@nathapp/nax 0.78.0 → 0.79.0

package/dist/nax.js

@@ -16640,7 +16640,10 @@ var init_schemas_context = __esm(() => {
       enabled: exports_external.boolean().default(true),
       maxStoryAge: exports_external.number().int().min(1).default(10),
       scoreMultiplier: exports_external.number().min(0).max(1).default(0.4)
-    }).default(() => ({ enabled: true, maxStoryAge: 10, scoreMultiplier: 0.4 }))
+    }).default(() => ({ enabled: true, maxStoryAge: 10, scoreMultiplier: 0.4 })),
+    manifest: exports_external.object({
+      retentionDays: exports_external.number().int().min(1)
+    }).optional()
   }).default(() => ({
     enabled: false,
     minScore: 0.1,
@@ -17984,9 +17987,9 @@ var init_severity = __esm(() => {
     info: 0,
     unverifiable: 0,
     low: 1,
-    warning: 1,
-    error: 2,
-    critical: 3
+    warning: 2,
+    error: 3,
+    critical: 4
   };
 });
 
@@ -18681,6 +18684,17 @@ var init_logger = __esm(() => {
 });
 
 // src/logger/index.ts
+var exports_logger = {};
+__export(exports_logger, {
+  resetLogger: () => resetLogger,
+  initLogger: () => initLogger,
+  getSafeLogger: () => getSafeLogger,
+  getLogger: () => getLogger,
+  formatJsonl: () => formatJsonl,
+  formatConsole: () => formatConsole,
+  addSink: () => addSink,
+  Logger: () => Logger
+});
 var init_logger2 = __esm(() => {
   init_logger();
   init_formatters();
@@ -18836,6 +18850,55 @@ var init_config_guards = __esm(() => {
   };
 });
 
+// src/config/dotenv.ts
+function parseDotenv(content) {
+  if (!content)
+    return {};
+  const result = {};
+  for (const rawLine of content.split(`
+`)) {
+    const line = rawLine.trim();
+    if (!line || line.startsWith("#"))
+      continue;
+    const stripped = line.startsWith("export ") ? line.slice(7).trim() : line;
+    const eqIndex = stripped.indexOf("=");
+    if (eqIndex === -1)
+      continue;
+    const key = stripped.slice(0, eqIndex).trim();
+    let value = stripped.slice(eqIndex + 1).trim();
+    if (value.startsWith('"') && value.endsWith('"') || value.startsWith("'") && value.endsWith("'")) {
+      value = value.slice(1, -1);
+    }
+    result[key] = value;
+  }
+  return result;
+}
+function resolveEnvVars(config2, env2) {
+  if (typeof config2 === "string") {
+    return resolveString(config2, env2);
+  }
+  if (Array.isArray(config2)) {
+    return config2.map((item) => resolveEnvVars(item, env2));
+  }
+  if (config2 !== null && typeof config2 === "object") {
+    const result = {};
+    for (const [key, value] of Object.entries(config2)) {
+      result[key] = resolveEnvVars(value, env2);
+    }
+    return result;
+  }
+  return config2;
+}
+function resolveString(str, env2) {
+  return str.replace(/\$\$([A-Za-z_][A-Za-z0-9_]*)/g, `${DOUBLE_DOLLAR_PLACEHOLDER}$1`).replace(/\$([A-Za-z_][A-Za-z0-9_]*)/g, (_match, varName) => {
+    if (!(varName in env2)) {
+      throw new Error(`Environment variable $${varName} (${varName}) is not defined`);
+    }
+    return env2[varName];
+  }).replace(new RegExp(`${DOUBLE_DOLLAR_PLACEHOLDER}([A-Za-z_][A-Za-z0-9_]*)`, "g"), "$$$1");
+}
+var DOUBLE_DOLLAR_PLACEHOLDER = "__DOLLAR_ESCAPE__";
+
 // src/config/merge.ts
 function mergePackageConfig(root, packageOverride) {
   const hasAnyMergeableField = packageOverride.agent !== undefined || packageOverride.models !== undefined || packageOverride.routing !== undefined || packageOverride.execution !== undefined || packageOverride.review !== undefined || packageOverride.acceptance !== undefined || packageOverride.quality !== undefined || packageOverride.context !== undefined || packageOverride.project !== undefined;
@@ -18874,6 +18937,10 @@ function mergePackageConfig(root, packageOverride) {
       mutationCheck: {
         ...root.execution.mutationCheck,
         ...packageOverride.execution?.mutationCheck
+      },
+      rectification: {
+        ...root.execution.rectification,
+        ...packageOverride.execution?.rectification
       }
     },
     review: {
@@ -18910,11 +18977,13 @@ function mergePackageConfig(root, packageOverride) {
         },
         ...packageOverride.review?.commands
       },
-      semantic: packageOverride.review?.semantic !== undefined ? { ...root.review.semantic, ...packageOverride.review.semantic } : root.review.semantic
+      semantic: packageOverride.review?.semantic !== undefined ? { ...root.review.semantic, ...packageOverride.review.semantic } : root.review.semantic,
+      adversarial: packageOverride.review?.adversarial !== undefined ? { ...root.review.adversarial, ...packageOverride.review.adversarial } : root.review.adversarial
     },
     acceptance: {
       ...root.acceptance,
-      ...packageOverride.acceptance
+      ...packageOverride.acceptance,
+      fix: packageOverride.acceptance?.fix !== undefined ? { ...root.acceptance.fix, ...packageOverride.acceptance.fix } : root.acceptance.fix
     },
     quality: {
       ...root.quality,
@@ -18922,7 +18991,9 @@ function mergePackageConfig(root, packageOverride) {
         ...root.quality.commands,
         ...packageOverride.quality?.commands
       },
-      testing: packageOverride.quality?.testing !== undefined ? { ...root.quality.testing, ...packageOverride.quality.testing } : root.quality.testing
+      testing: packageOverride.quality?.testing !== undefined ? { ...root.quality.testing, ...packageOverride.quality.testing } : root.quality.testing,
+      autofix: packageOverride.quality?.autofix !== undefined ? { ...root.quality.autofix, ...packageOverride.quality.autofix } : root.quality.autofix,
+      lintOutput: packageOverride.quality?.lintOutput !== undefined ? { ...root.quality.lintOutput, ...packageOverride.quality.lintOutput } : root.quality.lintOutput
     },
     context: {
       ...root.context,
@@ -18935,6 +19006,10 @@ function mergePackageConfig(root, packageOverride) {
         stages: {
           ...root.context.v2?.stages,
           ...packageOverride.context?.v2?.stages
+        },
+        rules: {
+          ...root.context.v2?.rules,
+          ...packageOverride.context?.v2?.rules
         }
       }
     },
@@ -19153,55 +19228,6 @@ function projectConfigDir(projectRoot) {
 var GLOBAL_CONFIG_DIR_ENV = "NAX_GLOBAL_CONFIG_DIR", PROJECT_NAX_DIR = ".nax";
 var init_paths = () => {};
 
-// src/config/dotenv.ts
-function parseDotenv(content) {
-  if (!content)
-    return {};
-  const result = {};
-  for (const rawLine of content.split(`
-`)) {
-    const line = rawLine.trim();
-    if (!line || line.startsWith("#"))
-      continue;
-    const stripped = line.startsWith("export ") ? line.slice(7).trim() : line;
-    const eqIndex = stripped.indexOf("=");
-    if (eqIndex === -1)
-      continue;
-    const key = stripped.slice(0, eqIndex).trim();
-    let value = stripped.slice(eqIndex + 1).trim();
-    if (value.startsWith('"') && value.endsWith('"') || value.startsWith("'") && value.endsWith("'")) {
-      value = value.slice(1, -1);
-    }
-    result[key] = value;
-  }
-  return result;
-}
-function resolveEnvVars(config2, env2) {
-  if (typeof config2 === "string") {
-    return resolveString(config2, env2);
-  }
-  if (Array.isArray(config2)) {
-    return config2.map((item) => resolveEnvVars(item, env2));
-  }
-  if (config2 !== null && typeof config2 === "object") {
-    const result = {};
-    for (const [key, value] of Object.entries(config2)) {
-      result[key] = resolveEnvVars(value, env2);
-    }
-    return result;
-  }
-  return config2;
-}
-function resolveString(str, env2) {
-  return str.replace(/\$\$([A-Za-z_][A-Za-z0-9_]*)/g, `${DOUBLE_DOLLAR_PLACEHOLDER}$1`).replace(/\$([A-Za-z_][A-Za-z0-9_]*)/g, (_match, varName) => {
-    if (!(varName in env2)) {
-      throw new Error(`Environment variable $${varName} (${varName}) is not defined`);
-    }
-    return env2[varName];
-  }).replace(new RegExp(`${DOUBLE_DOLLAR_PLACEHOLDER}([A-Za-z_][A-Za-z0-9_]*)`, "g"), "$$$1");
-}
-var DOUBLE_DOLLAR_PLACEHOLDER = "__DOLLAR_ESCAPE__";
-
 // src/config/profile.ts
 import { readdirSync } from "fs";
 import { join as join2 } from "path";
@@ -19471,8 +19497,9 @@ async function loadConfig(startDir, cliOverrides) {
   }
   for (const name of overlayChain) {
     const profileData = await loadProfile(name, projectRoot);
-    rawConfig = deepMergeConfig(rawConfig, profileData);
-    await loadProfileEnv(name, projectRoot);
+    const profileEnv = await loadProfileEnv(name, projectRoot);
+    const resolvedProfileData = Object.keys(profileEnv).length > 0 ? resolveEnvVars(profileData, profileEnv) : profileData;
+    rawConfig = deepMergeConfig(rawConfig, resolvedProfileData);
   }
   if (cliOverrides) {
     rawConfig = deepMergeConfig(rawConfig, cliOverrides);
@@ -20052,6 +20079,7 @@ __export(exports_config, {
   DESCRIPTION_QUALITY_RULES: () => DESCRIPTION_QUALITY_RULES,
   DEFAULT_CONFIG: () => DEFAULT_CONFIG,
   DEFAULT_AGENT_TIMEOUT_RETRY_CONFIG: () => DEFAULT_AGENT_TIMEOUT_RETRY_CONFIG,
+  ContextV2ConfigSchema: () => ContextV2ConfigSchema,
   ConfiguredModelSchema: () => ConfiguredModelSchema,
   COMPLEXITY_GUIDE: () => COMPLEXITY_GUIDE,
   AutoRouteConfigSchema: () => AutoRouteConfigSchema,
@@ -20097,9 +20125,11 @@ var CompleteError, SessionFailureError, SessionTurnError;
 var init_types3 = __esm(() => {
   CompleteError = class CompleteError extends Error {
     exitCode;
-    constructor(message, exitCode) {
+    retryable;
+    constructor(message, exitCode, retryable) {
       super(message);
       this.exitCode = exitCode;
+      this.retryable = retryable;
       this.name = "CompleteError";
     }
   };
@@ -20276,6 +20306,21 @@ var init_bun_deps = __esm(() => {
 });
 
 // src/agents/acp/parse-agent-error.ts
+function classifyCompleteError(error48) {
+  if (error48.retryable === undefined)
+    return null;
+  return {
+    output: error48.message,
+    tokenUsage: { inputTokens: 0, outputTokens: 0 },
+    estimatedCostUsd: 0,
+    adapterFailure: {
+      category: "quality",
+      outcome: "fail-adapter-error",
+      retriable: error48.retryable,
+      message: error48.message.slice(0, 500)
+    }
+  };
+}
 function parseAgentError(stderr) {
   if (!stderr) {
     return { type: "unknown" };
@@ -20603,42 +20648,55 @@ function parseSessionIds(stdout) {
   return { sessionId: undefined, recordId: undefined };
 }
 
-// src/agents/acp/spawn-client.ts
-import { randomUUID } from "crypto";
-async function readAndParseLines(stream, state, onActivity) {
+// src/agents/acp/stdout-line-reader.ts
+function readAndParseLines(stream, state, onActivity) {
   const decoder = new TextDecoder;
   let remainder = "";
   const reader = stream.getReader();
-  try {
-    while (true) {
-      const { done, value } = await reader.read();
-      if (done)
-        break;
-      remainder += decoder.decode(value, { stream: true });
-      for (;; ) {
-        const nl = remainder.indexOf(`
-`);
-        if (nl < 0)
+  const promise2 = (async () => {
+    try {
+      while (true) {
+        const { done, value } = await reader.read();
+        if (done)
           break;
-        const line = remainder.slice(0, nl);
-        remainder = remainder.slice(nl + 1);
-        if (line.trim()) {
-          const activity = parseAcpxJsonLine(line, state);
-          if (activity && onActivity)
-            onActivity(activity);
+        remainder += decoder.decode(value, { stream: true });
+        for (;; ) {
+          const nl = remainder.indexOf(`
+`);
+          if (nl < 0)
+            break;
+          const line = remainder.slice(0, nl);
+          remainder = remainder.slice(nl + 1);
+          if (line.trim()) {
+            const activity = parseAcpxJsonLine(line, state);
+            if (activity && onActivity)
+              onActivity(activity);
+          }
         }
       }
+      remainder += decoder.decode();
+      if (remainder.trim()) {
+        const activity = parseAcpxJsonLine(remainder.trim(), state);
+        if (activity && onActivity)
+          onActivity(activity);
+      }
+    } finally {
+      reader.releaseLock();
     }
-    remainder += decoder.decode();
-    if (remainder.trim()) {
-      const activity = parseAcpxJsonLine(remainder.trim(), state);
-      if (activity && onActivity)
-        onActivity(activity);
+  })();
+  return {
+    promise: promise2,
+    cancel: () => {
+      reader.cancel().catch(() => {});
     }
-  } finally {
-    reader.releaseLock();
-  }
+  };
 }
+var init_stdout_line_reader = __esm(() => {
+  init_agents();
+});
+
+// src/agents/acp/spawn-client.ts
+import { randomUUID } from "crypto";
 
 class SpawnAcpSession {
   agentName;
@@ -20793,7 +20851,8 @@ class SpawnAcpSession {
           });
         }
       } : undefined;
-      const parsePromise = readAndParseLines(proc.stdout, parseState, onActivity).catch(() => {});
+      const parseHandle = readAndParseLines(proc.stdout, parseState, onActivity);
+      const parsePromise = parseHandle.promise.catch(() => {});
       const stderrPromise = new Response(proc.stderr).text().catch(() => "");
       const exitCode = await proc.exited;
       const makeDrain = (ms) => {
@@ -20805,10 +20864,16 @@ class SpawnAcpSession {
       };
       const drainA = makeDrain(_spawnClientDeps.streamDrainTimeoutMs);
       const drainB = makeDrain(_spawnClientDeps.streamDrainTimeoutMs);
-      const [, stderr] = await Promise.all([
-        Promise.race([parsePromise, drainA.promise]).finally(() => drainA.cancel()),
+      const stdoutRaceResult = Promise.race([
+        parsePromise.then(() => "parsed"),
+        drainA.promise.then(() => "drain")
+      ]).finally(() => drainA.cancel());
+      const [stdoutWinner, stderr] = await Promise.all([
+        stdoutRaceResult,
         Promise.race([stderrPromise, drainB.promise]).finally(() => drainB.cancel())
       ]);
+      if (stdoutWinner === "drain")
+        parseHandle.cancel();
       emit?.({ ...baseEvent, kind: "agent.process_update", status: "exited", exitCode, timestamp: now() });
       if (exitCode !== 0) {
         const parsedOnError = finalizeParseState(parseState);
@@ -21079,6 +21144,7 @@ var init_spawn_client = __esm(() => {
   init_env();
   init_model_spec();
   init_reasoning_effort();
+  init_stdout_line_reader();
   _spawnClientDeps = {
     spawn: typedSpawn,
     streamDrainTimeoutMs: ACPX_STREAM_DRAIN_TIMEOUT_MS
@@ -21372,11 +21438,54 @@ var init_adapter_output = __esm(() => {
   CONTEXT_TOOL_CALL_PATTERN = /<nax_tool_call\s+name="([^"]+)">\s*([\s\S]*?)\s*<\/nax_tool_call>/i;
 });
 
-// src/agents/acp/adapter.ts
+// src/agents/acp/agent-entries.ts
 function resolveRegistryEntry(agentName) {
   return AGENT_REGISTRY[agentName] ?? DEFAULT_ENTRY;
 }
+var AGENT_REGISTRY, DEFAULT_ENTRY, ACP_ADAPTER_NAMES;
+var init_agent_entries = __esm(() => {
+  AGENT_REGISTRY = {
+    claude: {
+      binary: "claude",
+      displayName: "Claude Code (ACP)",
+      supportedTiers: ["fast", "balanced", "powerful"],
+      maxContextTokens: 200000
+    },
+    codex: {
+      binary: "codex",
+      displayName: "OpenAI Codex (ACP)",
+      supportedTiers: ["fast", "balanced"],
+      maxContextTokens: 128000
+    },
+    gemini: {
+      binary: "gemini",
+      displayName: "Gemini CLI (ACP)",
+      supportedTiers: ["fast", "balanced", "powerful"],
+      maxContextTokens: 1e6
+    },
+    opencode: {
+      binary: "opencode",
+      displayName: "opencode (ACP)",
+      supportedTiers: ["fast", "balanced", "powerful"],
+      maxContextTokens: 128000
+    },
+    pi: {
+      binary: "pi",
+      displayName: "Pi Coding Agent (ACP)",
+      supportedTiers: ["fast", "balanced", "powerful"],
+      maxContextTokens: 128000
+    }
+  };
+  DEFAULT_ENTRY = {
+    binary: "claude",
+    displayName: "ACP Agent",
+    supportedTiers: ["balanced"],
+    maxContextTokens: 128000
+  };
+  ACP_ADAPTER_NAMES = new Set(Object.keys(AGENT_REGISTRY));
+});
 
+// src/agents/acp/adapter.ts
 class AcpAgentAdapter {
   name;
   displayName;
@@ -21428,7 +21537,9 @@ class AcpAgentAdapter {
         timeoutPromise.catch(() => {});
         let response;
         try {
-          response = await Promise.race([session.prompt(prompt), timeoutPromise]);
+          const promptPromise = session.prompt(prompt);
+          promptPromise.catch(() => {});
+          response = await Promise.race([promptPromise, timeoutPromise]);
         } finally {
           clearTimeout(timeoutId);
         }
@@ -21441,7 +21552,7 @@ class AcpAgentAdapter {
               cancelled: true
             };
           }
-          throw new CompleteError("complete() failed: stop reason is error");
+          throw new CompleteError("complete() failed: stop reason is error", undefined, response.retryable);
         }
         const text = response.messages.filter((m) => m.role === "assistant").map((m) => m.content).join(`
 `).trim();
@@ -21456,7 +21567,7 @@ class AcpAgentAdapter {
           throw new CompleteError("complete() returned empty output");
         }
         const tokenUsage = response.cumulative_token_usage ? this._mapper.toInternal(response.cumulative_token_usage) : { inputTokens: 0, outputTokens: 0 };
-        const estimatedCostUsd = tokenUsage.inputTokens > 0 ? estimateCostFromTokenUsage(tokenUsage, _options.modelDef.model) : 0;
+        const estimatedCostUsd = tokenUsage.inputTokens > 0 || tokenUsage.outputTokens > 0 ? estimateCostFromTokenUsage(tokenUsage, _options.modelDef.model) : 0;
         const exactCostUsd = response.exactCostUsd;
         if (exactCostUsd !== undefined) {
           getSafeLogger()?.info("acp-adapter", "complete() cost", {
@@ -21481,6 +21592,11 @@ class AcpAgentAdapter {
       return await tryOneAgent(this.name);
     } catch (err) {
       const error48 = err instanceof Error ? err : new Error(String(err));
+      if (error48 instanceof CompleteError) {
+        const classified = classifyCompleteError(error48);
+        if (classified)
+          return classified;
+      }
       const parsed = _fallbackDeps.parseAgentError(error48.message);
       if (parsed.type === "auth") {
         return {
@@ -21747,7 +21863,7 @@ class AcpAgentAdapter {
     }
   }
 }
-var INTERACTION_TIMEOUT_MS, AGENT_REGISTRY, DEFAULT_ENTRY, ACP_ADAPTER_NAMES;
+var INTERACTION_TIMEOUT_MS;
 var init_adapter = __esm(() => {
   init_errors();
   init_logger2();
@@ -21756,42 +21872,11 @@ var init_adapter = __esm(() => {
   init_token_mapper();
   init_adapter_lifecycle();
   init_adapter_output();
+  init_agent_entries();
   init_adapter_lifecycle();
   init_adapter_output();
+  init_agent_entries();
   INTERACTION_TIMEOUT_MS = 5 * 60 * 1000;
-  AGENT_REGISTRY = {
-    claude: {
-      binary: "claude",
-      displayName: "Claude Code (ACP)",
-      supportedTiers: ["fast", "balanced", "powerful"],
-      maxContextTokens: 200000
-    },
-    codex: {
-      binary: "codex",
-      displayName: "OpenAI Codex (ACP)",
-      supportedTiers: ["fast", "balanced"],
-      maxContextTokens: 128000
-    },
-    gemini: {
-      binary: "gemini",
-      displayName: "Gemini CLI (ACP)",
-      supportedTiers: ["fast", "balanced", "powerful"],
-      maxContextTokens: 1e6
-    },
-    opencode: {
-      binary: "opencode",
-      displayName: "opencode (ACP)",
-      supportedTiers: ["fast", "balanced", "powerful"],
-      maxContextTokens: 128000
-    }
-  };
-  DEFAULT_ENTRY = {
-    binary: "claude",
-    displayName: "ACP Agent",
-    supportedTiers: ["balanced"],
-    maxContextTokens: 128000
-  };
-  ACP_ADAPTER_NAMES = new Set(Object.keys(AGENT_REGISTRY));
 });
 
 // src/agents/acp/parser.ts
@@ -21802,12 +21887,17 @@ function createParseState() {
     exactCostUsd: undefined,
     stopReason: undefined,
     error: undefined,
-    retryable: false
+    retryable: false,
+    sawJsonLine: false
   };
 }
 function parseAcpxJsonLine(line, state) {
   try {
     const event = JSON.parse(line);
+    if (!state.sawJsonLine) {
+      state.text = "";
+      state.sawJsonLine = true;
+    }
     if (event.jsonrpc === "2.0") {
       if (event.method === "session/update" && event.params?.update) {
         const update = event.params.update;
@@ -21860,11 +21950,18 @@ function parseAcpxJsonLine(line, state) {
           state.stopReason = result.stop_reason;
         if (result.usage && typeof result.usage === "object") {
           const u = result.usage;
+          const asNumber = (...values) => {
+            for (const v of values) {
+              if (typeof v === "number" && Number.isFinite(v))
+                return v;
+            }
+            return 0;
+          };
           state.tokenUsage = {
-            input_tokens: u.inputTokens ?? u.input_tokens ?? 0,
-            output_tokens: u.outputTokens ?? u.output_tokens ?? 0,
-            cache_read_input_tokens: u.cachedReadTokens ?? u.cache_read_input_tokens ?? 0,
-            cache_creation_input_tokens: u.cachedWriteTokens ?? u.cache_creation_input_tokens ?? 0
+            input_tokens: asNumber(u.inputTokens, u.input_tokens),
+            output_tokens: asNumber(u.outputTokens, u.output_tokens),
+            cache_read_input_tokens: asNumber(u.cachedReadTokens, u.cache_read_input_tokens),
+            cache_creation_input_tokens: asNumber(u.cachedWriteTokens, u.cache_creation_input_tokens)
           };
         }
       }
@@ -21907,7 +22004,7 @@ function parseAcpxJsonLine(line, state) {
       state.error = typeof event.error === "string" ? event.error : event.error.message ?? JSON.stringify(event.error);
     }
   } catch {
-    if (!state.text)
+    if (!state.text && !state.sawJsonLine)
       state.text = line;
   }
   return;
@@ -21996,7 +22093,7 @@ var KNOWN_AGENT_NAMES, _registryTestAdapters;
 var init_registry = __esm(() => {
   init_logger2();
   init_adapter();
-  KNOWN_AGENT_NAMES = ["claude", "codex", "opencode", "gemini", "aider"];
+  KNOWN_AGENT_NAMES = ["claude", "codex", "opencode", "gemini", "aider", "pi"];
   _registryTestAdapters = new Map;
 });
 
@@ -22336,7 +22433,7 @@ function trySameAgentRetry(result, state, deps) {
         outcome: "timeout-retry",
         timeoutRetryAttempts: newAttempts,
         kind: { kind: "timeout-retry", attempt: newAttempts },
-        currentRunOptions: resolveTimeoutRetryOptions(currentRunOptions, timeoutConfig, config2.execution),
+        currentRunOptions: resolveTimeoutRetryOptions(currentRunOptions, timeoutConfig, config2.execution, requestRunOptions),
         fallbackRecord: {
           outcome: result.adapterFailure?.outcome ?? "fail-timeout",
           category: result.adapterFailure?.category ?? "quality",
@@ -22375,8 +22472,9 @@ function extractTimeoutRetryConfig(config2) {
     budgetMultiplier: fromConfig?.budgetMultiplier ?? DEFAULT_AGENT_TIMEOUT_RETRY_CONFIG.budgetMultiplier
   };
 }
-function resolveTimeoutRetryOptions(prev, timeoutConfig, executionConfig) {
-  const budget = prev.timeoutSeconds ?? executionConfig?.sessionTimeoutSeconds ?? DEFAULT_CONFIG.execution.sessionTimeoutSeconds;
+function resolveTimeoutRetryOptions(prev, timeoutConfig, executionConfig, baseRunOptions) {
+  const baseBudget = baseRunOptions?.timeoutSeconds ?? prev.timeoutSeconds;
+  const budget = baseBudget ?? executionConfig?.sessionTimeoutSeconds ?? DEFAULT_CONFIG.execution.sessionTimeoutSeconds;
   return { ...prev, timeoutSeconds: budget * timeoutConfig.budgetMultiplier };
 }
 function timeoutRetryShouldRetry(attempts, config2) {
@@ -30156,7 +30254,7 @@ function validateStory(raw, index, allIds) {
   const rawDeps = s.dependencies;
   const dependencies = Array.isArray(rawDeps) ? rawDeps : [];
   for (const dep of dependencies) {
-    if (!allIds.has(dep)) {
+    if (!allIds.has(normalizeStoryId(dep))) {
       throw new NaxError(`[schema] story[${index}].dependencies references unknown story ID "${dep}"`, "SCHEMA_VALIDATION_FAILED", { stage: "schema", index, dep });
     }
   }
@@ -30418,6 +30516,12 @@ async function loadPRD(path) {
     throw new Error(`PRD file is too large (${sizeMB} MB exceeds ${limitMB} MB limit). Split this feature into smaller features or reduce story count.`);
   }
   const prd = await Bun.file(path).json();
+  if (!Array.isArray(prd.userStories)) {
+    throw new NaxError(`PRD file is missing or has a corrupt "userStories" array: ${path}`, "PRD_INVALID", {
+      stage: "prd",
+      path
+    });
+  }
   for (const story of prd.userStories) {
     story.attempts = story.attempts ?? 0;
     story.priorErrors = story.priorErrors ?? [];
@@ -30464,7 +30568,7 @@ function getNextStory(prd, currentStoryId, maxRetries) {
       return currentStory;
     }
   }
-  const eligible = prd.userStories.filter((s) => !s.passes && s.status !== "passed" && s.status !== "skipped" && s.status !== "blocked" && s.status !== "failed" && s.status !== "paused" && s.status !== "decomposed" && hasSatisfiedDependencies(s, storyIds, completedIds));
+  const eligible = prd.userStories.filter((s) => !s.passes && s.status !== "passed" && s.status !== "skipped" && s.status !== "blocked" && s.status !== "failed" && s.status !== "paused" && s.status !== "decomposed" && s.status !== "regression-failed" && hasSatisfiedDependencies(s, storyIds, completedIds));
   if (eligible.length === 0)
     return null;
   return eligible.reduce((best, s) => (s.priority ?? 0) > (best.priority ?? 0) ? s : best);
@@ -30495,7 +30599,7 @@ function markStoryPassed(prd, storyId, _statusWriter) {
     const parent = prd.userStories.find((s) => s.id === parentId);
     if (parent && parent.status === "decomposed") {
       const siblings = prd.userStories.filter((s) => s.parentStoryId === parentId);
-      const allSiblingsPassed = siblings.length > 0 && siblings.every((s) => s.passes || s.status === "passed");
+      const allSiblingsPassed = siblings.length > 0 && siblings.every((s) => s.passes || s.status === "passed" || s.status === "skipped");
       if (allSiblingsPassed) {
         parent.passes = true;
         parent.status = "passed";
@@ -31572,19 +31676,17 @@ ${newContextSection}`);
       result += sections.acceptanceCriteria;
       remainingChars -= sections.acceptanceCriteria.length;
     }
-    if (sections.context && remainingChars > 0) {
-      const reserveForMessage = sections.context.length > remainingChars ? trimmedMessage.length : 0;
+    const trimmable = sections.context ?? sections.other;
+    if (trimmable && remainingChars > 0) {
+      const reserveForMessage = trimmable.length > remainingChars ? trimmedMessage.length : 0;
       const maxContextChars = Math.max(0, remainingChars - reserveForMessage);
-      const trimmedContext = sections.context.substring(0, maxContextChars);
+      const trimmedContext = trimmable.substring(0, maxContextChars);
       result += trimmedContext;
-      if (trimmedContext.length < sections.context.length) {
+      if (trimmedContext.length < trimmable.length) {
         result += trimmedMessage;
       }
     }
-    if (sections.other && remainingChars > sections.other.length) {
-      result += sections.other;
-    }
-    return result;
+    return result.trim() ? result : prompt;
   }
   extractSections(prompt) {
     const sections = {};
@@ -32911,6 +33013,80 @@ var init_tool_runtime = __esm(() => {
   init_pull_tools();
 });
 
+// src/context/engine/manifest-purge.ts
+import { dirname as dirname7, resolve as resolve11 } from "path";
+async function purgeStaleManifests(projectDir, retentionDays) {
+  const allEntries = await _manifestPurgeDeps.scan(MANIFEST_PATTERN, projectDir, MAX_MANIFEST_SCAN);
+  if (allEntries.length >= MAX_MANIFEST_SCAN) {
+    _manifestPurgeDeps.debugLog("manifest-purge", `Manifest scan reached MAX_MANIFEST_SCAN=${MAX_MANIFEST_SCAN}; stopping further examination`, { cap: MAX_MANIFEST_SCAN, projectDir });
+  }
+  const entries = allEntries.slice(0, MAX_MANIFEST_SCAN);
+  const cutoffMs = _manifestPurgeDeps.now() - retentionDays * DAY_MS;
+  let deleted = 0;
+  const touchedDirs = new Set;
+  for (const relPath of entries) {
+    const absPath = resolve11(projectDir, relPath);
+    let mtimeMs;
+    try {
+      mtimeMs = await _manifestPurgeDeps.statMtime(absPath);
+    } catch {
+      continue;
+    }
+    if (mtimeMs >= cutoffMs)
+      continue;
+    try {
+      await _manifestPurgeDeps.unlink(absPath);
+      deleted++;
+      touchedDirs.add(dirname7(absPath));
+    } catch {}
+  }
+  for (const storyDir of touchedDirs) {
+    await _manifestPurgeDeps.rmdirIfEmpty(storyDir);
+  }
+  return deleted;
+}
+var MAX_MANIFEST_SCAN = 5000, DAY_MS = 86400000, MANIFEST_PATTERN = ".nax/features/*/stories/*/{context-manifest-*,rebuild-manifest}.json", _manifestPurgeDeps;
+var init_manifest_purge = __esm(() => {
+  init_logger2();
+  _manifestPurgeDeps = {
+    now: () => Date.now(),
+    scan: async (pattern, cwd, cap) => {
+      const results = [];
+      const g = new Bun.Glob(pattern);
+      for (const entry of g.scanSync({ cwd, absolute: false, dot: true })) {
+        if (results.length >= cap)
+          break;
+        results.push(entry);
+      }
+      return results;
+    },
+    statMtime: async (path3) => {
+      const file3 = Bun.file(path3);
+      if (!await file3.exists())
+        throw new Error(`stat: file not found: ${path3}`);
+      const stat = await file3.stat();
+      return stat.mtimeMs;
+    },
+    unlink: async (path3) => {
+      const { unlink: nodeUnlink } = await import("fs/promises");
+      await nodeUnlink(path3);
+    },
+    rmdirIfEmpty: async (path3) => {
+      const { rmdir } = await import("fs/promises");
+      try {
+        await rmdir(path3);
+        return true;
+      } catch {
+        return false;
+      }
+    },
+    debugLog: (stage, message, data) => {
+      const logger = getLogger();
+      logger?.debug(stage, message, data);
+    }
+  };
+});
+
 // src/context/engine/index.ts
 var init_engine = __esm(() => {
   init_orchestrator();
@@ -32936,6 +33112,7 @@ var init_engine = __esm(() => {
   init_stage_assembler();
   init_tool_runtime();
   init_manifest_store();
+  init_manifest_purge();
 });
 
 // src/prompts/core/section-accumulator.ts
@@ -35606,12 +35783,12 @@ function acceptanceDiagnoseRawArrayToFindings(raw) {
 }
 
 // src/findings/path-utils.ts
-import { relative as relative8, resolve as resolve11 } from "path";
+import { relative as relative8, resolve as resolve12 } from "path";
 function rebaseToWorkdir(rawPath, cwd, workdir) {
   if (rawPath.startsWith("/")) {
     return relative8(workdir, rawPath);
   }
-  return relative8(workdir, resolve11(cwd, rawPath));
+  return relative8(workdir, resolve12(cwd, rawPath));
 }
 var init_path_utils = () => {};
 
@@ -36549,7 +36726,7 @@ function validateRoutingDecision(parsed, config2, story) {
     throw new Error(`Invalid complexity: ${parsed.complexity}`);
   }
   const modelTier = parsed.modelTier;
-  const tierExistsInAnyAgent = Object.values(config2.models).some((agentTiers) => (modelTier in agentTiers));
+  const tierExistsInAnyAgent = Object.values(config2.models).some((agentTiers) => typeof modelTier === "string" && Object.hasOwn(agentTiers, modelTier));
   if (!tierExistsInAnyAgent) {
     throw new Error(`Invalid modelTier: ${modelTier} (not found in any agent's tier map)`);
   }
@@ -37806,10 +37983,13 @@ function validateAdversarialShape(parsed) {
   const acks = extractAcks(obj.acks);
   return {
     passed: obj.passed,
-    findings: obj.findings,
+    findings: obj.findings.filter(isAdversarialFindingShaped),
     ...acks.length > 0 && { acks }
   };
 }
+function isAdversarialFindingShaped(f) {
+  return typeof f === "object" && f !== null && !Array.isArray(f);
+}
 function formatFindings(findings) {
   return findings.map((f) => `[${f.severity}][${f.category}] ${f.file}:${f.line} \u2014 ${f.issue}
   Suggestion: ${f.suggestion}`).join(`
@@ -39653,9 +39833,10 @@ var init_debate_hybrid = __esm(() => {
           return { ...proposal, output: `Agent "failed" during rebuttal`, estimatedCostUsd: totalCostUsd };
         }
         if (round < ctx.input.rounds) {
-          const settledRound = await raceAgainstAbort(Promise.all(ctx.input.rebutBarriers[round - 1].map((b) => b.promise)), ctx.input.signal, ctx.input.storyId);
-          priorRoundOutputs.push(settledRound);
-          roundInputs = settledRound;
+          const settledRound = await raceAgainstAbort(Promise.allSettled(ctx.input.rebutBarriers[round - 1].map((b) => b.promise)), ctx.input.signal, ctx.input.storyId);
+          const roundOutputs = settledRound.map((r) => r.status === "fulfilled" ? r.value : "");
+          priorRoundOutputs.push(roundOutputs);
+          roundInputs = roundOutputs;
         }
       }
       return { ...lastTurn, estimatedCostUsd: totalCostUsd };
@@ -39701,7 +39882,8 @@ var init_debate_plan = __esm(() => {
           return proposal;
         }
       }
-      const peerProposals = await raceAgainstAbort(Promise.all(ctx.input.proposalBarriers.map((barrier) => barrier.promise)), ctx.input.signal, ctx.input.storyId);
+      const peerProposalsSettled = await raceAgainstAbort(Promise.allSettled(ctx.input.proposalBarriers.map((barrier) => barrier.promise)), ctx.input.signal, ctx.input.storyId);
+      const peerProposals = peerProposalsSettled.map((r) => r.status === "fulfilled" ? r.value : "");
       const rebutResult = ctx.input.turnSemaphore ? await ctx.input.turnSemaphore.run(() => ctx.send(ctx.input.buildRebutPrompt(peerProposals))) : await ctx.send(ctx.input.buildRebutPrompt(peerProposals));
       ctx.input.rebuttalBarrier.resolve(rebutResult.output);
       const decision = await raceAgainstAbort(ctx.input.selectionSignal, ctx.input.signal, ctx.input.storyId);
@@ -39740,8 +39922,18 @@ async function getChangedFiles(workdir, fromRef = "HEAD") {
     stdout: "pipe",
     stderr: "pipe"
   });
-  const output = await Bun.readableStreamToText(proc.stdout);
-  await proc.exited;
+  const [output, stderr, exitCode] = await Promise.all([
+    Bun.readableStreamToText(proc.stdout),
+    Bun.readableStreamToText(proc.stderr),
+    proc.exited
+  ]);
+  if (exitCode !== 0) {
+    throw new NaxError(`git diff --name-only ${fromRef} failed (exit ${exitCode}): ${stderr.trim()}`, "GIT_DIFF_FAILED", {
+      stage: "tdd-isolation",
+      fromRef,
+      exitCode
+    });
+  }
   return output.trim().split(`
 `).filter(Boolean);
 }
@@ -39816,6 +40008,7 @@ async function verifyImplementerIsolation(workdir, beforeRef, testFilePatterns =
 }
 var _isolationDeps, SRC_PATTERNS, LITE_STUB_ADDED_LINES_CEILING = 20;
 var init_isolation = __esm(() => {
+  init_errors();
   init_test_runners();
   init_bun_deps();
   _isolationDeps = { spawn };
@@ -41323,17 +41516,18 @@ async function executeWithTimeout(command, timeoutSeconds, env2, options) {
     stdout: "pipe",
     stderr: "pipe",
     env: env2 || normalizeEnvironment(process.env),
-    cwd: options?.cwd
+    cwd: options?.cwd,
+    detached: true
   });
   const stdoutPromise = new Response(proc.stdout).text().catch(() => "");
   const stderrPromise = new Response(proc.stderr).text().catch(() => "");
   const timeoutMs = timeoutSeconds * 1000;
   let timedOut = false;
   const timer = { id: undefined };
-  const timeoutPromise = new Promise((resolve12) => {
+  const timeoutPromise = new Promise((resolve13) => {
     timer.id = setTimeout(() => {
       timedOut = true;
-      resolve12();
+      resolve13();
     }, timeoutMs);
   });
   const processPromise = proc.exited;
@@ -42197,8 +42391,8 @@ function makeDeclarationSink() {
 var {spawn: spawn2 } = globalThis.Bun;
 function createDrainDeadline(deadlineMs) {
   let timeoutId;
-  const promise2 = new Promise((resolve12) => {
-    timeoutId = setTimeout(() => resolve12(""), deadlineMs);
+  const promise2 = new Promise((resolve13) => {
+    timeoutId = setTimeout(() => resolve13(""), deadlineMs);
   });
   return {
     promise: promise2,
@@ -45080,14 +45274,14 @@ var init_prepare_inputs = __esm(() => {
 });
 
 // src/utils/nax-project-root.ts
-import { dirname as dirname7, join as join27, resolve as resolve12 } from "path";
+import { dirname as dirname8, join as join27, resolve as resolve13 } from "path";
 async function findNaxProjectRoot(startDir) {
-  let dir = resolve12(startDir);
+  let dir = resolve13(startDir);
   for (let depth = 0;depth < MAX_NAX_WALK_DEPTH; depth++) {
     if (await _naxProjectRootDeps.exists(join27(dir, ".nax", "config.json"))) {
       return dir;
     }
-    const parent = dirname7(dir);
+    const parent = dirname8(dir);
     if (parent === dir)
       break;
     dir = parent;
@@ -45108,7 +45302,7 @@ var package_default;
 var init_package = __esm(() => {
   package_default = {
     name: "@nathapp/nax",
-    version: "0.78.0",
+    version: "0.79.0",
     description: "AI Coding Agent Orchestrator \u2014 loops until done",
     type: "module",
     bin: {
@@ -45155,9 +45349,14 @@ var init_package = __esm(() => {
       "check:dispatch-context": "bash scripts/check-dispatch-context.sh",
       "check:naxconfig-cast": "bash scripts/check-no-silent-naxconfig-cast.sh",
       "check:runtime-cleanup": "bash scripts/check-runtime-cleanup.sh",
+      "check:scripts": "bash scripts/check-scripts.sh",
       "check:adapter-no-config-import": "bash scripts/check-adapter-no-config-import.sh",
+      "check:test-typecheck": "bun run scripts/check-test-typecheck.ts",
+      "check:test-typecheck:update": "bun run scripts/check-test-typecheck.ts --update-baseline",
+      "check:test-as-unknown-as": "bun run scripts/check-test-as-unknown-as.ts",
+      "check:test-as-unknown-as:update": "bun run scripts/check-test-as-unknown-as.ts --update-baseline",
       "check:gate-reachability": "bun run scripts/check-gate-reachability.ts",
-      "check:all": "bun run lint && bun run check:test-mocks && bun run check:process-cwd && bun run check:no-adapter-wrap && bun run check:dispatch-context && bun run check:naxconfig-cast && bun run check:runtime-cleanup && bun run check:adapter-no-config-import && bun run check:gate-reachability",
+      "check:all": "bun run lint && bun run check:test-mocks && bun run check:process-cwd && bun run check:no-adapter-wrap && bun run check:scripts && bun run check:dispatch-context && bun run check:naxconfig-cast && bun run check:runtime-cleanup && bun run check:adapter-no-config-import && bun run check:test-typecheck && bun run check:test-as-unknown-as && bun run check:gate-reachability",
       prepublishOnly: "bun run build",
       "test:full": "FULL=1 NAX_PRECHECK=1 bun test test/ --timeout=60000"
     },
@@ -45216,8 +45415,8 @@ var init_version = __esm(() => {
   NAX_VERSION = package_default.version;
   NAX_COMMIT = (() => {
     try {
-      if (/^[0-9a-f]{6,10}$/.test("af86acb4"))
-        return "af86acb4";
+      if (/^[0-9a-f]{6,10}$/.test("fdfb7e0e"))
+        return "fdfb7e0e";
     } catch {}
     try {
       const result = Bun.spawnSync(["git", "rev-parse", "--short", "HEAD"], {
@@ -46054,7 +46253,7 @@ function appendFilesToCommand(command, files) {
 }
 async function listChangedFiles(workdir, baseRef) {
   const proc = Bun.spawn({
-    cmd: ["git", "diff", "--name-only", `${baseRef}..HEAD`],
+    cmd: ["git", "diff", "--relative", "--name-only", `${baseRef}..HEAD`],
     cwd: workdir,
     stdout: "pipe",
     stderr: "pipe"
@@ -50239,7 +50438,7 @@ function createPackageRegistry(loader, repoRoot) {
       return "";
     return packageDir;
   }
-  function resolve13(packageDir) {
+  function resolve14(packageDir) {
     const key = toRelativeKey(packageDir);
     const cached2 = cache.get(key);
     if (cached2 !== undefined) {
@@ -50276,9 +50475,9 @@ function createPackageRegistry(loader, repoRoot) {
     all() {
       return [...cache.values()];
     },
-    resolve: resolve13,
+    resolve: resolve14,
     repo() {
-      return resolve13(undefined);
+      return resolve14(undefined);
     },
     hydrate
   };
@@ -51956,6 +52155,11 @@ var init_session = __esm(() => {
 });
 
 // src/verification/flake-probe.ts
+function probeRanNoTests(output) {
+  if (!output)
+    return false;
+  return NO_TESTS_EXECUTED_MARKERS.some((re) => re.test(output));
+}
 function escapeRegex2(input) {
   return input.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
 }
@@ -51998,7 +52202,7 @@ async function runFlakeProbe(input) {
     } catch {
       continue;
     }
-    if (result.success && result.countsTowardEscalation) {
+    if (result.success && result.countsTowardEscalation && !probeRanNoTests(result.output)) {
       probePasses += 1;
     }
   }
@@ -52007,10 +52211,11 @@ async function runFlakeProbe(input) {
   }
   return { verdict: "consistent-failure", probeRuns };
 }
-var _flakeProbeDeps;
+var NO_TESTS_EXECUTED_MARKERS, _flakeProbeDeps;
 var init_flake_probe = __esm(() => {
   init_errors();
   init_executor();
+  NO_TESTS_EXECUTED_MARKERS = [/no tests? to run/i, /^ran 0 tests?/im];
   _flakeProbeDeps = {
     execute: executeWithTimeout
   };
@@ -52586,9 +52791,9 @@ async function buildProjectMetadata(workdir, config2) {
     name: detected?.name,
     language: detected?.lang,
     dependencies: detected?.dependencies ?? [],
-    testCommand: config2.execution?.testCommand ?? undefined,
-    lintCommand: config2.execution?.lintCommand ?? undefined,
-    typecheckCommand: config2.execution?.typecheckCommand ?? undefined
+    testCommand: config2.quality?.commands?.test ?? undefined,
+    lintCommand: config2.quality?.commands?.lint ?? undefined,
+    typecheckCommand: config2.quality?.commands?.typecheck ?? undefined
   };
 }
 function formatMetadataSection(metadata) {
@@ -53892,7 +54097,9 @@ async function finalizePlanRun(ctx, opts, successful, rebuttalList, outputPaths,
   } : await resolveOutcome(proposalOutputs, critiqueOutputs, ctx.stageConfig, ctx.config, ctx.callContext, ctx.storyId, resolverTimeoutMs, opts.workdir, opts.feature, buildPlanSynthesisSuffix(opts.specContent), finalizedProposals.map((p) => p.debater), agentManager);
   let finalOutcome = outcome.outcome;
   let winningOutput = outcome.output ?? finalizedProposals[0]?.output;
-  winningOutput = await readWinnerOutput(selectionSummary.winnerOutputPath ?? outputPaths[0], winningOutput);
+  if (selectionSummary.winnerOutputPath) {
+    winningOutput = await readWinnerOutput(selectionSummary.winnerOutputPath, winningOutput);
+  }
   let runCostUsd = totalCostUsd;
   if (config2.postDebateVerifier && winningOutput) {
     const verifierCtx = {
@@ -54039,7 +54246,8 @@ async function runPlan(ctx, taskContext, outputFormat, opts) {
     const settled = await Promise.allSettled(callOpPromises);
     for (let i = 0;i < settled.length; i++) {
       const res = settled[i];
-      if (res.status === "fulfilled") {
+      const succeeded = res.status === "fulfilled" && res.value.success;
+      if (succeeded && res.status === "fulfilled") {
         successful.push({
           debater: resolved[i].debater,
           agentName: resolved[i].agentName,
@@ -54064,7 +54272,7 @@ async function runPlan(ctx, taskContext, outputFormat, opts) {
             stage: ctx.stage,
             debaterIndex: i,
             agent: resolved[i].debater.agent,
-            error: res.reason instanceof Error ? res.reason.message : String(res.reason)
+            error: res.status === "rejected" ? res.reason instanceof Error ? res.reason.message : String(res.reason) : `debate op returned success:false \u2014 ${res.value.rebut}`
           });
         }
       }
@@ -54075,6 +54283,8 @@ async function runPlan(ctx, taskContext, outputFormat, opts) {
       resolver.resolve({});
     const proposalBarriers = resolved.map(() => Promise.withResolvers());
     const rebuttalBarriers = resolved.map(() => Promise.withResolvers());
+    for (const barrier of proposalBarriers)
+      barrier.promise.catch(() => {});
     const rebutBuilder = new DebatePromptBuilder({ taskContext, outputFormat: "", stage: "plan" }, { debaters: resolved.map((e) => e.debater), sessionMode: "stateful" });
     const callOpPromisesB = resolved.map(({ debater, agentName }, index) => {
       const debaterCtx = {
@@ -54100,6 +54310,7 @@ async function runPlan(ctx, taskContext, outputFormat, opts) {
       callOpPromisesB[i].then((result) => {
         rebuttalBarriers[i].resolve(result.rebut ?? "");
       }, (err) => {
+        proposalBarriers[i].reject(err);
         rebuttalBarriers[i].reject(err);
       });
     }
@@ -54221,7 +54432,6 @@ async function runStateful(ctx, prompt) {
   const rebuttalBuilder = buildRebuttalPromptBuilder(ctx.stage, prompt, resolved.map((entry) => entry.debater));
   const signal = resolveStatefulSignal(ctx);
   const noopBuildRebutPrompt = () => "";
-  const localProposalBarrier = () => [Promise.withResolvers()];
   const debaterRole = (index) => `debate-${ctx.stage}-${index}`;
   const debaterCallContext = (agentName, index) => ({
     ...createDebaterCallContext(ctx, agentName),
@@ -54233,12 +54443,13 @@ async function runStateful(ctx, prompt) {
       throw new NaxError("[debate] Stateful debate aborted", "CALL_OP_ABORTED", { storyId: ctx.storyId });
     }
   };
+  const proposalBarriers = resolved.map(() => Promise.withResolvers());
   const proposalSettled = await allSettledBounded(resolved.map(({ debater, agentName }, index) => () => callOp(debaterCallContext(agentName, index), statefulDebaterOp, {
     debater,
     index,
     proposePrompt: proposalBuilder.buildProposalPrompt(index),
     buildRebutPrompt: noopBuildRebutPrompt,
-    proposalBarriers: localProposalBarrier(),
+    proposalBarriers,
     signal,
     storyId: ctx.storyId,
     skipRebuttal: true
@@ -54304,6 +54515,7 @@ async function runStateful(ctx, prompt) {
     });
     return buildFailedResult(ctx.storyId, ctx.stage, ctx.stageConfig, 0);
   }
+  const rebuttalRoundBarriers = successfulProposals.map(() => Promise.withResolvers());
   const rebuttals = shouldRunRebuttal ? (await allSettledBounded(successfulProposals.map((proposal, index) => () => callOp(debaterCallContext(proposal.agentName, proposal.resolvedIndex), statefulDebaterOp, {
     debater: proposal.debater,
     index,
@@ -54312,7 +54524,7 @@ async function runStateful(ctx, prompt) {
       output: entry.output
     }))),
     buildRebutPrompt: noopBuildRebutPrompt,
-    proposalBarriers: localProposalBarrier(),
+    proposalBarriers: rebuttalRoundBarriers,
     signal,
     storyId: ctx.storyId,
     skipRebuttal: true
@@ -54962,9 +55174,9 @@ ${request.summary}
       throw new Error("CLI plugin not initialized");
     }
     let timeoutId;
-    const timeoutPromise = new Promise((resolve14) => {
+    const timeoutPromise = new Promise((resolve15) => {
       timeoutId = setTimeout(() => {
-        resolve14({
+        resolve15({
           requestId: request.id,
           action: "skip",
           respondedBy: "timeout",
@@ -55120,9 +55332,9 @@ ${request.summary}
     if (!this.rl) {
       throw new Error("CLI plugin not initialized");
     }
-    return new Promise((resolve14) => {
+    return new Promise((resolve15) => {
       this.rl?.question(prompt, (answer) => {
-        resolve14(answer);
+        resolve15(answer);
       });
     });
   }
@@ -55480,9 +55692,9 @@ ${partLabel}${chunks[i]}`;
     parseUpdate(requestId, update) {
       if (update.callback_query) {
         const data = update.callback_query.data;
-        if (!data.startsWith(requestId))
-          return null;
         const parts = data.split(":");
+        if (parts[0] !== requestId)
+          return null;
         if (parts.length < 2)
           return null;
         const action = parts[1];
@@ -55609,11 +55821,11 @@ function installServePortZeroCompat() {
   const originalFetch = globalThis.fetch.bind(globalThis);
   const patchedServe = (options) => {
     const requestedPort = typeof options.port === "number" ? options.port : 0;
-    if (requestedPort !== 0 && !inMemoryServers.has(requestedPort)) {
+    if (!inMemoryServers.has(requestedPort)) {
       try {
         return originalServe(options);
       } catch {
-        return createInMemoryServer(options, requestedPort);
+        return createInMemoryServer(options, requestedPort === 0 ? nextCompatPort() : requestedPort);
       }
     }
     return createInMemoryServer(options, nextCompatPort());
@@ -55736,7 +55948,7 @@ class WebhookInteractionPlugin {
       this.registeredRequestIds.delete(requestId);
       return early;
     }
-    return new Promise((resolve14) => {
+    return new Promise((resolve15) => {
       const existingCallback = this.receiveCallbacks.get(requestId);
       if (existingCallback) {
         this.clearReceiveTimer(requestId);
@@ -55751,7 +55963,7 @@ class WebhookInteractionPlugin {
         this.clearReceiveTimer(requestId);
         this.receiveCallbacks.delete(requestId);
         this.registeredRequestIds.delete(requestId);
-        resolve14({
+        resolve15({
           requestId,
           action: "skip",
           respondedBy: "timeout",
@@ -55763,7 +55975,7 @@ class WebhookInteractionPlugin {
         this.clearReceiveTimer(requestId);
         this.receiveCallbacks.delete(requestId);
         this.registeredRequestIds.delete(requestId);
-        resolve14(response);
+        resolve15(response);
       });
     });
   }
@@ -56039,8 +56251,8 @@ Options:`);
         stage: "run"
       });
     }
-    if (parsed.confidence < 0 || parsed.confidence > 1) {
-      throw new NaxError(`Invalid confidence: ${parsed.confidence} (must be 0-1)`, "AUTO_APPROVE_PARSE_FAILED", {
+    if (typeof parsed.confidence !== "number" || !Number.isFinite(parsed.confidence) || parsed.confidence < 0 || parsed.confidence > 1) {
+      throw new NaxError(`Invalid confidence: ${parsed.confidence} (must be a number 0-1)`, "AUTO_APPROVE_PARSE_FAILED", {
         stage: "run"
       });
     }
@@ -56136,7 +56348,7 @@ function createTriggerRequest(trigger, context, config2) {
   const metadata = TRIGGER_METADATA[trigger];
   const { fallback, timeout } = getTriggerConfig(trigger, config2);
   const summary = substituteTemplate(metadata.defaultSummary, context);
-  const id = `trigger-${trigger}-${Date.now()}`;
+  const id = `trigger-${trigger}-${Date.now()}-${crypto.randomUUID().slice(0, 8)}`;
   return {
     id,
     type: "confirm",
@@ -56315,10 +56527,10 @@ function validateFeatureName(feature) {
 
 // src/plan/critic.ts
 import { mkdir as mkdir6 } from "fs/promises";
-import { dirname as dirname8, join as join43 } from "path";
+import { dirname as dirname9, join as join43 } from "path";
 async function writeSpecDeltas(findings, workdir, runId, storyId, manifest) {
   const path8 = join43(workdir, ".nax", "runs", runId, "plan", storyId, "spec-deltas.md");
-  await mkdir6(dirname8(path8), { recursive: true });
+  await mkdir6(dirname9(path8), { recursive: true });
   await Bun.write(path8, formatSpecDeltas(findings, manifest));
   return path8;
 }
@@ -56393,13 +56605,13 @@ function createCliInteractionBridge() {
       process.stdout.write(`
 \uD83E\uDD16 Agent: ${text}
 You: `);
-      return new Promise((resolve14) => {
+      return new Promise((resolve15) => {
         const rl = createInterface2({ input: process.stdin, terminal: false });
         rl.once("line", (line) => {
           rl.close();
-          resolve14(line.trim());
+          resolve15(line.trim());
         });
-        rl.once("close", () => resolve14(""));
+        rl.once("close", () => resolve15(""));
       });
     }
   };
@@ -58463,14 +58675,14 @@ var init_status_cost = __esm(() => {
 
 // src/commands/common.ts
 import { existsSync as existsSync16, readdirSync as readdirSync2, realpathSync as realpathSync4 } from "fs";
-import { join as join46, resolve as resolve14 } from "path";
+import { join as join46, resolve as resolve15 } from "path";
 function resolveProject2(options = {}) {
   const { dir, feature } = options;
   let projectRoot;
   let naxDir;
   let configPath;
   if (dir) {
-    projectRoot = realpathSync4(resolve14(dir));
+    projectRoot = realpathSync4(resolve15(dir));
     naxDir = join46(projectRoot, ".nax");
     if (!existsSync16(naxDir)) {
       throw new NaxError(`Directory does not contain a nax project: ${projectRoot}
@@ -58527,12 +58739,28 @@ No features found in this project.`;
     featureDir
   };
 }
+function resolveSingleFeature(naxDir, remediationHint = "pass -f <name>") {
+  const featuresDir = join46(naxDir, "features");
+  const available = existsSync16(featuresDir) ? readdirSync2(featuresDir, { withFileTypes: true }).filter((entry) => entry.isDirectory()).map((entry) => entry.name).sort() : [];
+  if (available.length === 1)
+    return available[0];
+  if (available.length === 0) {
+    throw new NaxError(`No feature specified and no features found \u2014 ${remediationHint}.`, "FEATURE_NOT_SPECIFIED", {
+      featuresDir
+    });
+  }
+  throw new NaxError(`No feature specified and multiple features exist \u2014 ${remediationHint}.
+
+Available features:
+${available.map((f) => `  - ${f}`).join(`
+`)}`, "FEATURE_AMBIGUOUS", { featuresDir, available });
+}
 async function resolveProjectAsync(options = {}) {
   const { dir } = options;
   if (!dir) {
     return resolveProject2(options);
   }
-  if (existsSync16(resolve14(dir))) {
+  if (existsSync16(resolve15(dir))) {
     return resolveProject2(options);
   }
   const isPlainName = !dir.includes("/") && !dir.includes("\\");
@@ -58548,17 +58776,17 @@ async function resolveProjectAsync(options = {}) {
       } catch {}
     }
     throw new NaxError(`No project found for name or path: "${dir}"
-Checked filesystem path: ${resolve14(dir)}
+Checked filesystem path: ${resolve15(dir)}
 Checked identity registry: ${registryIdentityPath}
-Tip: use an absolute or relative path, or run "nax init" in your project directory first.`, "PROJECT_NOT_FOUND", { dir, resolvedPath: resolve14(dir), registryIdentityPath });
+Tip: use an absolute or relative path, or run "nax init" in your project directory first.`, "PROJECT_NOT_FOUND", { dir, resolvedPath: resolve15(dir), registryIdentityPath });
   }
   try {
     return resolveProject2(options);
   } catch (err) {
     if (err instanceof Error && "code" in err && err.code === "ENOENT") {
-      throw new NaxError(`Path does not exist: ${resolve14(dir)}`, "PROJECT_NOT_FOUND", {
+      throw new NaxError(`Path does not exist: ${resolve15(dir)}`, "PROJECT_NOT_FOUND", {
         dir,
-        resolvedPath: resolve14(dir),
+        resolvedPath: resolve15(dir),
         cause: err
       });
     }
@@ -58566,7 +58794,7 @@ Tip: use an absolute or relative path, or run "nax init" in your project directo
   }
 }
 function findProjectRoot(startDir) {
-  let current = resolve14(startDir);
+  let current = resolve15(startDir);
   let depth = 0;
   while (depth < MAX_DIRECTORY_DEPTH) {
     const naxDir = join46(current, ".nax");
@@ -58596,7 +58824,7 @@ __export(exports_status_features, {
   _statusFeaturesDeps: () => _statusFeaturesDeps
 });
 import { existsSync as existsSync17, readdirSync as readdirSync3 } from "fs";
-import { basename as basename10, join as join47, resolve as resolve15 } from "path";
+import { basename as basename10, join as join47, resolve as resolve16 } from "path";
 function isPidAlive(pid) {
   try {
     process.kill(pid, 0);
@@ -58911,7 +59139,7 @@ async function displayFeatureStatus(options = {}) {
   if (options.feature) {
     let featureDir;
     if (options.dir) {
-      const projectDir = resolve15(options.dir);
+      const projectDir = resolve16(options.dir);
       const config2 = await _statusFeaturesDeps.loadConfig(projectDir).catch(() => null);
       const projectKey = config2?.name?.trim() || basename10(projectDir);
       const outputDir = _statusFeaturesDeps.projectOutputDir(projectKey, config2?.outputDir);
@@ -59150,9 +59378,11 @@ var init_events = () => {};
 // src/acceptance/fix-generator.ts
 function findRelatedStories(failedAC, prd) {
   const relatedStoryIds = [];
+  const escapedAC = failedAC.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+  const acPattern = new RegExp(`(?<![\\w-])${escapedAC}(?!\\d)`);
   for (const story of prd.userStories) {
     for (const ac of story.acceptanceCriteria) {
-      if (ac.includes(failedAC)) {
+      if (acPattern.test(ac)) {
         relatedStoryIds.push(story.id);
         break;
       }
@@ -59525,6 +59755,58 @@ function logTestOutput(logger, stage, output, opts = {}) {
     output: lines
   });
 }
+// src/verification/flake-baseline-diff.ts
+async function resolveFlakeBaselineDiff(config2, workdir, storyWorkdir) {
+  try {
+    const resolved = await resolveTestFilePatterns(config2, workdir, storyWorkdir);
+    const baseRef = await getMergeBase(workdir);
+    if (baseRef === undefined) {
+      throw new NaxError("getMergeBase() found no usable ref (empty/detached repo)", "FLAKE_BASELINE_NO_MERGE_BASE", {
+        stage: "flake-triage",
+        workdir
+      });
+    }
+    const preflight = await gitWithTimeout(["diff", "--name-only", baseRef], workdir);
+    if (preflight.exitCode !== 0) {
+      throw new NaxError(`git diff --name-only ${baseRef} failed (exit ${preflight.exitCode})`, "FLAKE_BASELINE_GIT_DIFF_FAILED", {
+        stage: "flake-triage",
+        baseRef,
+        exitCode: preflight.exitCode
+      });
+    }
+    const changedTestFiles = await getChangedTestFiles(workdir, workdir, baseRef, storyWorkdir, [...resolved.regex]);
+    const changedNonTestFiles = await getChangedNonTestFiles(workdir, baseRef, storyWorkdir, [...resolved.regex], undefined, workdir);
+    const mappedTestFiles = await mapSourceToTests(changedNonTestFiles, workdir, storyWorkdir, [...resolved.globs]);
+    return { changedTestFiles, mappedTestFiles };
+  } catch (err) {
+    getSafeLogger()?.warn("flake-triage", "Baseline diff resolution failed \u2014 skipping triage this gate (fail closed)", {
+      error: errorMessage(err)
+    });
+    return null;
+  }
+}
+var init_flake_baseline_diff = __esm(() => {
+  init_errors();
+  init_logger2();
+  init_test_runners();
+  init_git();
+  init_smart_runner();
+});
+
+// src/verification/shell-quote.ts
+function shellQuoteArg(arg) {
+  return `'${arg.replaceAll("'", `'\\''`)}'`;
+}
+
+// src/verification/index.ts
+var init_verification = __esm(() => {
+  init_executor();
+  init_runners();
+  init_flake_probe();
+  init_flake_triage();
+  init_flake_baseline_diff();
+  init_mutation();
+});
 
 // src/pipeline/stages/acceptance.ts
 var exports_acceptance2 = {};
@@ -59546,6 +59828,7 @@ var init_acceptance3 = __esm(() => {
   init_logger2();
   init_prd();
   init_test_runners();
+  init_verification();
   _acceptanceStageDeps = {
     runHardeningPass: async (ctx) => {
       const { runHardeningPass: runHardeningPass2 } = await Promise.resolve().then(() => (init_acceptance2(), exports_acceptance));
@@ -59624,18 +59907,9 @@ var init_acceptance3 = __esm(() => {
           cmd: testCmdParts.join(" "),
           packageDir
         });
-        const proc = Bun.spawn(testCmdParts, {
-          cwd: packageDir,
-          stdout: "pipe",
-          stderr: "pipe"
-        });
-        const [exitCode, stdout, stderr] = await Promise.all([
-          proc.exited,
-          new Response(proc.stdout).text(),
-          new Response(proc.stderr).text()
-        ]);
-        const output = `${stdout}
-${stderr}`;
+        const execution = await executeWithTimeout(testCmdParts.map(shellQuoteArg).join(" "), Math.ceil(ctx.config.acceptance.timeoutMs / 1000), undefined, { cwd: packageDir });
+        const exitCode = execution.exitCode ?? (execution.success ? 0 : 1);
+        const output = execution.output ?? "";
         allOutputParts.push(output);
         const failedACs = parseTestFailures2(output);
         const overrides = ctx.prd.acceptanceOverrides ?? {};
@@ -60049,7 +60323,7 @@ async function runAcceptanceSetup(ctx, featureDir, phaseStartTime) {
       cmd: runCmd.join(" "),
       packageDir
     });
-    const { exitCode } = await _acceptanceSetupDeps.runTest(testPath, packageDir, runCmd);
+    const { exitCode } = await _acceptanceSetupDeps.runTest(testPath, packageDir, runCmd, ctx.config.acceptance.timeoutMs);
     if (exitCode !== 0) {
       redFailCount++;
     }
@@ -60086,6 +60360,7 @@ var init_acceptance_setup = __esm(() => {
   init_logger2();
   init_operations();
   init_git();
+  init_verification();
   init_event_bus();
   _acceptanceSetupDeps = {
     getAgent: (_name) => {
@@ -60146,20 +60421,14 @@ var init_acceptance_setup = __esm(() => {
     loadGroupConfig: async (projectDir, relativeWorkdir) => {
       return loadConfigForWorkdir(path13.join(projectDir, ".nax", "config.json"), relativeWorkdir || undefined);
     },
-    runTest: async (_testPath, _workdir, _cmd) => {
-      const cmd = _cmd;
-      const proc = Bun.spawn(cmd, {
-        cwd: _workdir,
-        stdout: "pipe",
-        stderr: "pipe"
+    runTest: async (_testPath, _workdir, _cmd, timeoutMs = 1800000) => {
+      const execution = await executeWithTimeout(_cmd.map(shellQuoteArg).join(" "), Math.ceil(timeoutMs / 1000), undefined, {
+        cwd: _workdir
       });
-      const [exitCode, stdout, stderr] = await Promise.all([
-        proc.exited,
-        new Response(proc.stdout).text(),
-        new Response(proc.stderr).text()
-      ]);
-      return { exitCode, output: `${stdout}
-${stderr}` };
+      return {
+        exitCode: execution.exitCode ?? (execution.success ? 0 : 1),
+        output: execution.output ?? ""
+      };
     },
     callOp: async (pipelineCtx, packageDir, op, input, storyId) => {
       if (!pipelineCtx.runtime) {
@@ -60591,7 +60860,7 @@ var init_constitution = __esm(() => {
 });
 
 // src/pipeline/stages/constitution.ts
-import { dirname as dirname9 } from "path";
+import { dirname as dirname10 } from "path";
 var constitutionStage;
 var init_constitution2 = __esm(() => {
   init_constitution();
@@ -60601,7 +60870,7 @@ var init_constitution2 = __esm(() => {
     enabled: (ctx) => ctx.config.constitution.enabled,
     async execute(ctx) {
       const logger = getLogger();
-      const ngentDir = ctx.featureDir ? dirname9(dirname9(ctx.featureDir)) : `${ctx.workdir}/nax`;
+      const ngentDir = ctx.featureDir ? dirname10(dirname10(ctx.featureDir)) : `${ctx.workdir}/nax`;
       const result = await loadConstitution(ngentDir, ctx.config.constitution);
       if (result) {
         ctx.constitution = result;
@@ -61133,11 +61402,11 @@ async function spawnWithTimeout(proc, timeoutMs) {
       ]);
       return { stdout, exitCode };
     })(),
-    new Promise((resolve16) => setTimeout(() => {
+    new Promise((resolve17) => setTimeout(() => {
       try {
         proc.kill("SIGKILL");
       } catch {}
-      resolve16({ stdout: "", exitCode: 1 });
+      resolve17({ stdout: "", exitCode: 1 });
     }, timeoutMs))
   ]);
   return result;
@@ -61908,38 +62177,6 @@ var init_story_orchestrator_logging = __esm(() => {
   init_logger2();
   init_phase_eval();
 });
-// src/verification/flake-baseline-diff.ts
-async function resolveFlakeBaselineDiff(config2, workdir, storyWorkdir) {
-  try {
-    const resolved = await resolveTestFilePatterns(config2, workdir, storyWorkdir);
-    const baseRef = await getMergeBase(workdir);
-    const changedTestFiles = await getChangedTestFiles(workdir, workdir, baseRef, storyWorkdir, [...resolved.regex]);
-    const changedNonTestFiles = await getChangedNonTestFiles(workdir, baseRef, storyWorkdir, [...resolved.regex], undefined, workdir);
-    const mappedTestFiles = await mapSourceToTests(changedNonTestFiles, workdir, storyWorkdir, [...resolved.globs]);
-    return { changedTestFiles, mappedTestFiles };
-  } catch (err) {
-    getSafeLogger()?.warn("flake-triage", "Baseline diff resolution failed \u2014 skipping triage this gate (fail closed)", {
-      error: errorMessage(err)
-    });
-    return null;
-  }
-}
-var init_flake_baseline_diff = __esm(() => {
-  init_logger2();
-  init_test_runners();
-  init_git();
-  init_smart_runner();
-});
-
-// src/verification/index.ts
-var init_verification = __esm(() => {
-  init_executor();
-  init_runners();
-  init_flake_probe();
-  init_flake_triage();
-  init_flake_baseline_diff();
-  init_mutation();
-});
 
 // src/execution/story-orchestrator/flake-triage-seam.ts
 var productionTriageSeam = async (gateFindings, { ctx, rawOutput, quarantineMemo }) => {
@@ -63036,7 +63273,7 @@ var init_story_orchestrator = __esm(() => {
 });
 
 // src/execution/build-plan-for-strategy.ts
-import { join as join52, normalize as normalize5, resolve as resolve16, sep as sep6 } from "path";
+import { join as join52, normalize as normalize5, resolve as resolve17, sep as sep6 } from "path";
 function requiresInitialRefCapture(strategy) {
   return isThreeSessionStrategy(strategy);
 }
@@ -63051,7 +63288,7 @@ function resolveStoryPathAnchors(ctxPackageDir, storyWorkdir) {
   if (segments.length === 0) {
     return { repoRoot: base, packageDir: base };
   }
-  const candidateRoot = resolve16(base, ...Array(segments.length).fill(".."));
+  const candidateRoot = resolve17(base, ...Array(segments.length).fill(".."));
   if (join52(candidateRoot, normalizedRel) === base) {
     return { repoRoot: candidateRoot, packageDir: base };
   }
@@ -67451,19 +67688,20 @@ function h2PullToolEmptyResult(observations, threshold) {
   const byKeyword = new Map;
   for (const obs of pulls) {
     const keyword = obs.payload.keyword;
+    const site = `${obs.featureId}/${obs.storyId}`;
     const existing = byKeyword.get(keyword);
     if (existing) {
-      existing.storyIds.push(obs.storyId);
+      existing.sites.push(site);
     } else {
-      byKeyword.set(keyword, { storyIds: [obs.storyId], featureId: obs.featureId });
+      byKeyword.set(keyword, { sites: [site], featureId: obs.featureId });
     }
   }
   const proposals = [];
   for (const [keyword, data] of byKeyword.entries()) {
-    if (data.storyIds.length < threshold)
+    if (data.sites.length < threshold)
       continue;
-    const count = data.storyIds.length;
-    const unique = uniqueStoryIds(data.storyIds);
+    const count = data.sites.length;
+    const unique = uniqueStoryIds(data.sites);
     proposals.push({
       id: "H2",
       severity: "MED",
@@ -67480,23 +67718,24 @@ function h3RepeatedRectification(observations, threshold) {
   const cycles = observations.filter((o) => o.kind === "rectify-cycle");
   const byStory = new Map;
   for (const obs of cycles) {
-    const existing = byStory.get(obs.storyId);
+    const key = `${obs.featureId}/${obs.storyId}`;
+    const existing = byStory.get(key);
     if (existing) {
       existing.count++;
     } else {
-      byStory.set(obs.storyId, { count: 1, featureId: obs.featureId });
+      byStory.set(key, { count: 1, featureId: obs.featureId, storyId: obs.storyId });
     }
   }
   const proposals = [];
-  for (const [storyId, data] of byStory.entries()) {
-    if (data.count < threshold)
+  for (const { count, featureId, storyId } of byStory.values()) {
+    if (count < threshold)
       continue;
     proposals.push({
       id: "H3",
       severity: "HIGH",
-      target: { canonicalFile: `.nax/features/${data.featureId}/context.md`, action: "add" },
-      description: `Repeated rectification cycle: story ${storyId} required ${data.count} rectify attempts`,
-      evidence: `Story ${storyId} triggered ${data.count} rectify cycles`,
+      target: { canonicalFile: `.nax/features/${featureId}/context.md`, action: "add" },
+      description: `Repeated rectification cycle: story ${storyId} required ${count} rectify attempts`,
+      evidence: `Story ${storyId} triggered ${count} rectify cycles`,
       sourceKinds: ["rectify-cycle"],
       storyIds: [storyId]
     });
@@ -67508,19 +67747,20 @@ function h4EscalationChain(observations, threshold) {
   const byPath = new Map;
   for (const obs of escalations) {
     const key = `${obs.payload.from}->${obs.payload.to}`;
+    const site = `${obs.featureId}/${obs.storyId}`;
     const existing = byPath.get(key);
     if (existing) {
-      existing.storyIds.push(obs.storyId);
+      existing.sites.push(site);
     } else {
-      byPath.set(key, { storyIds: [obs.storyId], featureId: obs.featureId });
+      byPath.set(key, { sites: [site], featureId: obs.featureId });
     }
   }
   const proposals = [];
   for (const [escalationPath, data] of byPath.entries()) {
-    if (data.storyIds.length < threshold)
+    if (data.sites.length < threshold)
       continue;
-    const count = data.storyIds.length;
-    const unique = uniqueStoryIds(data.storyIds);
+    const count = data.sites.length;
+    const unique = uniqueStoryIds(data.sites);
     proposals.push({
       id: "H4",
       severity: "MED",
@@ -67567,15 +67807,17 @@ function h6FixCycleUnchanged(observations, threshold) {
   const iterations = observations.filter((o) => o.kind === "fix-cycle-iteration");
   const byStory = new Map;
   for (const obs of iterations) {
-    const existing = byStory.get(obs.storyId);
+    const key = `${obs.featureId}/${obs.storyId}`;
+    const existing = byStory.get(key);
     if (existing) {
       existing.push(obs);
     } else {
-      byStory.set(obs.storyId, [obs]);
+      byStory.set(key, [obs]);
     }
   }
   const proposals = [];
-  for (const [storyId, storyIterations] of byStory.entries()) {
+  for (const storyIterations of byStory.values()) {
+    const storyId = storyIterations[0].storyId;
     const ordered = [...storyIterations].sort((a, b) => (a.payload.iterationNum ?? a.payload.iteration) - (b.payload.iterationNum ?? b.payload.iteration));
     let currentStreak = 0;
     let maxStreak = 0;
@@ -69697,6 +69939,15 @@ async function loadPlugins(globalDir, projectDir, configPlugins, projectRoot, di
   const effectiveProjectRoot = projectRoot || projectDir;
   const pluginNames = new Set;
   const disabledSet = new Set(disabledPlugins ?? []);
+  const registerLoadedPlugin = (entry) => {
+    const existingIndex = loadedPlugins.findIndex((p) => p.plugin.name === entry.plugin.name);
+    if (existingIndex >= 0) {
+      loadedPlugins[existingIndex] = entry;
+    } else {
+      loadedPlugins.push(entry);
+    }
+    pluginNames.add(entry.plugin.name);
+  };
   const logger = getSafeLogger6();
   if (!disabledSet.has(curatorPlugin.name)) {
     if (curatorPlugin.setup) {
@@ -69784,11 +70035,10 @@ async function loadPlugins(globalDir, projectDir, configPlugins, projectRoot, di
       if (pluginNames.has(validated.name)) {
         logger?.warn("plugins", `Plugin name collision: '${validated.name}' (global directory)`);
       }
-      loadedPlugins.push({
+      registerLoadedPlugin({
         plugin: validated,
         source: { type: "global", path: plugin.path }
       });
-      pluginNames.add(validated.name);
     }
   }
   const projectPlugins = await discoverPlugins(projectDir, isTestFileFn);
@@ -69803,11 +70053,10 @@ async function loadPlugins(globalDir, projectDir, configPlugins, projectRoot, di
       if (pluginNames.has(validated.name)) {
         logger?.warn("plugins", `Plugin name collision: '${validated.name}' (project directory overrides global)`);
       }
-      loadedPlugins.push({
+      registerLoadedPlugin({
         plugin: validated,
         source: { type: "project", path: plugin.path }
       });
-      pluginNames.add(validated.name);
     }
   }
   for (const entry of configPlugins) {
@@ -69821,11 +70070,10 @@ async function loadPlugins(globalDir, projectDir, configPlugins, projectRoot, di
       if (pluginNames.has(validated.name)) {
         logger?.warn("plugins", `Plugin name collision: '${validated.name}' (config entry overrides previous)`);
       }
-      loadedPlugins.push({
+      registerLoadedPlugin({
         plugin: validated,
         source: { type: "config", path: entry.module }
       });
-      pluginNames.add(validated.name);
     }
   }
   return new PluginRegistry(loadedPlugins, builtinPostRunActions);
@@ -70158,8 +70406,8 @@ var init_types10 = __esm(() => {
 import { join as join88 } from "path";
 function createDrainDeadline2(deadlineMs) {
   let timeoutId;
-  const promise2 = new Promise((resolve21) => {
-    timeoutId = setTimeout(() => resolve21(""), deadlineMs);
+  const promise2 = new Promise((resolve22) => {
+    timeoutId = setTimeout(() => resolve22(""), deadlineMs);
   });
   return {
     promise: promise2,
@@ -70279,14 +70527,17 @@ async function executeHook(hookDef, ctx, workdir) {
     env: buildAllowedEnv({ env: env2 })
   });
   let timedOut = false;
+  let killTimeoutId;
   const timeoutId = setTimeout(() => {
     timedOut = true;
     killProcessGroup(proc.pid, "SIGTERM");
+    killTimeoutId = setTimeout(() => killProcessGroup(proc.pid, "SIGKILL"), HOOK_KILL_GRACE_MS);
   }, timeout);
   const stdoutPromise = new Response(proc.stdout).text().catch(() => "");
   const stderrPromise = new Response(proc.stderr).text().catch(() => "");
   const exitCode = await proc.exited;
   clearTimeout(timeoutId);
+  clearTimeout(killTimeoutId);
   const [stdout, stderr] = timedOut ? await (async () => {
     const stdoutDrain = createDrainDeadline2(STREAM_DRAIN_TIMEOUT_MS2);
     const stderrDrain = createDrainDeadline2(STREAM_DRAIN_TIMEOUT_MS2);
@@ -70339,7 +70590,7 @@ async function fireHook(config2, event, ctx, workdir) {
     }
   }
 }
-var DEFAULT_TIMEOUT = 5000, STREAM_DRAIN_TIMEOUT_MS2 = 2000;
+var DEFAULT_TIMEOUT = 5000, STREAM_DRAIN_TIMEOUT_MS2 = 2000, HOOK_KILL_GRACE_MS = 5000;
 var init_runner5 = __esm(() => {
   init_env();
   init_logger2();
@@ -70697,7 +70948,7 @@ var init_crash_recovery = __esm(() => {
 });
 
 // src/acceptance/import-resolution.ts
-import { resolve as resolve21, sep as sep9 } from "path";
+import { resolve as resolve22, sep as sep9 } from "path";
 function languageFromExtension(testFilePath) {
   if (!testFilePath)
     return;
@@ -70719,8 +70970,8 @@ async function resolveLanguage(opts) {
   return "typescript";
 }
 async function readCapped(relPath, packageDir) {
-  const resolvedPackageDir = resolve21(packageDir);
-  const fullPath = resolve21(resolvedPackageDir, relPath);
+  const resolvedPackageDir = resolve22(packageDir);
+  const fullPath = resolve22(resolvedPackageDir, relPath);
   if (fullPath !== resolvedPackageDir && !fullPath.startsWith(resolvedPackageDir + sep9)) {
     return null;
   }
@@ -71306,7 +71557,7 @@ async function runAcceptanceLoop(ctx) {
   const prdDirty = false;
   logger?.info("acceptance", "All stories complete, running acceptance validation");
   const { acceptanceStage: acceptanceStage2 } = await _runAcceptanceTestsOnceDeps.importAcceptanceStage();
-  while (acceptanceRetries < maxRetries) {
+  do {
     const attemptCtx = { ...ctx, acceptanceRetries };
     const firstStory = prd.userStories[0];
     const acceptanceContext = buildAcceptanceContext(attemptCtx, prd);
@@ -71412,7 +71663,7 @@ async function runAcceptanceLoop(ctx) {
     const success2 = finalCheck.passed && remainingFindings.length === 0;
     const failureMessages = !success2 ? finalCheck.failedACs.length > 0 ? finalCheck.failedACs : remainingFindings.length > 0 ? remainingFindings.map((f) => f.message) : ["acceptance validation failed (unknown cause)"] : undefined;
     return buildResult(success2, prd, totalCost2, iterations, storiesCompleted, prdDirty, failureMessages, acceptanceRetries + totalInternalIterations, finalCheck.missingTargets);
-  }
+  } while (acceptanceRetries < maxRetries);
   return buildResult(false, prd, totalCost2, iterations, storiesCompleted, prdDirty);
 }
 var _acceptanceLoopDeps, _acceptanceFixCycleDeps, _runAcceptanceTestsOnceDeps, MAX_STUB_REGENS = 2;
@@ -71441,7 +71692,7 @@ var init_acceptance_loop = __esm(() => {
 
 // src/session/scratch-purge.ts
 import { mkdir as mkdir12, rename as rename2, rm } from "fs/promises";
-import { dirname as dirname15, join as join89 } from "path";
+import { dirname as dirname16, join as join89 } from "path";
 async function purgeStaleScratch(projectDir, featureName, retentionDays, archiveInsteadOfDelete = false) {
   const sessionsDir = join89(projectDir, ".nax", "features", featureName, "sessions");
   const sessionIds = await _scratchPurgeDeps.listSessionDirs(sessionsDir);
@@ -71492,7 +71743,7 @@ var init_scratch_purge = __esm(() => {
     readFile: (path26) => Bun.file(path26).text(),
     remove: (path26) => rm(path26, { recursive: true, force: true }),
     move: async (src, dest) => {
-      await mkdir12(dirname15(dest), { recursive: true });
+      await mkdir12(dirname16(dest), { recursive: true });
       await rename2(src, dest);
     },
     now: () => Date.now()
@@ -71566,10 +71817,11 @@ async function runRegressionFlakeTriage(params) {
     testCommand,
     quarantineMemo,
     triageFn,
+    resolveBaselineDiffFn,
     flakeDetection
   } = params;
   const logger = getSafeLogger();
-  const baselineDiff = await resolveFlakeBaselineDiff(config2, workdir);
+  const baselineDiff = await resolveBaselineDiffFn(config2, workdir);
   if (baselineDiff === null) {
     const untriaged = regressionFindings.filter((f) => f.category === "failed-test");
     const testFilesInFailures2 = new Set;
@@ -71625,7 +71877,6 @@ async function runRegressionFlakeTriage(params) {
 var init_run_regression_triage = __esm(() => {
   init_logger2();
   init_test_runners();
-  init_verification();
 });
 
 // src/execution/lifecycle/run-regression.ts
@@ -71779,6 +72030,7 @@ async function runDeferredRegression(options) {
     testCommand,
     quarantineMemo,
     triageFn: _regressionDeps.triageFlakyFindings,
+    resolveBaselineDiffFn: _regressionDeps.resolveFlakeBaselineDiff,
     flakeDetection: config2.execution.flakeDetection
   });
   if (triageOutcome.shortCircuit) {
@@ -71957,7 +72209,8 @@ var init_run_regression = __esm(() => {
     runVerification: fullSuite,
     runFixCycle: (cycle, ctx, name) => runFixCycle(cycle, ctx, name),
     parseTestOutput,
-    triageFlakyFindings
+    triageFlakyFindings,
+    resolveFlakeBaselineDiff
   };
 });
 
@@ -72221,6 +72474,17 @@ async function handleRunCompletion(options) {
       logger?.warn("run.complete", "Failed to purge stale session scratch", { error: String(err) });
     }
   }
+  const manifestCfg = config2.context?.v2?.manifest;
+  if (manifestCfg?.retentionDays) {
+    try {
+      const purged = await _runCompletionDeps.purgeStaleManifests(effectiveProjectDir, manifestCfg.retentionDays);
+      if (purged > 0) {
+        logger?.info("run.complete", "Purged stale context manifests", { purged });
+      }
+    } catch (err) {
+      logger?.warn("run.complete", "Failed to purge stale context manifests", { error: String(err) });
+    }
+  }
   const storyMetricsSummary = allStoryMetrics.map((sm) => ({
     storyId: sm.storyId,
     complexity: sm.complexity,
@@ -72274,6 +72538,7 @@ async function handleRunCompletion(options) {
 }
 var _runCompletionDeps;
 var init_run_completion = __esm(() => {
+  init_engine();
   init_pipeline();
   init_agents();
   init_runner5();
@@ -72289,7 +72554,8 @@ var init_run_completion = __esm(() => {
   _runCompletionDeps = {
     runDeferredRegression,
     fireHook,
-    closeAllRunSessions
+    closeAllRunSessions,
+    purgeStaleManifests
   };
 });
 
@@ -74636,7 +74902,18 @@ function selectNextStories(prd, config2, batchPlan, currentBatchIndex, lastStory
     const batch = batchPlan[currentBatchIndex];
     const storiesToExecute = batch.stories.filter((s) => !s.passes && s.status !== "passed" && s.status !== "skipped" && s.status !== "blocked" && s.status !== "failed" && s.status !== "paused" && s.status !== "decomposed");
     if (storiesToExecute.length === 0) {
-      return null;
+      const fallbackStory = getNextStory(prd, lastStoryId, config2.execution.rectification?.maxAttemptsTotal ?? 12);
+      if (!fallbackStory)
+        return null;
+      return {
+        selection: {
+          story: fallbackStory,
+          storiesToExecute: [fallbackStory],
+          routing: buildPreviewRouting(fallbackStory, config2),
+          isBatchExecution: false
+        },
+        nextBatchIndex: currentBatchIndex + 1
+      };
     }
     const story2 = storiesToExecute[0];
     return {
@@ -74833,6 +75110,8 @@ async function runParallelBatch(options) {
   const worktreeManager = await _parallelBatchDeps.createWorktreeManager();
   const worktreePaths = new Map;
   const storyStartTimes = new Map;
+  const preExecutionFailures = [];
+  const preExecutionFailureEndTimes = new Map;
   for (const story of stories) {
     storyStartTimes.set(story.id, Date.now());
     try {
@@ -74842,7 +75121,18 @@ async function runParallelBatch(options) {
         storyId: story.id,
         error: error48 instanceof Error ? error48.message : String(error48)
       });
-      throw error48;
+      preExecutionFailures.push({
+        story,
+        pipelineResult: {
+          success: false,
+          finalAction: "fail",
+          reason: error48 instanceof Error ? error48.message : String(error48),
+          stoppedAtStage: "worktree-create",
+          context: { ...pipelineContext, story, stories: [story], workdir }
+        }
+      });
+      preExecutionFailureEndTimes.set(story.id, Date.now());
+      continue;
     }
     worktreePaths.set(story.id, path29.join(workdir, ".nax-wt", story.id));
   }
@@ -74872,7 +75162,6 @@ async function runParallelBatch(options) {
   }
   const dependencyContexts = new Map;
   const readyStories = [];
-  const preExecutionFailures = [];
   for (const story of stories) {
     const worktreeRoot = worktreePaths.get(story.id);
     if (!worktreeRoot)
@@ -74967,7 +75256,7 @@ async function runParallelBatch(options) {
     storyEndTimes.set(story.id, batchEndMs);
   }
   for (const { story } of failed) {
-    storyEndTimes.set(story.id, batchEndMs);
+    storyEndTimes.set(story.id, preExecutionFailureEndTimes.get(story.id) ?? batchEndMs);
   }
   const mergeConflicts = [];
   for (const conflict of workerResult.mergeConflicts) {
@@ -75238,7 +75527,7 @@ async function executeUnified(ctx, initialPrd) {
           });
           for (const { story, pipelineResult } of batchResult.failed) {
             const storyRouting = prd.userStories.find((s) => s.id === story.id)?.routing;
-            await handlePipelineFailure({
+            const failureResult = await handlePipelineFailure({
               config: ctx.config,
               prd,
               prdPath: ctx.prdPath,
@@ -75267,12 +75556,13 @@ async function executeUnified(ctx, initialPrd) {
               runtime: ctx.runtime,
               abortSignal: ctx.abortSignal
             }, pipelineResult);
+            prd = failureResult.prd;
           }
           reconcileBatchOutcome(prd, batchResult);
           await savePRD(prd, ctx.prdPath);
           await pipelineEventBus.drain();
           totalCost2 += batchResult.totalCost;
-          storiesCompleted += batchResult.completed.length;
+          storiesCompleted += batchResult.completed.length + batchResult.mergeConflicts.filter((c) => c.rectified).length;
           prdDirty = true;
           if (ctx.sessionManager) {
             for (const story of batchResult.completed) {
@@ -75695,7 +75985,7 @@ var init_runner_execution = __esm(() => {
 
 // src/execution/status-file.ts
 import { rename as rename3, unlink as unlink4 } from "fs/promises";
-import { resolve as resolve22 } from "path";
+import { resolve as resolve23 } from "path";
 function countProgress(prd) {
   const stories = prd.userStories;
   const passed = stories.filter((s) => s.status === "passed").length;
@@ -75740,7 +76030,7 @@ function buildStatusSnapshot(state) {
   return snapshot;
 }
 async function writeStatusFile(filePath, status) {
-  const resolvedPath = resolve22(filePath);
+  const resolvedPath = resolve23(filePath);
   if (filePath.includes("../") || filePath.includes("..\\")) {
     throw new Error("Invalid status file path: path traversal detected");
   }
@@ -77052,8 +77342,10 @@ async function run(options) {
   const runId = `run-${new Date().toISOString().replace(/[:.]/g, "-")}`;
   const origLoadCheckpoints = _storyOrchestratorDeps.loadCheckpoints;
   const origRecordGreen = _storyOrchestratorDeps.recordGreen;
-  applyResumeModeDeps(featureDir ?? "", resumeMode);
-  applyRecordGreenDeps(featureDir ?? "", runId);
+  if (featureDir) {
+    applyResumeModeDeps(featureDir, resumeMode);
+    applyRecordGreenDeps(featureDir, runId);
+  }
   let iterations = 0;
   let storiesCompleted = 0;
   let totalCost2 = 0;
@@ -77740,14 +78032,14 @@ See https://react.dev/link/invalid-hook-call for tips about how to debug and fix
       prevActScopeDepth !== actScopeDepth - 1 && console.error("You seem to have overlapping act() calls, this is not supported. Be sure to await previous act() calls before making a new one. ");
       actScopeDepth = prevActScopeDepth;
     }
-    function recursivelyFlushAsyncActWork(returnValue, resolve23, reject) {
+    function recursivelyFlushAsyncActWork(returnValue, resolve24, reject) {
       var queue = ReactSharedInternals.actQueue;
       if (queue !== null)
         if (queue.length !== 0)
           try {
             flushActQueue(queue);
             enqueueTask(function() {
-              return recursivelyFlushAsyncActWork(returnValue, resolve23, reject);
+              return recursivelyFlushAsyncActWork(returnValue, resolve24, reject);
             });
             return;
           } catch (error48) {
@@ -77755,7 +78047,7 @@ See https://react.dev/link/invalid-hook-call for tips about how to debug and fix
           }
         else
           ReactSharedInternals.actQueue = null;
-      0 < ReactSharedInternals.thrownErrors.length ? (queue = aggregateErrors(ReactSharedInternals.thrownErrors), ReactSharedInternals.thrownErrors.length = 0, reject(queue)) : resolve23(returnValue);
+      0 < ReactSharedInternals.thrownErrors.length ? (queue = aggregateErrors(ReactSharedInternals.thrownErrors), ReactSharedInternals.thrownErrors.length = 0, reject(queue)) : resolve24(returnValue);
     }
     function flushActQueue(queue) {
       if (!isFlushing) {
@@ -77931,14 +78223,14 @@ See https://react.dev/link/invalid-hook-call for tips about how to debug and fix
           didAwaitActCall || didWarnNoAwaitAct || (didWarnNoAwaitAct = true, console.error("You called act(async () => ...) without await. This could lead to unexpected testing behaviour, interleaving multiple act calls and mixing their scopes. You should - await act(async () => ...);"));
         });
         return {
-          then: function(resolve23, reject) {
+          then: function(resolve24, reject) {
             didAwaitActCall = true;
             thenable.then(function(returnValue) {
               popActScope(prevActQueue, prevActScopeDepth);
               if (prevActScopeDepth === 0) {
                 try {
                   flushActQueue(queue), enqueueTask(function() {
-                    return recursivelyFlushAsyncActWork(returnValue, resolve23, reject);
+                    return recursivelyFlushAsyncActWork(returnValue, resolve24, reject);
                   });
                 } catch (error$0) {
                   ReactSharedInternals.thrownErrors.push(error$0);
@@ -77949,7 +78241,7 @@ See https://react.dev/link/invalid-hook-call for tips about how to debug and fix
                   reject(_thrownError);
                 }
               } else
-                resolve23(returnValue);
+                resolve24(returnValue);
             }, function(error48) {
               popActScope(prevActQueue, prevActScopeDepth);
               0 < ReactSharedInternals.thrownErrors.length ? (error48 = aggregateErrors(ReactSharedInternals.thrownErrors), ReactSharedInternals.thrownErrors.length = 0, reject(error48)) : reject(error48);
@@ -77965,11 +78257,11 @@ See https://react.dev/link/invalid-hook-call for tips about how to debug and fix
       if (0 < ReactSharedInternals.thrownErrors.length)
         throw callback = aggregateErrors(ReactSharedInternals.thrownErrors), ReactSharedInternals.thrownErrors.length = 0, callback;
       return {
-        then: function(resolve23, reject) {
+        then: function(resolve24, reject) {
           didAwaitActCall = true;
           prevActScopeDepth === 0 ? (ReactSharedInternals.actQueue = queue, enqueueTask(function() {
-            return recursivelyFlushAsyncActWork(returnValue$jscomp$0, resolve23, reject);
-          })) : resolve23(returnValue$jscomp$0);
+            return recursivelyFlushAsyncActWork(returnValue$jscomp$0, resolve24, reject);
+          })) : resolve24(returnValue$jscomp$0);
         }
       };
     };
@@ -80811,8 +81103,8 @@ It can also happen if the client has a browser extension installed which messes
         currentEntangledActionThenable = {
           status: "pending",
           value: undefined,
-          then: function(resolve23) {
-            entangledListeners.push(resolve23);
+          then: function(resolve24) {
+            entangledListeners.push(resolve24);
           }
         };
       }
@@ -80836,8 +81128,8 @@ It can also happen if the client has a browser extension installed which messes
         status: "pending",
         value: null,
         reason: null,
-        then: function(resolve23) {
-          listeners.push(resolve23);
+        then: function(resolve24) {
+          listeners.push(resolve24);
         }
       };
       thenable.then(function() {
@@ -107009,7 +107301,7 @@ __export(exports_curator, {
 });
 import { readdirSync as readdirSync9 } from "fs";
 import { unlink as unlink6 } from "fs/promises";
-import { join as join104, resolve as resolve23, sep as sep10 } from "path";
+import { join as join104, resolve as resolve24, sep as sep10 } from "path";
 function listRunIds(runsDir) {
   try {
     return readdirSync9(runsDir, { withFileTypes: true }).filter((e) => e.isDirectory()).map((e) => e.name).sort();
@@ -107127,15 +107419,15 @@ async function curatorStatus(options) {
   }
 }
 function resolveCanonicalTargetPath(projectDir, canonicalFile) {
-  const target = resolve23(projectDir, canonicalFile);
-  const root = resolve23(projectDir);
+  const target = resolve24(projectDir, canonicalFile);
+  const root = resolve24(projectDir);
   if (target !== root && !target.startsWith(root + sep10))
     return null;
   const relative18 = target.slice(root.length + 1).replaceAll(sep10, "/");
   return CURATOR_TARGET_SHAPES.some((shape) => shape.test(relative18)) ? target : null;
 }
 function isWithinCanonicalRulesDir(projectDir, targetPath) {
-  const rulesRoot = resolve23(projectDir, CANONICAL_RULES_DIR);
+  const rulesRoot = resolve24(projectDir, CANONICAL_RULES_DIR);
   return targetPath === rulesRoot || targetPath.startsWith(rulesRoot + sep10);
 }
 async function curatorCommit(options) {
@@ -108076,6 +108368,12 @@ async function parseRunLog(logPath) {
     return [];
   }
 }
+function findRunStart(entries) {
+  return entries.find((e) => e.stage === "run.start");
+}
+function findRunSummary(entries) {
+  return entries.find((e) => e.stage === "run.complete" && e.data?.totalStories !== undefined);
+}
 async function runsListCommand(options) {
   const logger = getLogger();
   const { feature, workdir } = options;
@@ -108094,8 +108392,8 @@ async function runsListCommand(options) {
   for (const file3 of files.sort().reverse()) {
     const logPath = join48(runsDir, file3);
     const entries = await parseRunLog(logPath);
-    const startEvent = entries.find((e) => e.message === "run.start");
-    const completeEvent = entries.find((e) => e.message === "run.complete");
+    const startEvent = findRunStart(entries);
+    const completeEvent = findRunSummary(entries);
     if (!startEvent) {
       logger.warn("cli", "Run log missing run.start event", { file: file3 });
       continue;
@@ -108125,8 +108423,8 @@ async function runsShowCommand(options) {
     throw new NaxError("Run not found", "RUN_NOT_FOUND", { runId, feature, logPath });
   }
   const entries = await parseRunLog(logPath);
-  const startEvent = entries.find((e) => e.message === "run.start");
-  const completeEvent = entries.find((e) => e.message === "run.complete");
+  const startEvent = findRunStart(entries);
+  const completeEvent = findRunSummary(entries);
   const storyEvents = entries.filter((e) => e.stage === "execution" && e.data?.storyId);
   if (!startEvent) {
     logger.error("cli", "Run log missing run.start event", { runId });
@@ -108966,6 +109264,7 @@ async function profileUseCommand(profileName, startDir) {
     await Bun.write(configPath, JSON.stringify(rest, null, 2));
     return "Profile reset to default.";
   }
+  await loadProfile(profileName, startDir);
   const updated = { ...existing, profile: profileName };
   await Bun.write(configPath, JSON.stringify(updated, null, 2));
   return `Now using profile: ${profileName}`;
@@ -109098,7 +109397,7 @@ init_canonical_loader();
 init_errors();
 init_logger2();
 import { mkdir as mkdir11 } from "fs/promises";
-import { join as join76, resolve as resolve20, sep as sep8 } from "path";
+import { join as join76, resolve as resolve21, sep as sep8 } from "path";
 
 // src/cli/rules-lint.ts
 init_engine();
@@ -109250,13 +109549,13 @@ import { basename as basename15, join as join75 } from "path";
 
 // src/cli/rules-migrate-plan.ts
 init_errors();
-import { resolve as resolve19, sep as sep7 } from "path";
+import { resolve as resolve20, sep as sep7 } from "path";
 async function planMigration(sources, options) {
   const writes = [];
   const skips = [];
-  const resolvedTargetDir = resolve19(options.targetDir);
+  const resolvedTargetDir = resolve20(options.targetDir);
   for (const source of sources) {
-    const resolvedTargetPath = resolve19(source.targetPath);
+    const resolvedTargetPath = resolve20(source.targetPath);
     if (!resolvedTargetPath.startsWith(`${resolvedTargetDir}${sep7}`) && resolvedTargetPath !== resolvedTargetDir) {
       throw new NaxError(`Migration target escapes ${options.targetDir}: ${source.targetFileName} -> ${source.targetPath}`, "RULES_MIGRATE_TARGET_ESCAPE", { stage: "rules-migrate-plan", targetDir: options.targetDir, entry: source.targetPath });
     }
@@ -109469,8 +109768,8 @@ async function exportRuleDirectory(input) {
   const drifted = [];
   for (const rule of rules) {
     const rel = rule.path ?? rule.fileName;
-    const target = resolve20(workdir, ruleDir, rel);
-    if (!target.startsWith(`${resolve20(workdir, ruleDir)}${sep8}`)) {
+    const target = resolve21(workdir, ruleDir, rel);
+    if (!target.startsWith(`${resolve21(workdir, ruleDir)}${sep8}`)) {
       throw new NaxError(`Rule path escapes ${ruleDir}: ${rel}`, "RULES_EXPORT_PATH_ESCAPE", {
         stage: "rules-export",
         rule: rel
@@ -109490,9 +109789,9 @@ async function exportRuleDirectory(input) {
     }
     await _rulesCLIDeps.writeFile(target, content);
   }
-  const expected = new Set(rules.map((r) => resolve20(workdir, ruleDir, r.path ?? r.fileName)));
+  const expected = new Set(rules.map((r) => resolve21(workdir, ruleDir, r.path ?? r.fileName)));
   for (const existing of _rulesCLIDeps.globInDir(join76(workdir, ruleDir))) {
-    if (!expected.has(resolve20(existing))) {
+    if (!expected.has(resolve21(existing))) {
       _rulesCLIDeps.getLogger().warn("rules-export", "Generated rules dir contains a file with no canonical source", {
         file: existing,
         hint: `Delete it, or add the rule to ${CANONICAL_RULES_DIR}/`
@@ -110166,17 +110465,29 @@ async function resolveRunFileFromRegistry(runId) {
   } catch {
     throw new Error(`Run not found in registry: ${runId}`);
   }
-  let matched = null;
+  let exactMatch = null;
+  const prefixMatches = [];
   for (const entry of entries) {
     const metaPath = join81(runsDir, entry, "meta.json");
     try {
       const meta3 = await Bun.file(metaPath).json();
-      if (meta3.runId === runId || meta3.runId.startsWith(runId)) {
-        matched = meta3;
+      if (meta3.runId === runId) {
+        exactMatch = meta3;
         break;
       }
+      if (meta3.runId.startsWith(runId)) {
+        prefixMatches.push(meta3);
+      }
     } catch {}
   }
+  let matched = exactMatch;
+  if (!matched) {
+    if (prefixMatches.length > 1) {
+      const candidates = prefixMatches.map((m) => m.runId).join(", ");
+      throw new Error(`Ambiguous run ID "${runId}" matches multiple runs: ${candidates}`);
+    }
+    matched = prefixMatches[0] ?? null;
+  }
   if (!matched) {
     throw new Error(`Run not found in registry: ${runId}`);
   }
@@ -110398,13 +110709,7 @@ async function logsCommand(options) {
   }
   const resolved = resolveProject2({ dir: options.dir });
   const naxDir = join83(resolved.projectDir, ".nax");
-  const configPath = resolved.configPath;
-  const configFile = Bun.file(configPath);
-  const config2 = await configFile.json();
-  const featureName = config2.feature;
-  if (!featureName) {
-    throw new Error("No feature specified in config.json");
-  }
+  const featureName = resolveSingleFeature(naxDir, "pass -r <runId> (see `nax runs list`)");
   const featureDir = join83(naxDir, "features", featureName);
   const runsDir = join83(featureDir, "runs");
   if (!existsSync30(runsDir)) {
@@ -110444,17 +110749,16 @@ async function precheckCommand(options) {
     const result2 = await runEnvironmentPrecheck(config3, resolved.projectDir, { format });
     process.exit(result2.passed ? EXIT_CODES.SUCCESS : EXIT_CODES.BLOCKER);
   }
+  const naxDir = join84(resolved.projectDir, ".nax");
   let featureName = options.feature;
   if (!featureName) {
-    const configFile = Bun.file(resolved.configPath);
-    const config3 = await configFile.json();
-    featureName = config3.feature;
-    if (!featureName) {
-      console.error(source_default.red("No feature specified. Use -f flag or set feature in config.json"));
+    try {
+      featureName = resolveSingleFeature(naxDir);
+    } catch (err) {
+      console.error(source_default.red(err instanceof Error ? err.message : String(err)));
       process.exit(1);
     }
   }
-  const naxDir = join84(resolved.projectDir, ".nax");
   const featureDir = join84(naxDir, "features", featureName);
   const prdPath = join84(featureDir, "prd.json");
   if (!existsSync31(featureDir)) {
@@ -110478,7 +110782,7 @@ async function precheckCommand(options) {
 // src/commands/replay.ts
 init_errors();
 import { existsSync as existsSync32 } from "fs";
-import { dirname as dirname14 } from "path";
+import { dirname as dirname15 } from "path";
 
 // src/replay/discovery.ts
 init_errors();
@@ -110791,7 +111095,7 @@ async function readJsonOrUndefined(path25) {
 }
 async function readMetricsFromProject(meta3) {
   const { loadRunMetrics: loadRunMetrics2 } = await Promise.resolve().then(() => (init_tracker(), exports_tracker));
-  const outputDir = dirname14(dirname14(dirname14(meta3.eventsDir)));
+  const outputDir = dirname15(dirname15(dirname15(meta3.eventsDir)));
   const all = await loadRunMetrics2(outputDir);
   return all.find((m) => m.runId === meta3.runId);
 }
@@ -110924,10 +111228,11 @@ function registerResumeCommand(program2) {
     const { findProjectDir: findProjectDir2 } = await Promise.resolve().then(() => (init_config(), exports_config));
     const { run: run2 } = await Promise.resolve().then(() => (init_execution2(), exports_execution));
     const { applyResumeModeDeps: applyResumeModeDeps2 } = await Promise.resolve().then(() => (init_checkpoint(), exports_checkpoint));
-    const { existsSync: existsSync38 } = await import("fs");
+    const { existsSync: existsSync38, mkdirSync: mkdirSync8 } = await import("fs");
     const { loadConfig: loadConfig2 } = await Promise.resolve().then(() => (init_config(), exports_config));
     const { loadPRD: loadPRD2 } = await Promise.resolve().then(() => (init_prd(), exports_prd));
     const { loadHooksConfig: loadHooksConfig2 } = await Promise.resolve().then(() => (init_hooks(), exports_hooks));
+    const { initLogger: initLogger2 } = await Promise.resolve().then(() => (init_logger2(), exports_logger));
     const naxDir = findProjectDir2(cmdOpts.dir);
     if (!naxDir) {
       process.stderr.write(`nax not initialized. Run: nax init
@@ -110952,6 +111257,11 @@ function registerResumeCommand(program2) {
         const projectKey = config2.name?.trim() || basename19(cmdOpts.dir);
         const outputDir = projectOutputDir(projectKey, config2.outputDir);
         const statusFilePath = join99(outputDir, "status.json");
+        const runsDir = join99(outputDir, "features", feature, "runs");
+        mkdirSync8(runsDir, { recursive: true });
+        const runId = new Date().toISOString().replace(/:/g, "-").replace(/\..+/, "");
+        const logFilePath = join99(runsDir, `${runId}.jsonl`);
+        initLogger2({ level: "info", filePath: logFilePath, useChalk: true, headless: true, suppressConsole: false });
         const result = await run2({
           prdPath,
           workdir: cmdOpts.dir,
@@ -110962,7 +111272,7 @@ function registerResumeCommand(program2) {
           dryRun: false,
           useBatch: true,
           statusFile: statusFilePath,
-          logFilePath: undefined,
+          logFilePath,
           formatterMode: "normal",
           headless: true,
           skipPrecheck: false,
@@ -116785,8 +117095,8 @@ class Ink {
     }
   }
   async waitUntilExit() {
-    this.exitPromise ||= new Promise((resolve23, reject2) => {
-      this.resolveExitPromise = resolve23;
+    this.exitPromise ||= new Promise((resolve24, reject2) => {
+      this.resolveExitPromise = resolve24;
       this.rejectExitPromise = reject2;
     });
     if (!this.beforeExitHandler) {
@@ -118571,15 +118881,17 @@ function usePipelineBusEvents(initialStories) {
     });
     const unsubCompleted = pipelineEventBus.on("story:completed", (event) => {
       setState((prev) => {
+        const prevStoryCost = prev.stories.find((s) => s.story.id === event.storyId)?.cost ?? 0;
+        const costDelta = event.cost ?? 0;
+        const storyCost = prevStoryCost + costDelta;
+        const totalCost2 = prev.totalCost + costDelta;
         const newStories = prev.stories.map((s) => {
           if (s.story.id === event.storyId) {
             const status = event.passed ? "passed" : "failed";
-            const storyCost = event.cost ?? s.cost;
             return { ...s, status, cost: storyCost };
           }
           return s;
         });
-        const totalCost2 = newStories.reduce((sum2, s) => sum2 + (s.cost ?? 0), 0);
         const { [event.storyId]: _removed, ...remainingSteps } = prev.storySteps;
         const lastFailedStoryId = event.passed ? prev.lastFailedStoryId : event.storyId;
         return { ...prev, stories: newStories, totalCost: totalCost2, storySteps: remainingSteps, lastFailedStoryId };
@@ -118814,7 +119126,7 @@ function App2({ feature, version: version2, stories: initialStories, events, que
         break;
     }
   };
-  use_input_default((input) => {
+  use_input_default((input, key) => {
     if (showQuitConfirm || showAbortConfirm) {
       const inputKey = input.toLowerCase();
       if (inputKey === "y") {
@@ -118824,7 +119136,7 @@ function App2({ feature, version: version2, stories: initialStories, events, que
           writeQueueCommand(queueFilePath, { type: "ABORT" });
           setShowAbortConfirm(false);
         }
-      } else if (inputKey === "n" || input === "\x1B") {
+      } else if (inputKey === "n" || key.escape) {
         setShowQuitConfirm(false);
         setShowAbortConfirm(false);
       }
@@ -119051,7 +119363,7 @@ async function promptForConfirmation(question) {
   if (!process.stdin.isTTY) {
     return true;
   }
-  return new Promise((resolve24) => {
+  return new Promise((resolve25) => {
     process.stdout.write(source_default.bold(`${question} [Y/n] `));
     process.stdin.setRawMode(true);
     process.stdin.resume();
@@ -119060,13 +119372,17 @@ async function promptForConfirmation(question) {
       process.stdin.setRawMode(false);
       process.stdin.pause();
       process.stdin.removeListener("data", handler);
-      const answer = char.toLowerCase();
       process.stdout.write(`
 `);
+      if (char === "\x03") {
+        resolve25(false);
+        process.exit(130);
+      }
+      const answer = char.toLowerCase();
       if (answer === "n") {
-        resolve24(false);
+        resolve25(false);
       } else {
-        resolve24(true);
+        resolve25(true);
       }
     };
     process.stdin.on("data", handler);
@@ -119245,6 +119561,12 @@ program2.command("setup").description("Analyze repo and generate .nax/config.jso
   process.exit(exitCode);
 });
 program2.command("run").description("Run the orchestration loop for a feature").requiredOption("-f, --feature <name>", "Feature name").option("-a, --agent <name>", "Force a specific agent").option("-m, --max-iterations <n>", "Max iterations", "20").option("--max-cost <usd>", "Override cost limit (USD) for this run \u2014 aborts execution when exceeded").option("--dry-run", "Show plan without executing", false).option("--no-context", "Disable context builder (skip file context in prompts)").option("--no-batch", "Disable story batching (execute all stories individually)").option("--parallel <n>", "Max parallel sessions (0=auto, omit=sequential)").option("--plan", "Run plan phase first before execution", false).option("--from <spec-path>", "Path to spec file (required when --plan is used)").option("--one-shot", "Skip interactive planning Q&A, use single LLM call (ACP only)", false).option("--force", "Force overwrite existing prd.json when using --plan", false).option("--headless", "Force headless mode (disable TUI, use pipe mode)", false).option("--verbose", "Enable verbose logging (debug level)", false).option("--quiet", "Quiet mode (warnings and errors only)", false).option("--silent", "Silent mode (errors only)", false).option("--json", "JSON mode (raw JSONL output to stdout)", false).option("-d, --dir <path>", "Working directory", process.cwd()).option("--skip-precheck", "Skip precheck validations (advanced users only)", false).option("--profile <name>", "Profile(s) to overlay (comma-separated or repeated; later overrides earlier)", collectProfile, []).option("--schedule <when>", "Defer run start until <when> (e.g. 30m, 1h30m, 17:00, 2026-07-02T02:00)").option("--compare <agents>", "Bake-off mode: comma-separated list of contestant agents (e.g. claude,codex)").option("--fresh", "Ignore any existing checkpoint.jsonl and re-run every incomplete story from scratch", false).addOption(new Option("--no-resume", "Alias for --fresh: never auto-resume from a prior checkpoint").default("__UNSET__")).action(async (options) => {
+  try {
+    validateFeatureName(options.feature);
+  } catch (err) {
+    console.error(source_default.red(`Invalid feature name: ${err.message}`));
+    process.exit(1);
+  }
   let workdir;
   try {
     workdir = validateDirectory(options.dir);
@@ -119338,6 +119660,7 @@ program2.command("run").description("Run the orchestration loop for a feature").
     console.error(source_default.red("nax not initialized. Run: nax init"));
     process.exit(1);
   }
+  const projectRoot = join105(naxDir, "..");
   const featureDir = join105(naxDir, "features", options.feature);
   const prdPath = join105(featureDir, "prd.json");
   if (options.plan && options.from) {
@@ -119368,7 +119691,7 @@ program2.command("run").description("Run the orchestration loop for a feature").
       initLogger({ level: "info", filePath: planLogPath, useChalk: false, headless: true });
       console.log(source_default.dim(`   [Plan log: ${planLogPath}]`));
       console.log(source_default.dim("   [Planning phase: generating PRD from spec]"));
-      const planResult = await planCommand(workdir, config2, {
+      const planResult = await planCommand(projectRoot, config2, {
         from: options.from,
         feature: options.feature,
         auto: options.oneShot ?? false,
@@ -119432,7 +119755,12 @@ program2.command("run").description("Run the orchestration loop for a feature").
     config2.agent ??= {};
     config2.agent.default = options.agent;
   }
-  config2.execution.maxIterations = Number.parseInt(options.maxIterations, 10);
+  const maxIterations = Number.parseInt(options.maxIterations, 10);
+  if (!Number.isFinite(maxIterations) || maxIterations < 1) {
+    console.error(source_default.red("--max-iterations must be a positive integer"));
+    process.exit(1);
+  }
+  config2.execution.maxIterations = maxIterations;
   if (options.maxCost !== undefined) {
     const maxCost = Number(options.maxCost);
     if (!Number.isFinite(maxCost) || maxCost <= 0) {
@@ -119509,25 +119837,32 @@ Scheduled run cancelled.`));
     const exitOutcome = typeof bakeoffResult?.outcome === "number" ? bakeoffResult.outcome : 0;
     process.exit(exitOutcome);
   }
-  const result2 = await run({
-    prdPath,
-    workdir,
-    config: config2,
-    hooks,
-    feature: options.feature,
-    featureDir,
-    dryRun: options.dryRun,
-    useBatch: options.batch ?? true,
-    parallel,
-    eventEmitter,
-    statusFile: statusFilePath,
-    logFilePath,
-    formatterMode: useHeadless ? formatterMode : undefined,
-    headless: useHeadless,
-    skipPrecheck: options.skipPrecheck ?? false,
-    agentStreamEvents,
-    resumeMode: options.fresh === true || options.resume === false ? "fresh" : "auto"
-  });
+  let result2;
+  try {
+    result2 = await run({
+      prdPath,
+      workdir,
+      config: config2,
+      hooks,
+      feature: options.feature,
+      featureDir,
+      dryRun: options.dryRun,
+      useBatch: options.batch ?? true,
+      parallel,
+      eventEmitter,
+      statusFile: statusFilePath,
+      logFilePath,
+      formatterMode: useHeadless ? formatterMode : undefined,
+      headless: useHeadless,
+      skipPrecheck: options.skipPrecheck ?? false,
+      agentStreamEvents,
+      resumeMode: options.fresh === true || options.resume === false ? "fresh" : "auto"
+    });
+  } finally {
+    if (tuiInstance) {
+      tuiInstance.unmount();
+    }
+  }
   const latestSymlink = join105(runsDir, "latest.jsonl");
   try {
     if (existsSync39(latestSymlink)) {
@@ -119539,9 +119874,6 @@ Scheduled run cancelled.`));
   } catch (error48) {
     console.error(source_default.yellow(`Warning: Failed to create latest.jsonl symlink: ${error48}`));
   }
-  if (tuiInstance) {
-    tuiInstance.unmount();
-  }
   if (useHeadless) {
     console.log(source_default.dim(`
 \u2500\u2500 Summary \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500`));
@@ -119613,6 +119945,12 @@ function printHumanReadable(result2) {
 }
 var features = program2.command("features").description("Manage features");
 features.command("create <name>").description("Create a new feature").option("-d, --dir <path>", "Project directory", process.cwd()).action(async (name, options) => {
+  try {
+    validateFeatureName(name);
+  } catch (err) {
+    console.error(source_default.red(`Invalid feature name: ${err.message}`));
+    process.exit(1);
+  }
   let workdir;
   try {
     workdir = validateDirectory(options.dir);
@@ -119768,12 +120106,13 @@ Use: nax plan -f <feature> --from <spec>`));
     console.error(source_default.red("nax not initialized. Run: nax init"));
     process.exit(1);
   }
+  const projectRoot = join105(naxDir, "..");
   const cliOverrides = {};
   const cliProfiles = options.profile ?? [];
   if (cliProfiles.length > 0) {
     cliOverrides.profile = cliProfiles;
   }
-  const config2 = await loadConfig(workdir, cliOverrides);
+  const config2 = await loadConfig(projectRoot, cliOverrides);
   const featureLogDir = join105(naxDir, "features", options.feature, "plan");
   mkdirSync8(featureLogDir, { recursive: true });
   const planLogId = new Date().toISOString().replace(/:/g, "-").replace(/\..+/, "");
@@ -119782,7 +120121,7 @@ Use: nax plan -f <feature> --from <spec>`));
   console.log(source_default.dim(`   [Plan log: ${planLogPath}]`));
   try {
     if (options.decompose) {
-      await planDecomposeCommand(workdir, config2, {
+      await planDecomposeCommand(projectRoot, config2, {
         feature: options.feature,
         storyId: options.decompose
       });
@@ -119794,7 +120133,7 @@ Use: nax plan -f <feature> --from <spec>`));
         console.error(source_default.red("Error: --from <spec-path> is required unless --decompose is used"));
         process.exit(1);
       }
-      const planResult = await planCommand(workdir, config2, {
+      const planResult = await planCommand(projectRoot, config2, {
         from: options.from,
         feature: options.feature,
         auto: options.auto || options.oneShot,
@@ -119990,6 +120329,7 @@ runs.command("list").description("List all runs for a feature").requiredOption("
     console.error(source_default.red(`Invalid directory: ${err.message}`));
     process.exit(1);
   }
+  initLogger({ level: "info", useChalk: true });
   await runsListCommand({ feature: options.feature, workdir });
 });
 runs.command("show <run-id>").description("Show detailed information for a specific run").requiredOption("-f, --feature <name>", "Feature name").option("-d, --dir <path>", "Project directory", process.cwd()).action(async (runId, options) => {
@@ -120000,6 +120340,7 @@ runs.command("show <run-id>").description("Show detailed information for a speci
     console.error(source_default.red(`Invalid directory: ${err.message}`));
     process.exit(1);
   }
+  initLogger({ level: "info", useChalk: true });
   await runsShowCommand({ runId, feature: options.feature, workdir });
 });
 registerReplayCommand(program2);