated to 12 chars and collide
+                            // for entries written within ~2.8h; SmartRetrieval dedupes on id.
+                            id: JSON.stringify([e.namespace, e.key]),
                             key: e.key,
                             content: e.content,
                             score: e.score,
@@ -1592,6 +1594,13 @@ const exportCommand = {
                 namespace: ctx.flags.namespace,
                 includeVectors: ctx.flags.includeVectors ?? true,
             });
+            // memory_export reports failure as { error } rather than throwing; without
+            // this check the command printed "Exported to undefined" and then crashed
+            // reading result.exported.entries (#4204).
+            if (!result || result.error || !result.exported) {
+                output.printError(`Export error: ${result?.error ?? 'memory_export returned no export summary'}`);
+                return { success: false, exitCode: 1 };
+            }
             output.printSuccess(`Exported to ${result.outputPath}`);
             output.printList([
                 `Entries: ${result.exported.entries}`,
@@ -1657,6 +1666,21 @@ const importCommand = {
                 namespace: ctx.flags.namespace,
                 dbPath: resolveDbPath(ctx.flags.path),
             });
+            // memory_import reports a bad file as { error } rather than throwing, and
+            // a partial write as { success: false, error, imported }. Without this the
+            // command printed "Imported from undefined" and crashed on result.imported,
+            // or reported success for an import that dropped entries.
+            const failure = result?.error;
+            if (!result || failure || result.success === false || !result.imported) {
+                output.printError(`Import error: ${failure ?? 'memory_import returned no import summary'}`);
+                if (result?.imported) {
+                    output.printList([
+                        `Entries imported: ${result.imported.entries}`,
+                        `Failed: ${result.failed ?? 'unknown'}`,
+                    ]);
+                }
+                return { success: false, exitCode: 1 };
+            }
             output.printSuccess(`Imported from ${result.inputPath}`);
             output.printList([
                 `Entries: ${result.imported.entries}`,

package/v3/@claude-flow/cli/dist/src/commands/workflow.js

@@ -111,6 +111,12 @@ const runCommand = {
                     dryRun,
                 },
             });
+            const runError = toolError(result);
+            if (runError || !result.metrics) {
+                spinner.fail('Workflow failed');
+                output.printError(`Workflow error: ${runError ?? 'workflow_run returned no workflow summary'}`);
+                return { success: false, exitCode: 1 };
+            }
             if (dryRun) {
                 spinner.succeed('Workflow validated successfully');
             }
@@ -277,6 +283,11 @@ const listCommand = {
                 status: status || 'all',
                 limit,
             });
+            const listError = toolError(result);
+            if (listError || !Array.isArray(result.workflows)) {
+                output.printError(`Failed to list workflows: ${listError ?? 'workflow_list returned no workflows'}`);
+                return { success: false, exitCode: 1 };
+            }
             if (ctx.flags.format === 'json') {
                 output.printJson(result);
                 return { success: true, data: result };
@@ -290,13 +301,19 @@ const listCommand = {
             }
             output.printTable({
                 columns: [
-                    { key: 'id', header: 'ID', width: 15 },
-                    { key: 'template', header: 'Template', width: 15 },
+                    { key: 'id', header: 'ID', width: 30 },
+                    { key: 'name', header: 'Name', width: 24 },
                     { key: 'status', header: 'Status', width: 12, format: formatStageStatus },
-                    { key: 'progress', header: 'Progress', width: 10, align: 'right', format: (v) => `${v}%` },
-                    { key: 'startedAt', header: 'Started', width: 20, format: (v) => new Date(String(v)).toLocaleString() }
+                    { key: 'steps', header: 'Steps', width: 6, align: 'right' },
+                    { key: 'createdAt', header: 'Created', width: 20, format: (v) => new Date(String(v)).toLocaleString() }
                 ],
-                data: result.workflows
+                data: result.workflows.map(w => ({
+                    id: w.workflowId,
+                    name: w.name,
+                    status: w.status,
+                    steps: w.stepCount,
+                    createdAt: w.createdAt,
+                }))
             });
             output.writeln();
             output.printInfo(`Total: ${result.total} workflows`);
@@ -335,30 +352,37 @@ const statusCommand = {
         try {
             const result = await callMCPTool('workflow_status', {
                 workflowId,
+                verbose: true,
             });
+            const statusError = toolError(result);
+            if (statusError) {
+                output.printError(`Failed to get status: ${statusError}`);
+                return { success: false, exitCode: 1 };
+            }
             if (ctx.flags.format === 'json') {
                 output.printJson(result);
                 return { success: true, data: result };
             }
+            const started = result.startedAt ? Date.parse(result.startedAt) : NaN;
+            const ended = result.completedAt ? Date.parse(result.completedAt) : Date.now();
             output.writeln();
             output.printBox([
-                `ID: ${result.id}`,
-                `Template: ${result.template}`,
+                `ID: ${result.workflowId}`,
+                `Name: ${result.name}`,
                 `Status: ${formatStageStatus(result.status)}`,
-                `Progress: ${result.progress}%`,
-                `Duration: ${(result.metrics.duration / 1000).toFixed(1)}s`,
-                `Tokens: ${result.metrics.tokensUsed.toLocaleString()}`,
-                `Agents: ${result.metrics.agentsSpawned}`
+                `Progress: ${Math.round(result.progress)}% (${result.completedSteps}/${result.totalSteps} steps)`,
+                ...(Number.isNaN(started) ? [] : [`Duration: ${((ended - started) / 1000).toFixed(1)}s`]),
+                ...(result.error ? [`Error: ${result.error}`] : []),
             ].join('\n'), 'Workflow Status');
             output.writeln();
-            output.writeln(output.bold('Stage Progress'));
+            output.writeln(output.bold('Step Progress'));
             output.printTable({
                 columns: [
-                    { key: 'name', header: 'Stage', width: 20 },
+                    { key: 'name', header: 'Step', width: 24 },
+                    { key: 'type', header: 'Type', width: 10 },
                     { key: 'status', header: 'Status', width: 12, format: formatStageStatus },
-                    { key: 'agents', header: 'Agents', width: 25, format: (v) => Array.isArray(v) ? v.length.toString() : '0' }
                 ],
-                data: result.stages
+                data: result.steps ?? []
             });
             return { success: true, data: result };
         }
@@ -408,6 +432,11 @@ const stopCommand = {
                 workflowId,
                 graceful: !force,
             });
+            const stopError = toolError(result);
+            if (stopError || result.stopped !== true) {
+                output.printError(`Failed to stop workflow: ${stopError ?? 'the workflow was not stopped'}`);
+                return { success: false, exitCode: 1 };
+            }
             output.printSuccess(`Workflow ${workflowId} stopped`);
             return { success: true, data: result };
         }
@@ -556,6 +585,17 @@ export const workflowCommand = {
     }
 };
 // Helper functions
+/**
+ * The workflow MCP tools report failure as `{ error }` (or `{ success: false, error }`)
+ * instead of throwing, so a command that reads the result without checking it prints
+ * a false success or crashes on a field the error result does not have.
+ */
+function toolError(result) {
+    const r = result;
+    if (!r)
+        return 'the workflow tool returned no result';
+    return typeof r.error === 'string' && r.error.length > 0 ? r.error : undefined;
+}
 function formatStageStatus(status) {
     const statusStr = String(status);
     switch (statusStr) {

package/v3/@claude-flow/cli/dist/src/init/executor.js

@@ -18,7 +18,7 @@ import { generatePreCommitHook, generatePostCommitHook, generateSessionManager,
 import { getInstalledCliVersion, HELPERS_STAMP_FILE } from './helper-refresh.js';
 import { generateClaudeMd } from './claudemd-generator.js';
 import { recordMemoryPackagePath } from './memory-package-resolver.js';
-import { ensureCommonJsCompanions } from './helper-companions.js';
+import { COMMONJS_COMPANION_HELPERS, ensureCommonJsCompanions } from './helper-companions.js';
 import { scanSettingsForRisk, formatRiskFindingsAsWarnings } from './settings-risk-scanner.js';
 import { AUTO_MEMORY_HOOK_TIMEOUT_S, helperHookCommand, helperScopeFor, helperStatusLineCommand, pinToUserHelpers } from './helper-commands.js';
 /**
@@ -548,10 +548,14 @@ export async function executeUpgrade(targetDir, upgradeSettings = false) {
                 catch { }
             }
         }
-        // #3555: the refreshed hook-handler requires the .cjs companions; older
-        // installs only have session.js / memory.js, which can't load in ESM.
-        for (const name of await ensureCommonJsCompanions(path.join(targetDir, '.claude', 'helpers'))) {
-            result.created.push(`.claude/helpers/${name}`);
+        // #4198: refresh existing companions too, so upgraded hook handlers never
+        // keep obsolete session/memory logic. Generate from the CLI trust root.
+        const helpersDir = path.join(targetDir, '.claude', 'helpers');
+        const existingCompanions = new Set(COMMONJS_COMPANION_HELPERS.filter((name) => fs.existsSync(path.join(helpersDir, name))));
+        for (const name of await ensureCommonJsCompanions(helpersDir, true)) {
+            const changes = existingCompanions.has(name)
+                ? result.updated : result.created;
+            changes.push(`.claude/helpers/${name}`);
         }
         // Stamp the installed version so the startup auto-refresh treats these as
         // current (no redundant re-copy on the next command).

package/v3/@claude-flow/cli/dist/src/init/helper-companions.d.ts

@@ -1,3 +1,3 @@
 export declare const COMMONJS_COMPANION_HELPERS: readonly ["session.cjs", "memory.cjs"];
-export declare function ensureCommonJsCompanions(helpersDir: string): Promise<string[]>;
+export declare function ensureCommonJsCompanions(helpersDir: string, force?: boolean): Promise<string[]>;
 //# sourceMappingURL=helper-companions.d.ts.map

package/v3/@claude-flow/cli/dist/src/init/helper-companions.js

@@ -7,13 +7,14 @@
  * `.js` copies, which the refreshed hook-handler no longer requires, so the
  * refresh writes any missing `.cjs` companion from the CLI's own compiled
  * generators (the trust root; no external file to verify). Stale `.js` copies
- * are left in place and ignored. Existing `.cjs` files are never overwritten.
+ * are left in place and ignored. Existing `.cjs` files are preserved during
+ * startup refresh; an explicit init upgrade replaces them from the generators.
  */
 import * as fs from 'fs';
 import * as path from 'path';
 export const COMMONJS_COMPANION_HELPERS = ['session.cjs', 'memory.cjs'];
-export async function ensureCommonJsCompanions(helpersDir) {
-    const missing = COMMONJS_COMPANION_HELPERS.filter((name) => !fs.existsSync(path.join(helpersDir, name)));
+export async function ensureCommonJsCompanions(helpersDir, force = false) {
+    const missing = COMMONJS_COMPANION_HELPERS.filter((name) => force || !fs.existsSync(path.join(helpersDir, name)));
     if (missing.length === 0)
         return [];
     const gen = await import('./helpers-generator.js');

package/v3/@claude-flow/cli/dist/src/mcp-tools/hooks-tools.js

@@ -4175,12 +4175,12 @@ export const hooksIntelligenceLearn = {
 // Intelligence attention hook
 export const hooksIntelligenceAttention = {
     name: 'hooks_intelligence_attention',
-    description: 'Compute attention-weighted similarity using MoE/Flash/Hyperbolic Use when native Bash hooks (via Claude Code\'s settings.json) are wrong because you need Ruflo-side state — pattern persistence, neural training signals, model-routing learning, cost tracking, audit chain. For one-off shell commands, plain Bash hooks are fine.',
+    description: 'Compute attention-weighted similarity using MoE/Flash. Use when native Bash hooks (via Claude Code\'s settings.json) are wrong because you need Ruflo-side state — pattern persistence, neural training signals, model-routing learning, cost tracking, audit chain. For one-off shell commands, plain Bash hooks are fine.',
     inputSchema: {
         type: 'object',
         properties: {
             query: { type: 'string', description: 'Query for attention computation' },
-            mode: { type: 'string', description: 'Attention mode (flash, moe, hyperbolic)' },
+            mode: { type: 'string', description: 'Attention mode (flash, moe)' },
             topK: { type: 'number', description: 'Top-k results' },
         },
         required: ['query'],
@@ -4195,6 +4195,12 @@ export const hooksIntelligenceAttention = {
             if (!v.valid)
                 return { success: false, error: v.error };
         }
+        // #3548: only flash and moe have an implementation. Any other mode
+        // (including the previously advertised 'hyperbolic') used to return an
+        // empty stub whose note blamed a missing package; say so instead.
+        if (mode !== 'flash' && mode !== 'moe') {
+            return { success: false, error: `Attention mode "${mode}" is not implemented; supported modes: flash, moe` };
+        }
         let implementation = 'placeholder';
         let embeddingSource = 'none';
         const results = [];
@@ -4370,7 +4376,7 @@ export const hooksIntelligenceAttention = {
                 implementation,
                 _embeddingSource: embeddingSource,
                 _stub: implementation === 'none',
-                _note: implementation === 'none' ? 'No attention backend available. Install @ruvector/attention for real computation.' : undefined,
+                _note: implementation === 'none' ? 'No attention backend available: flash/moe attention from @claude-flow/neural could not be loaded or failed.' : undefined,
                 ...(embeddingSource === 'hash-fallback' && implementation !== 'none'
                     ? { _embeddingNote: 'Query embeddings are hash-based (not semantic). Install @claude-flow/embeddings for real ONNX embeddings.' }
                     : {}),

package/v3/@claude-flow/cli/dist/src/mcp-tools/memory-tools.js

@@ -227,15 +227,31 @@ function loadLegacyStore() {
 /**
  * Mark migration as complete
  */
-function markMigrationComplete() {
+function markMigrationComplete(counts) {
     const legacyDir = resolve(LEGACY_MEMORY_DIR);
     if (!existsSync(legacyDir))
         mkdirSync(legacyDir, { recursive: true });
     writeFileSync(resolve(join(LEGACY_MEMORY_DIR, MIGRATION_MARKER)), JSON.stringify({
         migratedAt: new Date().toISOString(),
         version: '3.0.0',
+        ...(counts ?? {}),
     }), 'utf-8');
 }
+/**
+ * Counts recorded by the migration that wrote the marker, or null when no
+ * marker (or an older marker without counts) is present.
+ */
+function readMigrationCounts() {
+    try {
+        const marker = JSON.parse(readFileSync(resolve(join(LEGACY_MEMORY_DIR, MIGRATION_MARKER)), 'utf-8'));
+        return typeof marker?.migrated === 'number' && typeof marker?.total === 'number'
+            ? { migrated: marker.migrated, total: marker.total }
+            : null;
+    }
+    catch {
+        return null;
+    }
+}
 /**
  * Lazy-load memory initializer functions to avoid circular deps
  */
@@ -391,7 +407,7 @@ async function ensureInitialized(dbPath) {
                         }
                     }
                     console.error(`[MCP Memory] Migrated ${migrated}/${Object.keys(legacyStore.entries).length} entries`);
-                    markMigrationComplete();
+                    markMigrationComplete({ migrated, total: Object.keys(legacyStore.entries).length });
                 }
             }
         }
@@ -636,7 +652,11 @@ export const memoryTools = [
                             });
                             return {
                                 results: r.results.map(e => ({
-                                    id: e.id,
+                                    // #2271: searchEntries() truncates ids to 12 chars ("entry_" +
+                                    // the leading digits of Date.now()), so entries written within
+                                    // ~2.8h share one id and RRF fused them into a single result.
+                                    // SmartRetrieval dedupes on id: give it the (namespace, key) tuple.
+                                    id: JSON.stringify([e.namespace, e.key]),
                                     key: e.key,
                                     content: e.content,
                                     score: e.score,
@@ -966,11 +986,17 @@ export const memoryTools = [
         },
         handler: async (input) => {
             const force = input.force;
-            // Remove migration marker if forcing
+            // Remove the migration marker if forcing. hasLegacyStore() checks the marker
+            // beside the legacy store, so that is the one force must clear (#4194);
+            // the old .swarm marker path is cleared too for compatibility.
             if (force) {
-                const markerPath = getMigrationMarkerPath();
-                if (existsSync(markerPath)) {
-                    unlinkSync(markerPath);
+                for (const markerPath of [
+                    resolve(join(LEGACY_MEMORY_DIR, MIGRATION_MARKER)),
+                    getMigrationMarkerPath(),
+                ]) {
+                    if (existsSync(markerPath)) {
+                        unlinkSync(markerPath);
+                    }
                 }
             }
             // Check for legacy data
@@ -982,12 +1008,35 @@ export const memoryTools = [
                     migrated: 0,
                 };
             }
+            // A marker beside the store means a migration already ran; ensureInitialized
+            // would move nothing, so say so instead of reporting the store's size.
+            if (!hasLegacyStore()) {
+                return {
+                    success: true,
+                    message: 'Legacy store already migrated (marker present); nothing was moved. Pass force: true to re-run.',
+                    migrated: 0,
+                    total: Object.keys(legacyStore.entries).length,
+                };
+            }
             // Run migration via ensureInitialized
             await ensureInitialized();
+            // ensureInitialized swallows errors and records what it moved in the marker.
+            const counts = readMigrationCounts();
+            if (!counts) {
+                return {
+                    success: false,
+                    message: 'Migration did not complete; no entries were recorded as migrated. See the MCP server log.',
+                    migrated: 0,
+                    total: Object.keys(legacyStore.entries).length,
+                };
+            }
             return {
                 success: true,
-                message: 'Migration completed',
-                migrated: Object.keys(legacyStore.entries).length,
+                message: counts.migrated === counts.total
+                    ? 'Migration completed'
+                    : `Migration completed with failures: ${counts.migrated} of ${counts.total} entries migrated`,
+                migrated: counts.migrated,
+                total: counts.total,
                 backend: await describeBackend(),
             };
         },

package/v3/@claude-flow/cli/dist/src/mcp-tools/workflow-tools.js

@@ -577,7 +577,8 @@ export const workflowTools = [
             const store = loadWorkflowStore();
             let workflows = Object.values(store.workflows);
             // Apply filters
-            if (input.status) {
+            // 'all' is the CLI's explicit "no filter" value (`workflow list` sends it by default).
+            if (input.status && input.status !== 'all') {
                 workflows = workflows.filter(w => w.status === input.status);
             }
             // Sort by creation date (newest first)

package/v3/@claude-flow/cli/dist/src/memory/graph-edge-writer.d.ts

@@ -30,10 +30,12 @@
  * @module v3/cli/memory/graph-edge-writer
  */
 /**
- * True iff the memory.db bridge at `customDbPath` (or the default location)
- * is currently RFE1-encrypted-at-rest. Callers that receive `null` from
- * getBridgeDb()/insertGraphEdge() can use this to avoid recommending the
- * destructive `memory init` command for this specific, non-corrupt case.
+ * True iff the memory.db bridge at `customDbPath` — or, when omitted, the
+ * path `resolveDbPath()` resolves from the `CLAUDE_FLOW_DB_PATH` env binding
+ * / memory root default (#4291) — is currently RFE1-encrypted-at-rest.
+ * Callers that receive `null` from getBridgeDb()/insertGraphEdge() can use
+ * this to avoid recommending the destructive `memory init` command for this
+ * specific, non-corrupt case.
  */
 export declare function isBridgeDbEncryptedAtRest(customDbPath?: string): boolean;
 /** Test-only: clear the once-per-path warning dedup set. */
@@ -60,6 +62,16 @@ export declare function releaseBridgeDb(dbPath?: string): boolean;
  * #2431 fix: better-sqlite3 + WAL mode replaces sql.js + whole-file
  * writeFileSync. Eliminates the dual-write race that corrupted memory.db
  * when called alongside the memory bridge's better-sqlite3 writer.
+ *
+ * #4291 fix: the file is resolved via `resolveDbPath()` — the project's one
+ * documented path-priority rule (explicit `customDbPath` argument wins, then
+ * the `CLAUDE_FLOW_DB_PATH` env binding, then the plain `memory.db` default
+ * under the memory root) — instead of a local `customDbPath ?? <default>`
+ * expression that silently ignored `CLAUDE_FLOW_DB_PATH`. A caller that
+ * explicitly selected a store via that env var no longer gets answers read
+ * from a different, unselected database file. When the resolved file is
+ * missing (and `createIfMissing` is false) or encrypted at rest, this
+ * refuses (returns null) rather than falling back to any other store.
  */
 export declare function getBridgeDb(customDbPath?: string, opts?: {
     createIfMissing?: boolean;

package/v3/@claude-flow/cli/dist/src/memory/graph-edge-writer.js

@@ -33,7 +33,7 @@ import * as path from 'path';
 import * as fs from 'fs';
 import * as crypto from 'crypto';
 import { execFileSync } from 'child_process';
-import { getMemoryRoot } from './memory-initializer.js';
+import { resolveDbPath } from './memory-initializer.js';
 import { encodeEmbedding } from './embedding-quantization.js';
 import { loadBetterSqlite3 } from './shared-sqlite.js';
 import { isEncryptedBlob } from '../encryption/vault.js';
@@ -125,13 +125,15 @@ function warnRfe1EncryptedOnce(dbPath) {
         'See #2889 (https://github.com/ruvnet/ruflo/issues/2889) for details and recovery options.');
 }
 /**
- * True iff the memory.db bridge at `customDbPath` (or the default location)
- * is currently RFE1-encrypted-at-rest. Callers that receive `null` from
- * getBridgeDb()/insertGraphEdge() can use this to avoid recommending the
- * destructive `memory init` command for this specific, non-corrupt case.
+ * True iff the memory.db bridge at `customDbPath` — or, when omitted, the
+ * path `resolveDbPath()` resolves from the `CLAUDE_FLOW_DB_PATH` env binding
+ * / memory root default (#4291) — is currently RFE1-encrypted-at-rest.
+ * Callers that receive `null` from getBridgeDb()/insertGraphEdge() can use
+ * this to avoid recommending the destructive `memory init` command for this
+ * specific, non-corrupt case.
  */
 export function isBridgeDbEncryptedAtRest(customDbPath) {
-    const dbPath = customDbPath ?? path.join(getMemoryRoot(), 'memory.db');
+    const dbPath = resolveDbPath(customDbPath);
     return fs.existsSync(dbPath) && isRfe1EncryptedAtRest(dbPath);
 }
 /** Test-only: clear the once-per-path warning dedup set. */
@@ -222,9 +224,19 @@ export function releaseBridgeDb(dbPath) {
  * #2431 fix: better-sqlite3 + WAL mode replaces sql.js + whole-file
  * writeFileSync. Eliminates the dual-write race that corrupted memory.db
  * when called alongside the memory bridge's better-sqlite3 writer.
+ *
+ * #4291 fix: the file is resolved via `resolveDbPath()` — the project's one
+ * documented path-priority rule (explicit `customDbPath` argument wins, then
+ * the `CLAUDE_FLOW_DB_PATH` env binding, then the plain `memory.db` default
+ * under the memory root) — instead of a local `customDbPath ?? <default>`
+ * expression that silently ignored `CLAUDE_FLOW_DB_PATH`. A caller that
+ * explicitly selected a store via that env var no longer gets answers read
+ * from a different, unselected database file. When the resolved file is
+ * missing (and `createIfMissing` is false) or encrypted at rest, this
+ * refuses (returns null) rather than falling back to any other store.
  */
 export async function getBridgeDb(customDbPath, opts) {
-    const dbPath = customDbPath ?? path.join(getMemoryRoot(), 'memory.db');
+    const dbPath = resolveDbPath(customDbPath);
     const createIfMissing = opts?.createIfMissing === true;
     if (_db && _dbPath === dbPath) {
         armIdleRelease();

package/v3/@claude-flow/cli/dist/src/memory/intelligence.js

@@ -1077,6 +1077,10 @@ export async function recordTrajectory(steps, verdict) {
         }
         bumpStat('trajectoriesRecorded');
         globalStats.lastAdaptation = Date.now();
+        // #4283: the bank's own save is debounced, and the one-shot bins exit as
+        // soon as the command resolves, so write the patterns now. Otherwise
+        // stats.json counts patterns that never reach patterns.json.
+        reasoningBank?.flushToDisk();
         savePersistedStats();
         return true;
     }

package/v3/@claude-flow/cli/dist/src/memory/memory-initializer.js

@@ -2131,15 +2131,19 @@ async function loadLocalEmbeddingChain(verbose = false, startTime = Date.now())
             if (verbose) {
                 console.log('Loading agentic-flow ReasoningBank embedding model...');
             }
+            // #3113: register a callable, like the ruvector branch below —
+            // generateLocalEmbedding() only invokes function models. The bundled
+            // model is all-MiniLM-L6-v2 (384-dim, per agentic-flow's
+            // getEmbeddingDimensions()).
             embeddingModelState = {
                 loaded: true,
-                model: { embed: reasoningBank.computeEmbedding },
+                model: (text) => reasoningBank.computeEmbedding(text),
                 tokenizer: null,
-                dimensions: 768
+                dimensions: 384
             };
             return {
                 success: true,
-                dimensions: 768,
+                dimensions: 384,
                 modelName: 'agentic-flow/reasoningbank',
                 loadTime: Date.now() - startTime
             };
@@ -2272,10 +2276,13 @@ export async function generateLocalEmbedding(text) {
     if (state.model && typeof state.model === 'function') {
         try {
             const output = await state.model(text, { pooling: 'mean', normalize: true });
-            // Handle both @xenova/transformers (output.data) and ruvector (plain array) formats
+            // Handle @xenova/transformers (output.data), ruvector (plain array) and
+            // typed-array (ReasoningBank Float32Array, #3114) formats. DataView is an
+            // ArrayBuffer view without an iterator (Array.from gives []), so exclude it.
             const embedding = output?.data
                 ? Array.from(output.data)
-                : Array.isArray(output) ? output : null;
+                : Array.isArray(output) ? output
+                    : ArrayBuffer.isView(output) && !(output instanceof DataView) ? Array.from(output) : null;
             if (embedding) {
                 return {
                     embedding,

package/v3/@claude-flow/cli/dist/src/services/memory-backup.d.ts

@@ -10,7 +10,12 @@ export interface BackupOptions {
     /** Injected epoch millis (tests pass a fixed value; avoids Date.now in logic). */
     timestamp?: number;
     verbose?: boolean;
+    /** Test seam: inject a fake better-sqlite3-shaped constructor instead of importing the real module. */
+    Database?: new (path: string, opts?: Record<string, unknown>) => any;
 }
+/** Which method actually produced the snapshot — downstream migration tooling
+ * should require `native-online-backup` rather than trusting a blanket `backedUp: true`. */
+export type BackupMethod = 'native-online-backup' | 'raw-copy-fallback';
 export interface BackupResult {
     backedUp: boolean;
     path?: string;
@@ -18,6 +23,7 @@ export interface BackupResult {
     rotatedAway?: string[];
     gcsUri?: string;
     skipped?: string;
+    method?: BackupMethod;
 }
 export declare function defaultMemoryDbPath(cwd?: string): string;
 export interface ProjectBackupResult extends BackupResult {

package/v3/@claude-flow/cli/dist/src/services/memory-backup.js

@@ -14,7 +14,7 @@
  */
 import * as fs from 'fs';
 import * as path from 'path';
-import { readFileMaybeEncrypted } from '../fs-secure.js';
+import { existingFileIsEncrypted, readFileMaybeEncrypted } from '../fs-secure.js';
 import { loadBetterSqlite3 } from '../memory/shared-sqlite.js';
 import { resolveMemoryRoot } from '../memory/memory-root.js';
 export function defaultMemoryDbPath(cwd = process.cwd()) {
@@ -37,12 +37,18 @@ export async function backupProjectMemoryDbs(cwd, opts = {}) {
     }
     const successful = backups.filter(result => result.backedUp);
     const failed = backups.find(result => !result.backedUp && result.skipped !== 'no-db');
+    // Only report an aggregate `method` when every successful store agrees — a
+    // mixed native/raw-copy result must not collapse to whichever store
+    // happened to be first, the exact false-confidence #4287 is about.
+    const methods = new Set(successful.map(result => result.method));
+    const aggregateMethod = methods.size === 1 ? successful[0]?.method : undefined;
     return {
         ...successful[0],
         backedUp: successful.length > 0 && !failed,
         sizeBytes: successful.reduce((sum, result) => sum + (result.sizeBytes ?? 0), 0),
         rotatedAway: successful.flatMap(result => result.rotatedAway ?? []),
         skipped: failed?.skipped ?? (successful.length === 0 ? 'no-db' : undefined),
+        method: aggregateMethod,
         backups,
     };
 }
@@ -63,88 +69,25 @@ function isSnapshotFor(file, dbPath) {
     return file.startsWith(prefix)
         && /^\d{4}-\d{2}-\d{2}T\d{2}-\d{2}-\d{2}-\d{3}Z\.db$/.test(file.slice(prefix.length));
 }
-export async function backupMemoryDb(opts = {}) {
-    const dbPath = opts.dbPath ?? defaultMemoryDbPath();
-    if (!dbPath || !fs.existsSync(dbPath))
-        return { backedUp: false, skipped: 'no-db' };
-    let Database;
+/**
+ * A plain file copy of a live WAL-mode SQLite database is not a consistent
+ * snapshot — committed data can live only in the `-wal` sidecar until it's
+ * checkpointed back into the main file. We can't open an RFE1-encrypted
+ * source natively to run a real `wal_checkpoint` probe (it isn't a SQLite
+ * image), so for the raw-copy-fallback path the only signal available is
+ * sidecar presence: a non-empty `-wal` file means there are frames that a
+ * copy of the main file alone would silently drop. Fail closed on that.
+ */
+function hasActiveWal(dbPath) {
     try {
-        const mod = 'better-sqlite3';
-        Database = (await import(mod)).default;
+        return fs.statSync(`${dbPath}-wal`).size > 0;
     }
     catch {
-        return { backedUp: false, skipped: 'better-sqlite3 unavailable' };
+        return false;
     }
-    const destDir = opts.destDir ?? path.join(path.dirname(dbPath), 'backups');
-    try {
-        fs.mkdirSync(destDir, { recursive: true });
-    }
-    catch { /* */ }
-    const destPath = path.join(destDir, `${snapshotPrefix(dbPath)}${fileStamp(opts.timestamp ?? Date.now())}.db`);
-    // WAL-safe online backup: read-only source, consistent snapshot to destPath.
-    let db;
-    try {
-        db = new Database(dbPath, { readonly: true });
-        await db.backup(destPath);
-        db.close();
-    }
-    catch (e) {
-        try {
-            db?.close();
-        }
-        catch { /* */ }
-        // #2798 — under CLAUDE_FLOW_ENCRYPT_AT_REST the source is an RFE1
-        // blob, not native SQLite, so better-sqlite3's online-backup API
-        // throws "file is not a database" and the run was silently recorded
-        // as skipped (users with encryption had ZERO backups behind a green
-        // status). The online-backup API only exists to avoid tearing a live
-        // WAL-mode DB; that concern doesn't apply to the encrypted file (sql.js
-        // rewrites it wholesale per flush), so a plain byte copy is a valid
-        // snapshot. Fall back to it before giving up.
-        try {
-            fs.copyFileSync(dbPath, destPath);
-            const copiedBytes = fs.statSync(destPath).size;
-            if (copiedBytes > 0) {
-                // Fall through to rotation/offsite/return below via a flag path.
-                // (Mirror the success path's tail by re-using the same code.)
-                const keep = typeof opts.keep === 'number' && opts.keep > 0 ? opts.keep : 7;
-                const rotatedAway = [];
-                try {
-                    const snaps = fs.readdirSync(destDir).filter(f => isSnapshotFor(f, dbPath)).sort();
-                    while (snaps.length > keep) {
-                        const old = snaps.shift();
-                        try {
-                            fs.rmSync(path.join(destDir, old), { force: true });
-                            rotatedAway.push(old);
-                        }
-                        catch { /* */ }
-                    }
-                }
-                catch { /* */ }
-                let gcsUri;
-                if (opts.gcs) {
-                    try {
-                        const { execFileSync } = await import('child_process');
-                        const dest = opts.gcs.replace(/\/+$/, '') + '/' + path.basename(destPath);
-                        execFileSync('gcloud', ['storage', 'cp', destPath, dest], { stdio: ['ignore', 'ignore', 'inherit'] });
-                        gcsUri = dest;
-                    }
-                    catch { /* offsite failed — local snapshot stands */ }
-                }
-                if (opts.verbose) {
-                    console.log(`memory DB backed up (byte-copy, encrypted-at-rest) → ${destPath} (${Math.round(copiedBytes / 1024)} KB)`);
-                }
-                return { backedUp: true, path: destPath, sizeBytes: copiedBytes, rotatedAway, gcsUri };
-            }
-        }
-        catch { /* byte-copy also failed — report the original error */ }
-        return { backedUp: false, skipped: `backup failed: ${e?.message ?? e}` };
-    }
-    let sizeBytes = 0;
-    try {
-        sizeBytes = fs.statSync(destPath).size;
-    }
-    catch { /* */ }
+}
+/** Shared tail: rotation + optional GCS offsite + verbose logging + the success receipt. */
+async function finishBackup(destPath, dbPath, destDir, opts, method, sizeBytes) {
     // Rotation — ISO-stamped names sort chronologically, so keep the tail.
     const keep = typeof opts.keep === 'number' && opts.keep > 0 ? opts.keep : 7;
     const rotatedAway = [];
@@ -172,11 +115,96 @@ export async function backupMemoryDb(opts = {}) {
         catch { /* offsite failed — local snapshot stands */ }
     }
     if (opts.verbose) {
-        console.log(`memory DB backed up → ${destPath} (${Math.round(sizeBytes / 1024)} KB)` +
+        const label = method === 'raw-copy-fallback' ? ' (byte-copy, encrypted-at-rest)' : '';
+        console.log(`memory DB backed up${label} → ${destPath} (${Math.round(sizeBytes / 1024)} KB)` +
             (rotatedAway.length ? `, rotated ${rotatedAway.length} old` : '') +
             (gcsUri ? `, offsite ${gcsUri}` : ''));
     }
-    return { backedUp: true, path: destPath, sizeBytes, rotatedAway, gcsUri };
+    return { backedUp: true, path: destPath, sizeBytes, rotatedAway, gcsUri, method };
+}
+export async function backupMemoryDb(opts = {}) {
+    const dbPath = opts.dbPath ?? defaultMemoryDbPath();
+    if (!dbPath || !fs.existsSync(dbPath))
+        return { backedUp: false, skipped: 'no-db' };
+    const destDir = opts.destDir ?? path.join(path.dirname(dbPath), 'backups');
+    try {
+        fs.mkdirSync(destDir, { recursive: true });
+    }
+    catch { /* */ }
+    const destPath = path.join(destDir, `${snapshotPrefix(dbPath)}${fileStamp(opts.timestamp ?? Date.now())}.db`);
+    let Database = opts.Database;
+    let nativeError = null;
+    if (!Database) {
+        try {
+            const mod = 'better-sqlite3';
+            Database = (await import(mod)).default;
+        }
+        catch {
+            nativeError = 'better-sqlite3 unavailable';
+        }
+    }
+    if (!nativeError) {
+        // WAL-safe online backup: read-only source, consistent snapshot to destPath.
+        let db;
+        try {
+            db = new Database(dbPath, { readonly: true });
+            await db.backup(destPath);
+            db.close();
+            let sizeBytes = 0;
+            try {
+                sizeBytes = fs.statSync(destPath).size;
+            }
+            catch { /* */ }
+            return await finishBackup(destPath, dbPath, destDir, opts, 'native-online-backup', sizeBytes);
+        }
+        catch (e) {
+            try {
+                db?.close();
+            }
+            catch { /* */ }
+            try {
+                fs.rmSync(destPath, { force: true });
+            }
+            catch { /* a native backup() that throws mid-write can leave a torn destPath */ }
+            nativeError = e?.message ?? String(e);
+        }
+    }
+    // #2798 — under CLAUDE_FLOW_ENCRYPT_AT_REST the source is an RFE1 blob, not
+    // native SQLite, so better-sqlite3's online-backup API throws "file is not
+    // a database" (or isn't even importable on a WASM-only host). The
+    // online-backup API exists to avoid tearing a live WAL-mode DB; that
+    // concern doesn't apply to the encrypted file (sql.js rewrites it wholesale
+    // per flush), so a plain byte copy IS a valid snapshot there.
+    //
+    // But this fallback must never fire for an ORDINARY (non-encrypted) source
+    // just because the native backup threw — SQLITE_BUSY, a disk error, or any
+    // other native-backup failure on a perfectly normal database must fail
+    // closed, not silently report `backedUp: true` off a raw copy. Positively
+    // verify encryption (4-byte RFE1 magic sniff) before ever taking this path;
+    // "the native backup threw" is never by itself evidence the source is
+    // encrypted.
+    if (existingFileIsEncrypted(dbPath) !== true) {
+        return { backedUp: false, skipped: `native backup failed: ${nativeError}` };
+    }
+    // Even for a confirmed-encrypted source, refuse the raw-copy fallback if
+    // there's an active WAL — a plain copy of the main file alone would miss
+    // uncommitted WAL frames and silently produce an inconsistent snapshot.
+    if (hasActiveWal(dbPath)) {
+        return { backedUp: false, skipped: 'active WAL present — refusing raw-copy fallback (would be inconsistent)' };
+    }
+    try {
+        fs.copyFileSync(dbPath, destPath);
+        const copiedBytes = fs.statSync(destPath).size;
+        if (copiedBytes > 0) {
+            return await finishBackup(destPath, dbPath, destDir, opts, 'raw-copy-fallback', copiedBytes);
+        }
+    }
+    catch { /* byte-copy also failed — report the original native error below */ }
+    try {
+        fs.rmSync(destPath, { force: true });
+    }
+    catch { /* */ }
+    return { backedUp: false, skipped: `native backup failed: ${nativeError}` };
 }
 /** Verify a snapshot without modifying it, including RFE1 images and WASM-only hosts. */
 async function verifiedBackupRows(file, Database) {

package/v3/@claude-flow/cli/dist/src/services/policy-ledger-anchor.d.ts

@@ -32,6 +32,8 @@ export type AnchorAssessment = {
 };
 export type AnchorWriter = (file: string, value: unknown) => Promise<void>;
 export type StreamingAnchorWriter = (file: string, value: AtomicJsonSource) => Promise<void>;
+export declare const ANCHOR_LOG_FILE = "ledger-anchors.json";
+export declare const ANCHOR_MIRROR_FILE = "ledger-anchor-head.json";
 export declare const anchorLogPath: (projectRoot: string) => string;
 /**
  * Directory holding per-project trust material (anchor mirror, HMAC key).

package/v3/@claude-flow/cli/dist/src/services/policy-ledger-anchor.js

@@ -33,9 +33,9 @@ import { closeSync, constants as fsConstants, fstatSync, existsSync, mkdtempSync
 import { isAbsolute, join, resolve } from 'node:path';
 import { homedir, tmpdir, userInfo } from 'node:os';
 import { AgenticPolicyEngine, canonicalizePolicy } from '@claude-flow/security/policy/index';
-const LOG_FILE = 'ledger-anchors.json';
-const MIRROR_FILE = 'ledger-anchor-head.json';
-export const anchorLogPath = (projectRoot) => join(resolve(projectRoot), '.claude-flow', 'policy', LOG_FILE);
+export const ANCHOR_LOG_FILE = 'ledger-anchors.json';
+export const ANCHOR_MIRROR_FILE = 'ledger-anchor-head.json';
+export const anchorLogPath = (projectRoot) => join(resolve(projectRoot), '.claude-flow', 'policy', ANCHOR_LOG_FILE);
 /**
  * The home directory trust material lives under: $HOME when it is an absolute path, else the account's home. An empty or relative
  * $HOME (an unset variable in a wrapper script, `HOME=. cmd`) would make join() yield a path relative to the working directory and
@@ -71,7 +71,7 @@ export function policyTrustRoot() {
 }
 function mirrorPath(projectRoot) {
     const id = createHash('sha256').update(realpathSync(projectRoot)).digest('hex');
-    return join(policyTrustRoot(), id, MIRROR_FILE);
+    return join(policyTrustRoot(), id, ANCHOR_MIRROR_FILE);
 }
 // Duplicated from policy-runtime.ts's RECEIPT_ARCHIVE_FILE rather than
 // imported, to avoid a circular dependency (policy-runtime.ts imports this

package/v3/@claude-flow/cli/dist/src/services/policy-runtime.js

@@ -7,17 +7,18 @@ import { AgenticPolicyEngine, POLICY_STATE_VERSION, createLegacyCompatibleState,
 import { isMcpCallerAuthEnabled, decodeTokenEnvelope, publicKeyFromHex, verifyInvocationToken, } from '@claude-flow/security/mcp-caller-identity';
 import { createHash, createHmac, randomBytes, randomUUID, timingSafeEqual } from 'node:crypto';
 import { execFileSync } from 'node:child_process';
-import { closeSync, constants as fsConstants, existsSync, fstatSync, fsyncSync, ftruncateSync, writeSync, lstatSync, mkdirSync, openSync, readFileSync, readSync, readlinkSync, realpathSync, renameSync, unlinkSync, writeFileSync, } from 'node:fs';
+import { closeSync, constants as fsConstants, existsSync, fstatSync, fsyncSync, ftruncateSync, writeSync, lstatSync, mkdirSync, openSync, readFileSync, readSync, readdirSync, readlinkSync, realpathSync, renameSync, unlinkSync, writeFileSync, } from 'node:fs';
 import { dirname, join, resolve } from 'node:path';
 import { hostname, userInfo } from 'node:os';
 import { syncPolicyProjection } from '../mods/policy-projection.js';
 import { ATOMIC_JSON_WRITER } from './policy-anchor-log.js';
 import { captureArchiveSnapshot, verifyFullPolicyLedger } from './policy-ledger-audit.js';
-import { assessAnchors, policyTrustRoot, recordAnchor } from './policy-ledger-anchor.js';
+import { ANCHOR_LOG_FILE, ANCHOR_MIRROR_FILE, assessAnchors, policyTrustRoot, recordAnchor } from './policy-ledger-anchor.js';
 const POLICY_DIR = join('.claude-flow', 'policy');
 const POLICY_FILE = 'state.json';
 const LOCK_FILE = 'state.lock';
 const RECEIPT_ARCHIVE_FILE = 'receipts.ledger.jsonl';
+const STATE_ANCHOR_FILE = 'state.anchor.json';
 const LOCK_WAIT_MS = 5_000;
 // #3164: without a bound, `state.receipts` grows forever and every
 // transaction's verify/clone/serialize cost is O(all receipts ever issued) —
@@ -362,11 +363,59 @@ async function writeJsonAtomic(file, value) {
         }
     }
 }
+// #3164: a writer killed between creating its temp file and renaming it
+// (SIGKILL from a caller's timeout, OOM) never reaches writeJsonAtomic's
+// cleanup, so a full-size copy of the file stays behind forever (~250 MB each
+// on a mature ledger). Every writer of these files holds the project's
+// state.lock, so while the lock is held no temp file for them can belong to a
+// write in progress. That invariant has known gaps: released versions before
+// the dead-owner fix take over any lock older than 30 s, even a live owner's
+// (a writer suspended mid-write, e.g. a sleeping laptop). So a temp is also
+// kept while its writer pid is alive on this host, and until it is
+// ORPHAN_TEMP_MIN_AGE_MS old; a skipped orphan is removed by a later call.
+const ORPHAN_TEMP_MIN_AGE_MS = 10 * 60_000;
+const ATOMIC_TEMP = /^(.+)\.(\d+)\.[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}\.tmp$/;
+const PROJECT_ATOMIC_FILES = new Set([POLICY_FILE, ANCHOR_LOG_FILE]);
+const TRUST_ATOMIC_FILES = new Set([STATE_ANCHOR_FILE, ANCHOR_MIRROR_FILE]);
+function reapOrphanedTemps(dir, files) {
+    let names;
+    try {
+        names = readdirSync(dir);
+    }
+    catch {
+        return;
+    }
+    const now = Date.now();
+    for (const name of names) {
+        const match = ATOMIC_TEMP.exec(name);
+        if (!match || !files.has(match[1]))
+            continue;
+        const pid = Number(match[2]);
+        if (Number.isSafeInteger(pid) && pid > 0 && isPidAlive(pid))
+            continue;
+        const file = join(dir, name);
+        try {
+            const stat = lstatSync(file);
+            if (!stat.isFile() || now - stat.mtimeMs < ORPHAN_TEMP_MIN_AGE_MS)
+                continue;
+            unlinkSync(file);
+        }
+        catch { /* already gone, or not removable: never fail the caller */ }
+    }
+}
+/** Call only while holding the project's state.lock. */
+function reapOrphanedPolicyTemps(projectRoot) {
+    reapOrphanedTemps(paths(projectRoot).dir, PROJECT_ATOMIC_FILES);
+    try {
+        reapOrphanedTemps(dirname(trustPaths(projectRoot).anchor), TRUST_ATOMIC_FILES);
+    }
+    catch { /* no trust dir yet */ }
+}
 function trustPaths(projectRoot) {
     const trustRoot = policyTrustRoot();
     const projectId = createHash('sha256').update(realpathSync(projectRoot)).digest('hex');
     const dir = join(trustRoot, projectId);
-    return { key: join(dir, 'anchor.key'), anchor: join(dir, 'state.anchor.json') };
+    return { key: join(dir, 'anchor.key'), anchor: join(dir, STATE_ANCHOR_FILE) };
 }
 function trustKey(projectRoot, create) {
     const { key } = trustPaths(projectRoot);
@@ -531,6 +580,7 @@ export async function withPolicyTransaction(projectRoot, operation, options = {}
     mkdirDurably(target.dir);
     const release = await acquireLock(target.lock);
     try {
+        reapOrphanedPolicyTemps(projectRoot);
         const loaded = loadPolicyState(projectRoot);
         const engine = AgenticPolicyEngine.fromState(loaded, {
             signingKey: process.env.CLAUDE_FLOW_POLICY_SIGNING_KEY,
@@ -691,6 +741,7 @@ export async function verifyPolicyLedger(projectRoot = process.cwd(), options =
     // strings, receipt arrays or maps. The descriptor pins path replacements.
     const release = await acquireLock(target.lock);
     try {
+        reapOrphanedPolicyTemps(projectRoot);
         const engine = AgenticPolicyEngine.fromState(loadPolicyState(projectRoot), engineOptions);
         const outcome = reconcileLedger(projectRoot, engine, options);
         if (outcome.persist) {

package/v3/@claude-flow/cli/dist/src/services/worker-daemon.js

@@ -1699,6 +1699,10 @@ export class WorkerDaemon extends EventEmitter {
                 rotatedAway: r.rotatedAway?.length ?? 0,
                 gcsUri: r.gcsUri,
                 skipped: r.skipped,
+                // Which method actually completed (per-store detail is in `backups`);
+                // migration tooling should require 'native-online-backup', not a
+                // blanket `backedUp: true` — see #4287.
+                method: r.method,
             };
         }
         catch (error) {

package/v3/@claude-flow/cli/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@claude-flow/cli",
-  "version": "3.57.1",
+  "version": "3.57.2",
   "type": "module",
   "description": "Ruflo CLI - Enterprise AI agent orchestration with 60+ specialized agents, swarm coordination, MCP server, self-learning hooks, and vector memory for Claude Code",
   "main": "dist/src/index.js",
@@ -48,6 +48,7 @@
       "import": "./dist/src/index.js"
     },
     "./dist/*": "./dist/*",
+    "./package.json": "./package.json",
     "./ruvector": {
       "types": "./dist/src/ruvector/index.d.ts",
       "import": "./dist/src/ruvector/index.js"
@@ -98,7 +99,7 @@
     "vitest": "^4.1.0"
   },
   "dependencies": {
-    "@claude-flow/cli-core": "3.7.4",
+    "@claude-flow/cli-core": "3.7.5",
     "@claude-flow/codex": "3.0.5",
     "@claude-flow/mcp": "3.1.1",
     "@claude-flow/neural": "3.0.0",
@@ -125,11 +126,11 @@
     "ws": "^8.21.0",
     "yaml": "^2.8.0",
     "zod": "^3.22.0",
-    "@claude-flow/memory": "3.0.5"
+    "@claude-flow/memory": "3.0.6"
   },
   "optionalDependencies": {
     "@agntcy/slim-bindings": "2.0.0-alpha.5",
-    "@claude-flow/memory": "3.0.5",
+    "@claude-flow/memory": "3.0.6",
     "@metaharness/darwin": "~0.12.0",
     "@metaharness/flywheel": "~0.1.10",
     "@metaharness/radio": "~0.1.0",