claude-flow 3.32.34 → 3.32.36

package/node_modules/@claude-flow/codex/dist/generators/skill-md.js.map

@@ -1 +1 @@
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package/node_modules/@claude-flow/codex/dist/initializer.d.ts.map

@@ -1 +1 @@
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package/node_modules/@claude-flow/codex/dist/initializer.js

@@ -7,7 +7,7 @@ import fs from 'fs-extra';
 import path from 'path';
 import { fileURLToPath } from 'node:url';
 import { generateAgentsMd } from './generators/agents-md.js';
-import { generateSkillMd, generateBuiltInSkill } from './generators/skill-md.js';
+import { BUILT_IN_SKILL_NAMES, generateSkillMd, generateBuiltInSkill, } from './generators/skill-md.js';
 import { generateConfigToml } from './generators/config-toml.js';
 import { DEFAULT_SKILLS_BY_TEMPLATE, AGENTS_OVERRIDE_TEMPLATE, GITIGNORE_ENTRIES } from './templates/index.js';
 import { getRufloMcpAddCommand } from './mcp-config.js';
@@ -506,16 +506,8 @@ web_search = "live"
         }
         await fs.ensureDir(skillDir);
         // Check if it's a built-in skill
-        const builtInSkills = [
-            'swarm-orchestration',
-            'memory-management',
-            'sparc-methodology',
-            'security-audit',
-            'performance-analysis',
-            'github-automation',
-        ];
         let skillMd;
-        if (builtInSkills.includes(skillName)) {
+        if (BUILT_IN_SKILL_NAMES.includes(skillName)) {
             const result = await generateBuiltInSkill(skillName);
             skillMd = result.skillMd;
             // Also write any associated scripts or references
@@ -523,14 +515,18 @@ web_search = "live"
                 const scriptsDir = path.join(skillDir, 'scripts');
                 await fs.ensureDir(scriptsDir);
                 for (const [scriptName, scriptContent] of Object.entries(result.scripts)) {
-                    await fs.writeFile(path.join(scriptsDir, scriptName), scriptContent, 'utf-8');
+                    const scriptPath = path.join(scriptsDir, scriptName);
+                    await fs.ensureDir(path.dirname(scriptPath));
+                    await fs.writeFile(scriptPath, scriptContent, 'utf-8');
                 }
             }
             if (Object.keys(result.references).length > 0) {
-                const refsDir = path.join(skillDir, 'docs');
+                const refsDir = path.join(skillDir, 'references');
                 await fs.ensureDir(refsDir);
                 for (const [refName, refContent] of Object.entries(result.references)) {
-                    await fs.writeFile(path.join(refsDir, refName), refContent, 'utf-8');
+                    const referencePath = path.join(refsDir, refName);
+                    await fs.ensureDir(path.dirname(referencePath));
+                    await fs.writeFile(referencePath, refContent, 'utf-8');
                 }
             }
         }

package/node_modules/@claude-flow/codex/dist/initializer.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "claude-flow",
-  "version": "3.32.34",
+  "version": "3.32.36",
   "workspaces": [
     "v3/@claude-flow/codex",
     "v3/@claude-flow/plugin-agent-federation",

package/v3/@claude-flow/cli/bin/cli.js

@@ -34,6 +34,30 @@ import { dirname, join } from 'path';
 const _origWarn = console.warn;
 const _origLog = console.log;
 const _origError = console.error;
+
+// #2726 — Some MCP clients place every advertised schema in every model
+// request. Keep "all" as the backwards-compatible default, but honor the
+// same category/namespace/exact-name selector as `mcp start --tools`.
+function _filterAdvertisedMcpTools(tools) {
+  const argv = process.argv.slice(2);
+  const toolsIndex = argv.findIndex((arg) => arg === '--tools');
+  const inlineTools = argv.find((arg) => arg.startsWith('--tools='));
+  const configured = process.env.CLAUDE_FLOW_MCP_TOOLS
+    || (toolsIndex >= 0 ? argv[toolsIndex + 1] : undefined)
+    || (inlineTools ? inlineTools.slice('--tools='.length) : undefined);
+  if (!configured || configured.trim().toLowerCase() === 'all') return tools;
+  const selectors = new Set(
+    configured.split(',').map((item) => item.trim().toLowerCase()).filter(Boolean),
+  );
+  if (selectors.size === 0) return tools;
+  return tools.filter((tool) => {
+    const name = tool.name.toLowerCase();
+    const category = typeof tool.category === 'string' ? tool.category.toLowerCase() : '';
+    return selectors.has(name)
+      || selectors.has(category)
+      || Array.from(selectors).some((selector) => name.startsWith(`${selector}_`));
+  });
+}
 const _isCosmeticAgentdbPatchNoise = (msg) =>
   msg.includes('[AgentDB Patch]') && msg.includes('Controller index not found');
 const _STDERR_REDIRECT_PREFIXES = [
@@ -237,7 +261,7 @@ if (isMCPMode) {
         };
 
       case 'tools/list': {
-        const tools = listMCPTools();
+        const tools = _filterAdvertisedMcpTools(listMCPTools());
         return {
           jsonrpc: '2.0',
           id: message.id,

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

@@ -1,11 +1,11 @@
 {
   "schemaVersion": 1,
-  "generation": 3,
-  "generatedAt": "2026-07-29T13:29:39.000Z",
-  "gitSha": "c3cf2d0e",
+  "generation": 4,
+  "generatedAt": "2026-07-29T19:08:51.000Z",
+  "gitSha": "67ff9898",
   "catalog": {
     "agents": 164,
-    "tools": 395,
+    "tools": 397,
     "skills": 34
   },
   "benchmark": null

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

@@ -230,7 +230,7 @@ const listCommand = {
             }
             // Format for display
             const displayAgents = result.agents.map(agent => ({
-                id: agent.id,
+                id: agent.agentId,
                 type: agent.agentType,
                 status: agent.status,
                 created: new Date(agent.createdAt).toLocaleTimeString(),
@@ -487,6 +487,39 @@ const metricsCommand = {
         const avgSuccessRate = tasksCompleted > 0
             ? `${Math.round(Object.values(typeCounts).reduce((a, d) => a + d.success, 0) / tasksCompleted * 100)}%`
             : 'N/A';
+        // ADR-330: expose the learned scheduling signal where operators already
+        // inspect agent metrics. Old/non-APSC installs simply omit this section.
+        let pheromone;
+        const swarmStatePath = join(process.cwd(), '.claude-flow', 'swarm', 'swarm-state.json');
+        if (existsSync(swarmStatePath)) {
+            try {
+                const store = JSON.parse(readFileSync(swarmStatePath, 'utf-8'));
+                const current = Object.values(store.swarms ?? {})
+                    .filter((swarm) => swarm.status === 'running' && swarm.topology === 'pheromone-adaptive')
+                    .sort((a, b) => String(b.updatedAt).localeCompare(String(a.updatedAt)))[0];
+                const apsc = current?.config?.apscState;
+                if (apsc) {
+                    const agents = Object.values(apsc.agents ?? {})
+                        .filter((agent) => !agentId || agent.agentId === agentId)
+                        .sort((a, b) => a.agentId.localeCompare(b.agentId))
+                        .map((agent) => ({
+                        agentId: agent.agentId,
+                        role: agent.role,
+                        pheromoneScore: agent.emaScore,
+                        rawScore: agent.rawScore,
+                        samples: agent.samples,
+                        eligibility: agent.status === 'suspended' ? 'suspended' : 'eligible',
+                    }));
+                    pheromone = {
+                        active: true,
+                        dryRun: apsc.config?.dryRun !== false,
+                        threshold: apsc.threshold ?? 0.5,
+                        agents,
+                    };
+                }
+            }
+            catch { /* malformed/legacy swarm state — preserve existing metrics */ }
+        }
         const metrics = {
             period,
             summary: {
@@ -501,7 +534,8 @@ const metricsCommand = {
             performance: {
                 memoryVectors: `${vectorCount} vectors`,
                 searchBackend: vectorCount > 0 ? 'HNSW-indexed' : 'none'
-            }
+            },
+            pheromone,
         };
         if (ctx.flags.format === 'json') {
             output.printJson(metrics);
@@ -544,6 +578,20 @@ const metricsCommand = {
             `Vectors: ${output.success(metrics.performance.memoryVectors)}`,
             `Backend: ${output.success(metrics.performance.searchBackend)}`
         ]);
+        if (metrics.pheromone) {
+            output.writeln();
+            output.writeln(output.bold(`Pheromone Scheduling (${metrics.pheromone.dryRun ? 'dry run' : 'live'})`));
+            output.printTable({
+                columns: [
+                    { key: 'agentId', header: 'Agent', width: 20 },
+                    { key: 'role', header: 'Role', width: 18 },
+                    { key: 'pheromoneScore', header: 'EMA Score', width: 12, align: 'right' },
+                    { key: 'samples', header: 'Samples', width: 9, align: 'right' },
+                    { key: 'eligibility', header: 'Eligibility', width: 12 },
+                ],
+                data: metrics.pheromone.agents,
+            });
+        }
         return { success: true, data: metrics };
     }
 };

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

@@ -120,8 +120,8 @@ async function checkConfigFile() {
 }
 // Check daemon status
 /**
- * #2448 — Detect the runaway `npx @claude-flow/cli@latest` statusLine / hook
- * commands left over in `.claude/settings.json` from pre-#2337 installs.
+ * #2448 / #2677 — Detect runaway `npx @claude-flow/cli@latest` commands
+ * left over in `.claude/settings.json` from pre-#2337 installs.
  *
  * These fire on every Claude Code event (statusLine refires every few hundred
  * ms, hooks fire per tool-use), each spawning a cold Node process + npm
@@ -138,7 +138,9 @@ async function checkStaleSettingsNpx() {
     // Same regex pattern the executor migration uses — kept in sync. Flag-list
     // repetition bounded at 10 (CodeQL js/redos — unbounded `*` here is
     // exponential-backtracking-prone on a crafted settings.json).
-    const BROKEN_RE = /npx\s+(?:--?\S+\s+){0,10}@?claude-flow\/cli@latest\s+hooks\s+(?:statusline|\S+)/;
+    // Every subcommand incurs the same cold npm process/registry cost. The
+    // previous `hooks` literal missed `memory`, `daemon`, `swarm`, etc.
+    const BROKEN_RE = /npx\s+(?:--?\S+\s+){0,10}@?claude-flow\/cli@latest\s+\S+/;
     // Look in both project-local and home-dir settings.
     const candidates = [
         join(process.cwd(), '.claude', 'settings.json'),
@@ -263,18 +265,21 @@ async function checkMemoryDatabase() {
 // The existing `checkMemoryDatabase` above asserts existence + statability
 // only, so it CANNOT distinguish a healthy DB from a 99.97%-empty or
 // SQLite-malformed one. Stuinfla reported both cases live (81-store fleet).
-// The three checks below layer functional assertions on top, ordered so
+// The checks below layer functional assertions on top, ordered so
 // the earliest chain-break is always the first red the user sees:
 //   1. Integrity          — can sql.js open it AND does PRAGMA integrity_check pass?
 //   2. Content            — do most memory_entries rows carry non-empty content?
 //   3. Embedding coverage — do most rows have a vector? (unembedded rows are
 //                           both unrecallable AND undistillable per ADR-174)
+//   6. Reflexion coverage — can episodes participate in retrieveRelevant's
+//                           required episode_embeddings INNER JOIN?
+//      Feedback critiques — do execution-tier episodes carry a real lesson?
 // Ordering matters: content ratio is meaningless on a DB that can't open;
 // embedding coverage is meaningless on rows with no content. First red wins.
 //
-// Recall probe (stuinfla check 4) requires actual write+search+delete round
-// trips through the CLI's own memory pipeline — deferred to a follow-up PR
-// to keep this one purely additive and safe.
+// Recall probe (stuinfla check 4) still requires an isolated write+search+
+// delete round trip through the CLI's own memory pipeline. It remains separate
+// because doctor otherwise stays read-only.
 //
 // Design rules (also from stuinfla's report):
 //   - "A check that cannot fail protects nothing" — every check has a
@@ -731,6 +736,102 @@ async function checkMemoryEmbeddingCoverage() {
         catch { /* best-effort */ }
     }
 }
+// #2677 check 6 — ReflexionMemory.retrieveRelevant() INNER JOINs episodes to
+// episode_embeddings. A populated episodes table with an empty/missing partner
+// table is therefore not degraded recall; it is structurally zero recall.
+async function checkMemoryReflexionCoverage() {
+    const dbPath = await resolveMemoryDbPath();
+    if (!dbPath)
+        return { name: 'Memory Reflexion Coverage', status: 'warn', message: 'no memory.db found' };
+    const db = await tryOpenSqlJs(dbPath);
+    if (!db)
+        return { name: 'Memory Reflexion Coverage', status: 'warn', message: 'DB unreadable (see Memory Integrity)' };
+    try {
+        const tables = new Set(db.exec("SELECT name FROM sqlite_master WHERE type='table' AND name IN ('episodes','episode_embeddings')")[0]?.values?.map((v) => String(v[0])) ?? []);
+        if (!tables.has('episodes')) {
+            return { name: 'Memory Reflexion Coverage', status: 'warn', message: 'episodes table absent — AgentDB Reflexion schema not initialized' };
+        }
+        const episodes = Number(db.exec('SELECT count(*) FROM episodes')[0]?.values?.[0]?.[0] ?? 0);
+        if (episodes === 0) {
+            return { name: 'Memory Reflexion Coverage', status: 'warn', message: `${dbPath} — 0 episodes (Reflexion has not been exercised)` };
+        }
+        if (!tables.has('episode_embeddings')) {
+            return {
+                name: 'Memory Reflexion Coverage',
+                status: 'fail',
+                message: `${dbPath} — episode embeddings 0/${episodes} (0.00%); retrieveRelevant() cannot return rows`,
+                fix: 'run `claude-flow memory distill run`; current distillation creates/backfills episode_embeddings',
+            };
+        }
+        const embedded = Number(db.exec('SELECT count(*) FROM episodes e JOIN episode_embeddings ee ON ee.episode_id=e.id')[0]?.values?.[0]?.[0] ?? 0);
+        const ratio = embedded / episodes;
+        const detail = `episode embeddings ${embedded}/${episodes} (${(ratio * 100).toFixed(2)}%)`;
+        if (ratio < 0.95) {
+            return {
+                name: 'Memory Reflexion Coverage',
+                status: 'fail',
+                message: `${dbPath} — ${detail} below 95% floor; retrieveRelevant() cannot see uncovered episodes`,
+                fix: 'run `claude-flow memory distill run` to populate retrievable episodes',
+            };
+        }
+        return { name: 'Memory Reflexion Coverage', status: 'pass', message: `${dbPath} — ${detail}` };
+    }
+    catch (e) {
+        return { name: 'Memory Reflexion Coverage', status: 'warn', message: `${dbPath} — probe threw: ${e.message || String(e)}` };
+    }
+    finally {
+        try {
+            db.close();
+        }
+        catch { /* best-effort */ }
+    }
+}
+// Execution-tier feedback should carry a lesson, not just reward/success bits.
+// Proxy episodes intentionally remain critique-free to avoid laundering a
+// structural summary into an observed failure explanation.
+async function checkMemoryCritiqueCoverage() {
+    const dbPath = await resolveMemoryDbPath();
+    if (!dbPath)
+        return { name: 'Memory Feedback Critiques', status: 'warn', message: 'no memory.db found' };
+    const db = await tryOpenSqlJs(dbPath);
+    if (!db)
+        return { name: 'Memory Feedback Critiques', status: 'warn', message: 'DB unreadable (see Memory Integrity)' };
+    try {
+        const hasEpisodes = (db.exec("SELECT count(*) FROM sqlite_master WHERE type='table' AND name='episodes'")[0]?.values?.[0]?.[0] ?? 0) > 0;
+        if (!hasEpisodes)
+            return { name: 'Memory Feedback Critiques', status: 'warn', message: 'episodes table absent' };
+        const row = db.exec(`
+      SELECT count(*),
+        sum(CASE WHEN length(trim(coalesce(critique,''))) > 0 THEN 1 ELSE 0 END)
+      FROM episodes WHERE session_id LIKE 'distill:feedback%'
+    `)[0]?.values?.[0] ?? [0, 0];
+        const feedback = Number(row[0] ?? 0);
+        const withCritique = Number(row[1] ?? 0);
+        if (feedback === 0) {
+            return { name: 'Memory Feedback Critiques', status: 'warn', message: `${dbPath} — 0 execution-feedback episodes to assess` };
+        }
+        const ratio = withCritique / feedback;
+        const detail = `feedback critiques ${withCritique}/${feedback} (${(ratio * 100).toFixed(2)}%)`;
+        if (ratio < 0.95) {
+            return {
+                name: 'Memory Feedback Critiques',
+                status: 'fail',
+                message: `${dbPath} — ${detail} below 95% floor`,
+                fix: 'run current `claude-flow memory distill run`; execution-tier episodes preserve observed critique/error text',
+            };
+        }
+        return { name: 'Memory Feedback Critiques', status: 'pass', message: `${dbPath} — ${detail}` };
+    }
+    catch (e) {
+        return { name: 'Memory Feedback Critiques', status: 'warn', message: `${dbPath} — probe threw: ${e.message || String(e)}` };
+    }
+    finally {
+        try {
+            db.close();
+        }
+        catch { /* best-effort */ }
+    }
+}
 // #2545: Check that the self-learning bridge can actually load @claude-flow/memory
 // the SAME way the SessionStart auto-memory hook does. On the documented `npx ruflo`
 // path the package lands in the npx cache — unreachable from the project — so the
@@ -1027,6 +1128,48 @@ async function checkMcpServers() {
         fix: 'claude mcp add ruflo -- npx -y ruflo@latest mcp start',
     };
 }
+// #2726 — tools/list is fixed prompt overhead on clients/backends that do not
+// defer MCP schemas. Measure the actual live registry and warn before a small
+// context window becomes unrecoverable even after compaction.
+async function checkMcpSchemaOverhead() {
+    try {
+        const [{ listMCPTools }, { assessMcpSchemaOverhead, filterAdvertisedMcpTools, parseMcpToolSelection, }] = await Promise.all([
+            import('../mcp-client.js'),
+            import('../mcp-server.js'),
+        ]);
+        // The `mcp start --tools` CLI flag takes precedence when the server is
+        // constructed. Doctor intentionally inspects the environment fallback so
+        // its estimate describes the configuration inherited by MCP clients.
+        const selection = parseMcpToolSelection(process.env.CLAUDE_FLOW_MCP_TOOLS);
+        const tools = filterAdvertisedMcpTools(listMCPTools(), selection);
+        // This is diagnostic metadata about the external client's context window,
+        // not Ruflo command configuration, so there is no corresponding CLI flag.
+        const rawWindow = process.env.CLAUDE_FLOW_CONTEXT_WINDOW_TOKENS;
+        const contextWindow = rawWindow ? Number.parseInt(rawWindow, 10) : undefined;
+        const assessment = assessMcpSchemaOverhead(tools, contextWindow);
+        const ratio = assessment.ratio === undefined
+            ? ''
+            : `, ${(assessment.ratio * 100).toFixed(1)}% of ${assessment.contextWindowTokens}-token window`;
+        const selectionLabel = selection === 'all' ? 'all tools' : `filtered: ${selection.join(',')}`;
+        const message = `${assessment.toolCount} advertised tools ≈ ${assessment.estimatedTokens} schema tokens (${selectionLabel}${ratio})`;
+        if (assessment.risk === 'high') {
+            return {
+                name: 'MCP Schema Overhead',
+                status: 'warn',
+                message,
+                fix: 'Set CLAUDE_FLOW_MCP_TOOLS to required categories/tool names (for example: memory,swarm,agent,hooks) and optionally CLAUDE_FLOW_CONTEXT_WINDOW_TOKENS to your backend limit.',
+            };
+        }
+        return { name: 'MCP Schema Overhead', status: 'pass', message };
+    }
+    catch (error) {
+        return {
+            name: 'MCP Schema Overhead',
+            status: 'warn',
+            message: `Unable to measure: ${error instanceof Error ? error.message : String(error)}`,
+        };
+    }
+}
 // Check disk space (async with proper env inheritance)
 async function checkDiskSpace() {
     try {
@@ -1843,7 +1986,7 @@ export const doctorCommand = {
         {
             name: 'component',
             short: 'c',
-            description: 'Check specific component (version, node, npm, config, daemon, memory, api, git, mcp, claude, disk, typescript, agentic-flow, encryption, federation, funnel, proxy, auth, metaharness)',
+            description: 'Check specific component (version, node, npm, config, daemon, memory, api, git, mcp, mcp-overhead, claude, disk, typescript, agentic-flow, encryption, federation, funnel, proxy, auth, metaharness)',
             type: 'string'
         },
         {
@@ -1958,13 +2101,14 @@ export const doctorCommand = {
             checkGit,
             checkGitRepo,
             checkConfigFile,
-            checkStaleSettingsNpx, // #2448 — runaway `npx @latest` in statusLine/hooks
+            checkStaleSettingsNpx, // #2448/#2677 — runaway `npx @latest` in settings
             checkDaemonStatus,
             checkMemoryDatabase,
             checkMemoryStructuralIntegrity, // #2737 — bounded, native quick_check on every default run
             checkLearningBridge, // #2545 — can the auto-memory hook actually load @claude-flow/memory?
             checkApiKeys,
             checkMcpServers,
+            checkMcpSchemaOverhead, // #2726 — fixed tools/list prompt cost
             checkAIDefence, // #1807
             checkDiskSpace,
             checkBuildTools,
@@ -1982,8 +2126,9 @@ export const doctorCommand = {
         // array — expanded at execution time. Stuinfla's report showed the
         // existence-only check reporting PASS on a 99.97%-empty and even a
         // SQLite-malformed DB; the array here layers integrity → content →
-        // embedding coverage over the existing existence probe, ordered so
-        // the earliest chain-break is always the first red the user sees.
+        // embedding coverage over the existing existence probe; check 6 then
+        // verifies that distilled episodes are actually Reflexion-retrievable and
+        // execution feedback carries a lesson.
         const componentMap = {
             'version': checkVersionFreshness,
             'freshness': checkVersionFreshness,
@@ -1998,12 +2143,15 @@ export const doctorCommand = {
                 checkMemoryIntegrity, // #2677 check 1: sql.js open + PRAGMA integrity_check
                 checkMemoryContent, // #2677 check 2: memory_entries content coverage
                 checkMemoryEmbeddingCoverage, // #2677 check 3: vector coverage on populated rows
+                checkMemoryReflexionCoverage, // #2677 check 6: episodes are retrievable
+                checkMemoryCritiqueCoverage, // #2677 check 6: feedback carries lessons
             ],
             'learning': checkLearningBridge, // #2545
             'learning-bridge': checkLearningBridge, // #2545
             'api': checkApiKeys,
             'git': checkGit,
             'mcp': checkMcpServers,
+            'mcp-overhead': checkMcpSchemaOverhead,
             'aidefence': checkAIDefence, // #1807
             'disk': checkDiskSpace,
             'typescript': checkBuildTools,