nexus-agents 2.113.0 → 2.114.1

package/dist/{chunk-5VGGVVPG.js → chunk-5KYKXB7Q.js}

@@ -7,7 +7,7 @@ import {
   toolStructuredError,
   toolSuccessStructured,
   wrapToolWithTimeout
-} from "./chunk-7E2ZCYKA.js";
+} from "./chunk-GMXRM2JU.js";
 import {
   createLogger,
   formatZodError,
@@ -15,7 +15,7 @@ import {
   getOutcomeStore,
   getPipelineEventBus,
   getTimeProvider
-} from "./chunk-JRBUSUYD.js";
+} from "./chunk-DHU2YECH.js";
 import {
   getNexusDataDir
 } from "./chunk-CH7QIDHQ.js";
@@ -1138,4 +1138,4 @@ export {
   runImprovementReview,
   registerImprovementReviewTool
 };
-//# sourceMappingURL=chunk-5VGGVVPG.js.map
+//# sourceMappingURL=chunk-5KYKXB7Q.js.map

package/dist/{chunk-N2HYXBQ6.js → chunk-7LS7HZU3.js}

@@ -4,7 +4,7 @@ import {
   getErrorMessage,
   getTimeProvider,
   ok
-} from "./chunk-JRBUSUYD.js";
+} from "./chunk-DHU2YECH.js";
 
 // src/context/session-memory.ts
 import * as fs from "fs";
@@ -351,4 +351,4 @@ export {
   SessionMemory,
   createSessionMemory
 };
-//# sourceMappingURL=chunk-N2HYXBQ6.js.map
+//# sourceMappingURL=chunk-7LS7HZU3.js.map

package/dist/{chunk-WDOJESN6.js → chunk-AH645A5N.js}

@@ -2,7 +2,7 @@ import {
   TASK_CATEGORIES,
   getAdaptiveBonus,
   getOutcomeStore
-} from "./chunk-JRBUSUYD.js";
+} from "./chunk-DHU2YECH.js";
 
 // src/cli/doctor-deep.ts
 var CLI_NAMES = ["claude", "gemini", "codex", "opencode"];
@@ -106,4 +106,4 @@ export {
   runDeepDiagnostics,
   formatDeepDiagnostics
 };
-//# sourceMappingURL=chunk-WDOJESN6.js.map
+//# sourceMappingURL=chunk-AH645A5N.js.map

package/dist/{chunk-LUCPCWIZ.js → chunk-BUHPYOT3.js}

@@ -1,7 +1,7 @@
 import {
   getRandomProvider,
   getTimeProvider
-} from "./chunk-JRBUSUYD.js";
+} from "./chunk-DHU2YECH.js";
 
 // src/utils/id-utils.ts
 import { randomUUID } from "crypto";
@@ -24,4 +24,4 @@ export {
   generateHyphenId,
   generateUUID
 };
-//# sourceMappingURL=chunk-LUCPCWIZ.js.map
+//# sourceMappingURL=chunk-BUHPYOT3.js.map

package/dist/{chunk-JRBUSUYD.js → chunk-DHU2YECH.js}

@@ -11896,7 +11896,7 @@ var CompositeRouter = class _CompositeRouter {
    */
   async consultUnifiedContext(task) {
     try {
-      const { getContextForTask, inferTaskCategory } = await import("./context-retriever-5VFAIPHM.js");
+      const { getContextForTask, inferTaskCategory } = await import("./context-retriever-JSP6PVSJ.js");
       const ctx = await getContextForTask({
         task: task.content,
         category: inferTaskCategory(task.content),
@@ -13246,11 +13246,11 @@ export {
   setDefaultAvailableModelsCache,
   isDynamicModelsEnabled,
   buildDefaultModelSources,
+  ParseError,
   CompositeRouter,
   createCompositeRouter,
   ModelCapability,
   AgentCapability,
-  ParseError,
   OrchestratorError
 };
-//# sourceMappingURL=chunk-JRBUSUYD.js.map
+//# sourceMappingURL=chunk-DHU2YECH.js.map

package/dist/chunk-FO4A6HA3.js

@@ -0,0 +1,149 @@
+import {
+  resolveInsideRoot
+} from "./chunk-NUBSJGQZ.js";
+import {
+  ParseError,
+  SecurityError,
+  err,
+  getErrorMessage,
+  ok,
+  parseBoolEnv
+} from "./chunk-DHU2YECH.js";
+
+// src/cli/research-helpers-io.ts
+import * as fs2 from "fs/promises";
+import { join, resolve as resolve2 } from "path";
+import { parse as parseYaml, stringify as stringifyYaml2 } from "yaml";
+
+// src/cli/research-scaffold.ts
+import * as fs from "fs/promises";
+import { existsSync } from "fs";
+import { dirname, resolve } from "path";
+import { stringify as stringifyYaml } from "yaml";
+var SCHEMA_VERSION = "1.0";
+var ANNOUNCED = /* @__PURE__ */ new Set();
+function announceOnce(path, kind) {
+  if (ANNOUNCED.has(path)) return;
+  ANNOUNCED.add(path);
+  process.stderr.write(
+    `[scaffold] Created empty ${kind} at ${path}; add entries via 'nexus-agents research add' or research_add MCP tool.
+`
+  );
+}
+function scaffoldDisabled() {
+  return parseBoolEnv("NEXUS_NO_SCAFFOLD", false);
+}
+function emptyPapersYaml() {
+  return stringifyYaml({ schema_version: SCHEMA_VERSION, papers: {} });
+}
+function emptyTechniquesYaml() {
+  return stringifyYaml({ schema_version: SCHEMA_VERSION, techniques: {} });
+}
+async function ensureRegistryFile(rootDir, filename) {
+  const filePath = resolve(rootDir, REGISTRY_PATH, filename);
+  if (existsSync(filePath)) return ok(filePath);
+  if (scaffoldDisabled()) {
+    return err(
+      new ParseError(
+        `Registry file missing: ${filePath}. Scaffolding disabled (NEXUS_NO_SCAFFOLD=1). Create the file manually or unset the env var.`
+      )
+    );
+  }
+  if (!existsSync(resolve(rootDir, "docs"))) {
+    return err(
+      new ParseError(
+        `Registry file missing: ${filePath}. ${rootDir}/docs/ does not exist; refusing to create a Nexus subtree in a non-documented root. Run 'nexus-agents init' first, or create ${rootDir}/docs/ manually.`
+      )
+    );
+  }
+  try {
+    await fs.mkdir(dirname(filePath), { recursive: true });
+    const content = filename === PAPERS_FILE ? emptyPapersYaml() : emptyTechniquesYaml();
+    await fs.writeFile(filePath, content, "utf-8");
+    announceOnce(filePath, filename);
+    return ok(filePath);
+  } catch (e) {
+    return err(
+      new ParseError(
+        `Failed to scaffold ${filename} at ${filePath}: ${getErrorMessage(e)}. Set NEXUS_NO_SCAFFOLD=1 and create manually if scaffolding is unwanted.`
+      )
+    );
+  }
+}
+
+// src/cli/research-helpers-io.ts
+var REGISTRY_PATH = "docs/research/registry";
+var TECHNIQUES_FILE = "techniques.yaml";
+var PAPERS_FILE = "papers.yaml";
+function getProjectRoot() {
+  return process.cwd();
+}
+function validatePath(constructedPath, allowedRoot) {
+  const resolved = resolveInsideRoot(constructedPath, allowedRoot);
+  if (resolved === null) {
+    return {
+      ok: false,
+      error: new SecurityError("Path traversal detected: path escapes allowed root directory", {
+        context: { constructedPath, allowedRoot: resolve2(allowedRoot) }
+      })
+    };
+  }
+  return { ok: true, value: resolved };
+}
+async function loadTechniquesRegistry(rootDir) {
+  const root = rootDir ?? process.cwd();
+  const filePath = join(root, REGISTRY_PATH, TECHNIQUES_FILE);
+  const pathValidation = validatePath(filePath, root);
+  if (!pathValidation.ok) {
+    return pathValidation;
+  }
+  await ensureRegistryFile(root, TECHNIQUES_FILE);
+  try {
+    const content = await fs2.readFile(pathValidation.value, "utf-8");
+    return { ok: true, value: parseYaml(content) };
+  } catch (error) {
+    const message = getErrorMessage(error);
+    return { ok: false, error: new ParseError(`Failed to load techniques registry: ${message}`) };
+  }
+}
+async function loadPapersRegistry(rootDir) {
+  const root = rootDir ?? process.cwd();
+  const filePath = join(root, REGISTRY_PATH, PAPERS_FILE);
+  const pathValidation = validatePath(filePath, root);
+  if (!pathValidation.ok) {
+    return pathValidation;
+  }
+  await ensureRegistryFile(root, PAPERS_FILE);
+  try {
+    const content = await fs2.readFile(pathValidation.value, "utf-8");
+    return { ok: true, value: parseYaml(content) };
+  } catch (error) {
+    const message = getErrorMessage(error);
+    return { ok: false, error: new ParseError(`Failed to load papers registry: ${message}`) };
+  }
+}
+async function savePapersRegistry(registry, rootDir) {
+  const root = rootDir ?? process.cwd();
+  const filePath = join(root, REGISTRY_PATH, PAPERS_FILE);
+  const pathValidation = validatePath(filePath, root);
+  if (!pathValidation.ok) {
+    return pathValidation;
+  }
+  try {
+    const content = stringifyYaml2(registry, { lineWidth: 100 });
+    await fs2.writeFile(pathValidation.value, content, "utf-8");
+    return { ok: true, value: void 0 };
+  } catch (error) {
+    const message = getErrorMessage(error);
+    return { ok: false, error: new ParseError(`Failed to save papers registry: ${message}`) };
+  }
+}
+
+export {
+  REGISTRY_PATH,
+  getProjectRoot,
+  loadTechniquesRegistry,
+  loadPapersRegistry,
+  savePapersRegistry
+};
+//# sourceMappingURL=chunk-FO4A6HA3.js.map

package/dist/chunk-FO4A6HA3.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli/research-helpers-io.ts","../src/cli/research-scaffold.ts"],"sourcesContent":["/**\n * Research Registry I/O Operations\n *\n * File operations for loading and saving research registry YAML files.\n * Includes path traversal protection per Issue #353.\n *\n * @see docs/research/RESEARCH_INDEX.md\n * @see Issue #237 (Epic #225)\n * @see Issue #353 (Security - Path traversal fix)\n */\n\nimport * as fs from 'node:fs/promises';\nimport { join, resolve } from 'node:path';\nimport { resolveInsideRoot } from '../security/safe-path.js';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport type { Result } from '../core/index.js';\nimport { SecurityError, getErrorMessage } from '../core/index.js';\nimport { ParseError } from '../core/types/workflow.js';\nimport type { TechniquesRegistry, PapersRegistry } from './research-types.js';\nimport { ensureRegistryFile } from './research-scaffold.js';\n\n// =============================================================================\n// CONSTANTS\n// =============================================================================\n\n/** Path to research registry directory relative to project root */\nexport const REGISTRY_PATH = 'docs/research/registry';\n\n/** Filename for techniques registry */\nexport const TECHNIQUES_FILE = 'techniques.yaml';\n\n/** Filename for papers registry */\nexport const PAPERS_FILE = 'papers.yaml';\n\n// =============================================================================\n// PROJECT ROOT\n// =============================================================================\n\n/**\n * Get the project root directory.\n * Note: Returns cwd since registry operations use explicit rootDir parameter\n */\nexport function getProjectRoot(): string {\n  return process.cwd();\n}\n\n// =============================================================================\n// PATH VALIDATION\n// =============================================================================\n\n/**\n * Validates that a constructed path stays within the allowed root directory.\n * Prevents path traversal attacks (e.g., ../../../etc/passwd).\n *\n * @param constructedPath - The full path to validate\n * @param allowedRoot - The root directory that paths must be within\n * @returns Result with validated absolute path or SecurityError\n */\nfunction validatePath(constructedPath: string, allowedRoot: string): Result<string, SecurityError> {\n  const resolved = resolveInsideRoot(constructedPath, allowedRoot);\n  if (resolved === null) {\n    return {\n      ok: false,\n      error: new SecurityError('Path traversal detected: path escapes allowed root directory', {\n        context: { constructedPath, allowedRoot: resolve(allowedRoot) },\n      }),\n    };\n  }\n  return { ok: true, value: resolved };\n}\n\n// =============================================================================\n// LOAD OPERATIONS\n// =============================================================================\n\n/**\n * Load techniques registry from YAML file.\n * Validates path to prevent directory traversal attacks.\n *\n * @param rootDir - Project root directory (defaults to cwd)\n * @returns Result with TechniquesRegistry or SecurityError/ParseError\n */\nexport async function loadTechniquesRegistry(\n  rootDir?: string\n): Promise<Result<TechniquesRegistry, SecurityError | ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const filePath = join(root, REGISTRY_PATH, TECHNIQUES_FILE);\n\n  const pathValidation = validatePath(filePath, root);\n  if (!pathValidation.ok) {\n    return pathValidation;\n  }\n\n  // #2470: try to scaffold an empty techniques.yaml on first run so research_*\n  // workflows don't error on a fresh install. No-op when file exists.\n  // When scaffold refuses (e.g. <rootDir>/docs/ doesn't exist, or\n  // NEXUS_NO_SCAFFOLD=1), fall through and let readFile produce the original\n  // ENOENT error — that's the existing contract.\n  await ensureRegistryFile(root, TECHNIQUES_FILE);\n\n  try {\n    const content = await fs.readFile(pathValidation.value, 'utf-8');\n    return { ok: true, value: parseYaml(content) as TechniquesRegistry };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return { ok: false, error: new ParseError(`Failed to load techniques registry: ${message}`) };\n  }\n}\n\n/**\n * Load papers registry from YAML file.\n * Validates path to prevent directory traversal attacks.\n *\n * @param rootDir - Project root directory (defaults to cwd)\n * @returns Result with PapersRegistry or SecurityError/ParseError\n */\nexport async function loadPapersRegistry(\n  rootDir?: string\n): Promise<Result<PapersRegistry, SecurityError | ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const filePath = join(root, REGISTRY_PATH, PAPERS_FILE);\n\n  const pathValidation = validatePath(filePath, root);\n  if (!pathValidation.ok) {\n    return pathValidation;\n  }\n\n  // #2470: try to scaffold an empty papers.yaml on first run so research_*\n  // workflows don't error on a fresh install. No-op when file exists; falls\n  // through silently when scaffold refuses (no docs/ root, or NEXUS_NO_SCAFFOLD).\n  await ensureRegistryFile(root, PAPERS_FILE);\n\n  try {\n    const content = await fs.readFile(pathValidation.value, 'utf-8');\n    return { ok: true, value: parseYaml(content) as PapersRegistry };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return { ok: false, error: new ParseError(`Failed to load papers registry: ${message}`) };\n  }\n}\n\n// =============================================================================\n// SAVE OPERATIONS\n// =============================================================================\n\n/**\n * Save techniques registry to YAML file.\n * Validates path to prevent directory traversal attacks.\n *\n * @param registry - The techniques registry to save\n * @param rootDir - Project root directory (defaults to cwd)\n * @returns Result with void on success or SecurityError/ParseError on failure\n */\nexport async function saveTechniquesRegistry(\n  registry: TechniquesRegistry,\n  rootDir?: string\n): Promise<Result<void, SecurityError | ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const filePath = join(root, REGISTRY_PATH, TECHNIQUES_FILE);\n\n  const pathValidation = validatePath(filePath, root);\n  if (!pathValidation.ok) {\n    return pathValidation;\n  }\n\n  try {\n    const content = stringifyYaml(registry, { lineWidth: 100 });\n    await fs.writeFile(pathValidation.value, content, 'utf-8');\n    return { ok: true, value: undefined };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return { ok: false, error: new ParseError(`Failed to save techniques registry: ${message}`) };\n  }\n}\n\n/**\n * Save papers registry to YAML file.\n * Validates path to prevent directory traversal attacks.\n *\n * @param registry - The papers registry to save\n * @param rootDir - Project root directory (defaults to cwd)\n * @returns Result with void on success or SecurityError/ParseError on failure\n */\nexport async function savePapersRegistry(\n  registry: PapersRegistry,\n  rootDir?: string\n): Promise<Result<void, SecurityError | ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const filePath = join(root, REGISTRY_PATH, PAPERS_FILE);\n\n  const pathValidation = validatePath(filePath, root);\n  if (!pathValidation.ok) {\n    return pathValidation;\n  }\n\n  try {\n    const content = stringifyYaml(registry, { lineWidth: 100 });\n    await fs.writeFile(pathValidation.value, content, 'utf-8');\n    return { ok: true, value: undefined };\n  } catch (error) {\n    const message = getErrorMessage(error);\n    return { ok: false, error: new ParseError(`Failed to save papers registry: ${message}`) };\n  }\n}\n","/**\n * research-scaffold — auto-create empty research registry files when missing.\n *\n * On a fresh install or in a sandboxed environment where the project doesn't\n * have `docs/research/registry/`, the research workflows previously errored\n * with `Failed to load papers registry: ENOENT`. The user has no idea what\n * to do.\n *\n * This module provides `ensureResearchRegistry()`: idempotent scaffolding\n * that creates empty YAML registries on ENOENT, announces what it did to\n * stderr (so the operator knows), and returns the path that's now safe to\n * read.\n *\n * Source: Issue #2470 (epic #2467 child).\n */\n\nimport * as fs from 'node:fs/promises';\nimport { existsSync } from 'node:fs';\nimport { dirname, resolve } from 'node:path';\nimport { stringify as stringifyYaml } from 'yaml';\n\nimport type { Result } from '../core/index.js';\nimport { ok, err, getErrorMessage } from '../core/index.js';\nimport { ParseError } from '../core/types/workflow.js';\n\nimport { REGISTRY_PATH, PAPERS_FILE, TECHNIQUES_FILE } from './research-helpers-io.js';\nimport { parseBoolEnv } from '../config/defaults-env.js';\n\n/**\n * Names of the registry files this scaffolder knows how to create.\n * `sources.yaml` and `alignments.yaml` live alongside but are populated by\n * different code paths; this scaffolder only owns the two YAML registries\n * that block `research_query` / `research_synthesize` on a fresh install.\n */\ntype ScaffoldedFile = typeof PAPERS_FILE | typeof TECHNIQUES_FILE;\n\nconst SCHEMA_VERSION = '1.0';\n\nconst ANNOUNCED = new Set<string>();\n\nfunction announceOnce(path: string, kind: ScaffoldedFile): void {\n  // De-dupe so that running multiple research commands in one session\n  // produces one announcement per scaffolded file, not per call.\n  if (ANNOUNCED.has(path)) return;\n  ANNOUNCED.add(path);\n  process.stderr.write(\n    `[scaffold] Created empty ${kind} at ${path}; add entries via 'nexus-agents research add' or research_add MCP tool.\\n`\n  );\n}\n\n/**\n * Operator opt-out. When set, scaffolding errors loudly with an actionable\n * message instead of silently writing files. Useful for CI and for\n * environments that want strict \"fail when state is wrong\" semantics.\n */\nfunction scaffoldDisabled(): boolean {\n  return parseBoolEnv('NEXUS_NO_SCAFFOLD', false);\n}\n\nfunction emptyPapersYaml(): string {\n  return stringifyYaml({ schema_version: SCHEMA_VERSION, papers: {} });\n}\n\nfunction emptyTechniquesYaml(): string {\n  return stringifyYaml({ schema_version: SCHEMA_VERSION, techniques: {} });\n}\n\n/**\n * Create the registry directory + an empty YAML file if either is missing.\n * Idempotent: existing files are left untouched.\n *\n * Scaffolds only when `<rootDir>/docs/` already exists. That guard keeps\n * tests, vitest's package cwd, and random scratch directories from getting\n * a `docs/research/` subtree implicitly. Operators on a real project root\n * (which always has `docs/`, either from cloning the repo or running\n * `nexus-agents init`) still get the auto-create behavior the issue asks for.\n *\n * Returns the resolved file path on success, or a ParseError when scaffolding\n * is disabled / refused (so the caller can pass the error through unchanged\n * for backwards compat with existing call sites).\n */\nexport async function ensureRegistryFile(\n  rootDir: string,\n  filename: ScaffoldedFile\n): Promise<Result<string, ParseError>> {\n  const filePath = resolve(rootDir, REGISTRY_PATH, filename);\n\n  if (existsSync(filePath)) return ok(filePath);\n\n  if (scaffoldDisabled()) {\n    return err(\n      new ParseError(\n        `Registry file missing: ${filePath}. Scaffolding disabled (NEXUS_NO_SCAFFOLD=1). Create the file manually or unset the env var.`\n      )\n    );\n  }\n\n  // Refuse to create a docs/ subtree in directories that aren't already\n  // documented project roots. The presence of `<rootDir>/docs/` is the\n  // strong signal we use.\n  if (!existsSync(resolve(rootDir, 'docs'))) {\n    return err(\n      new ParseError(\n        `Registry file missing: ${filePath}. ${rootDir}/docs/ does not exist; ` +\n          `refusing to create a Nexus subtree in a non-documented root. ` +\n          `Run 'nexus-agents init' first, or create ${rootDir}/docs/ manually.`\n      )\n    );\n  }\n\n  try {\n    await fs.mkdir(dirname(filePath), { recursive: true });\n    const content = filename === PAPERS_FILE ? emptyPapersYaml() : emptyTechniquesYaml();\n    await fs.writeFile(filePath, content, 'utf-8');\n    announceOnce(filePath, filename);\n    return ok(filePath);\n  } catch (e: unknown) {\n    return err(\n      new ParseError(\n        `Failed to scaffold ${filename} at ${filePath}: ${getErrorMessage(e)}. Set NEXUS_NO_SCAFFOLD=1 and create manually if scaffolding is unwanted.`\n      )\n    );\n  }\n}\n\n/**\n * Convenience: scaffold both papers.yaml and techniques.yaml. Used by the\n * research workflow startup paths that need both registries available.\n */\nexport async function ensureResearchRegistry(rootDir?: string): Promise<Result<void, ParseError>> {\n  const root = rootDir ?? process.cwd();\n  const papers = await ensureRegistryFile(root, PAPERS_FILE);\n  if (!papers.ok) return papers;\n  const techniques = await ensureRegistryFile(root, TECHNIQUES_FILE);\n  if (!techniques.ok) return techniques;\n  return ok(undefined);\n}\n\n/**\n * Test-only reset of the announcement de-dupe set. 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package/dist/{chunk-3DB4DEFY.js → chunk-G633EA23.js}

@@ -3,7 +3,7 @@ import {
   err,
   getErrorMessage,
   ok
-} from "./chunk-JRBUSUYD.js";
+} from "./chunk-DHU2YECH.js";
 
 // src/scm/types.ts
 var ScmError = class extends Error {
@@ -258,4 +258,4 @@ export {
   ScmError,
   GitHubProvider
 };
-//# sourceMappingURL=chunk-3DB4DEFY.js.map
+//# sourceMappingURL=chunk-G633EA23.js.map

package/dist/{chunk-7E2ZCYKA.js → chunk-GMXRM2JU.js}

@@ -11,7 +11,7 @@ import {
   getErrorMessage,
   getTimeProvider,
   ok
-} from "./chunk-JRBUSUYD.js";
+} from "./chunk-DHU2YECH.js";
 import {
   getNexusDataDir
 } from "./chunk-CH7QIDHQ.js";
@@ -2588,4 +2588,4 @@ export {
   VOTING_THRESHOLDS,
   ConsensusMetricsSchema
 };
-//# sourceMappingURL=chunk-7E2ZCYKA.js.map
+//# sourceMappingURL=chunk-GMXRM2JU.js.map

package/dist/{chunk-F2ULTSZ6.js → chunk-H4EXCQCF.js}

@@ -4,24 +4,24 @@ import {
   createStream,
   requireApiKey,
   validateApiKeyPresence
-} from "./chunk-5OOFU3EY.js";
+} from "./chunk-ZTMLKLVG.js";
 import {
   CUSTOM_API_BASE_URL_ENV,
   CUSTOM_API_DEFAULT_MODEL,
   PROVIDER_ENV_KEYS,
   assertCustomApiHostResolvesPublic,
   validateCustomApiBaseUrl
-} from "./chunk-3XGPHTO6.js";
+} from "./chunk-KPDRVYSN.js";
 import {
   CliCircuitBreaker,
   DEFAULT_CIRCUIT_BREAKER_CONFIG
-} from "./chunk-5EH7WMME.js";
+} from "./chunk-KISVLXVZ.js";
 import {
   getAvailabilityCache
-} from "./chunk-TIOXPJIO.js";
+} from "./chunk-25QNW65Q.js";
 import {
   generateHyphenId
-} from "./chunk-LUCPCWIZ.js";
+} from "./chunk-BUHPYOT3.js";
 import {
   CLI_SUBPROCESS_TIMEOUTS,
   CLI_TIMEOUTS,
@@ -55,7 +55,7 @@ import {
   loadModelsDevSnapshot,
   ok,
   resolveCliAlias
-} from "./chunk-JRBUSUYD.js";
+} from "./chunk-DHU2YECH.js";
 
 // src/cli-adapters/cli-to-model-adapter.ts
 var CliToModelAdapter = class {
@@ -4793,4 +4793,4 @@ export {
   SdkAdapter,
   createAutoAdapter
 };
-//# sourceMappingURL=chunk-F2ULTSZ6.js.map
+//# sourceMappingURL=chunk-H4EXCQCF.js.map

package/dist/{chunk-2QBR4RVO.js → chunk-HEDW5QDP.js}

@@ -2,7 +2,7 @@ import {
   createLogger,
   err,
   ok
-} from "./chunk-JRBUSUYD.js";
+} from "./chunk-DHU2YECH.js";
 
 // src/scm/token-resolver.ts
 import { execFile } from "child_process";
@@ -87,4 +87,4 @@ export {
   hasToken,
   getTokenEnvVars
 };
-//# sourceMappingURL=chunk-2QBR4RVO.js.map
+//# sourceMappingURL=chunk-HEDW5QDP.js.map

package/dist/{chunk-ZSJG7EB2.js → chunk-HN6X3WJB.js}

@@ -1,147 +1,13 @@
 import {
-  resolveInsideRoot
-} from "./chunk-NUBSJGQZ.js";
+  loadPapersRegistry
+} from "./chunk-FO4A6HA3.js";
 import {
-  ParseError,
-  SecurityError,
-  err,
-  getErrorMessage,
-  ok,
-  parseBoolEnv
-} from "./chunk-JRBUSUYD.js";
+  getErrorMessage
+} from "./chunk-DHU2YECH.js";
 
 // src/cli/research-helpers-synthesize.ts
 import { z } from "zod";
 
-// src/cli/research-helpers-io.ts
-import * as fs2 from "fs/promises";
-import { join, resolve as resolve2 } from "path";
-import { parse as parseYaml, stringify as stringifyYaml2 } from "yaml";
-
-// src/cli/research-scaffold.ts
-import * as fs from "fs/promises";
-import { existsSync } from "fs";
-import { dirname, resolve } from "path";
-import { stringify as stringifyYaml } from "yaml";
-var SCHEMA_VERSION = "1.0";
-var ANNOUNCED = /* @__PURE__ */ new Set();
-function announceOnce(path, kind) {
-  if (ANNOUNCED.has(path)) return;
-  ANNOUNCED.add(path);
-  process.stderr.write(
-    `[scaffold] Created empty ${kind} at ${path}; add entries via 'nexus-agents research add' or research_add MCP tool.
-`
-  );
-}
-function scaffoldDisabled() {
-  return parseBoolEnv("NEXUS_NO_SCAFFOLD", false);
-}
-function emptyPapersYaml() {
-  return stringifyYaml({ schema_version: SCHEMA_VERSION, papers: {} });
-}
-function emptyTechniquesYaml() {
-  return stringifyYaml({ schema_version: SCHEMA_VERSION, techniques: {} });
-}
-async function ensureRegistryFile(rootDir, filename) {
-  const filePath = resolve(rootDir, REGISTRY_PATH, filename);
-  if (existsSync(filePath)) return ok(filePath);
-  if (scaffoldDisabled()) {
-    return err(
-      new ParseError(
-        `Registry file missing: ${filePath}. Scaffolding disabled (NEXUS_NO_SCAFFOLD=1). Create the file manually or unset the env var.`
-      )
-    );
-  }
-  if (!existsSync(resolve(rootDir, "docs"))) {
-    return err(
-      new ParseError(
-        `Registry file missing: ${filePath}. ${rootDir}/docs/ does not exist; refusing to create a Nexus subtree in a non-documented root. Run 'nexus-agents init' first, or create ${rootDir}/docs/ manually.`
-      )
-    );
-  }
-  try {
-    await fs.mkdir(dirname(filePath), { recursive: true });
-    const content = filename === PAPERS_FILE ? emptyPapersYaml() : emptyTechniquesYaml();
-    await fs.writeFile(filePath, content, "utf-8");
-    announceOnce(filePath, filename);
-    return ok(filePath);
-  } catch (e) {
-    return err(
-      new ParseError(
-        `Failed to scaffold ${filename} at ${filePath}: ${getErrorMessage(e)}. Set NEXUS_NO_SCAFFOLD=1 and create manually if scaffolding is unwanted.`
-      )
-    );
-  }
-}
-
-// src/cli/research-helpers-io.ts
-var REGISTRY_PATH = "docs/research/registry";
-var TECHNIQUES_FILE = "techniques.yaml";
-var PAPERS_FILE = "papers.yaml";
-function getProjectRoot() {
-  return process.cwd();
-}
-function validatePath(constructedPath, allowedRoot) {
-  const resolved = resolveInsideRoot(constructedPath, allowedRoot);
-  if (resolved === null) {
-    return {
-      ok: false,
-      error: new SecurityError("Path traversal detected: path escapes allowed root directory", {
-        context: { constructedPath, allowedRoot: resolve2(allowedRoot) }
-      })
-    };
-  }
-  return { ok: true, value: resolved };
-}
-async function loadTechniquesRegistry(rootDir) {
-  const root = rootDir ?? process.cwd();
-  const filePath = join(root, REGISTRY_PATH, TECHNIQUES_FILE);
-  const pathValidation = validatePath(filePath, root);
-  if (!pathValidation.ok) {
-    return pathValidation;
-  }
-  await ensureRegistryFile(root, TECHNIQUES_FILE);
-  try {
-    const content = await fs2.readFile(pathValidation.value, "utf-8");
-    return { ok: true, value: parseYaml(content) };
-  } catch (error) {
-    const message = getErrorMessage(error);
-    return { ok: false, error: new ParseError(`Failed to load techniques registry: ${message}`) };
-  }
-}
-async function loadPapersRegistry(rootDir) {
-  const root = rootDir ?? process.cwd();
-  const filePath = join(root, REGISTRY_PATH, PAPERS_FILE);
-  const pathValidation = validatePath(filePath, root);
-  if (!pathValidation.ok) {
-    return pathValidation;
-  }
-  await ensureRegistryFile(root, PAPERS_FILE);
-  try {
-    const content = await fs2.readFile(pathValidation.value, "utf-8");
-    return { ok: true, value: parseYaml(content) };
-  } catch (error) {
-    const message = getErrorMessage(error);
-    return { ok: false, error: new ParseError(`Failed to load papers registry: ${message}`) };
-  }
-}
-async function savePapersRegistry(registry, rootDir) {
-  const root = rootDir ?? process.cwd();
-  const filePath = join(root, REGISTRY_PATH, PAPERS_FILE);
-  const pathValidation = validatePath(filePath, root);
-  if (!pathValidation.ok) {
-    return pathValidation;
-  }
-  try {
-    const content = stringifyYaml2(registry, { lineWidth: 100 });
-    await fs2.writeFile(pathValidation.value, content, "utf-8");
-    return { ok: true, value: void 0 };
-  } catch (error) {
-    const message = getErrorMessage(error);
-    return { ok: false, error: new ParseError(`Failed to save papers registry: ${message}`) };
-  }
-}
-
 // src/cli/research-alignment-map.ts
 var TECHNIQUE_IMPLEMENTATION_MAP = /* @__PURE__ */ new Map([
   // Routing techniques
@@ -1006,13 +872,8 @@ function attributeFindings(papers) {
 }
 
 export {
-  REGISTRY_PATH,
-  getProjectRoot,
-  loadTechniquesRegistry,
-  loadPapersRegistry,
-  savePapersRegistry,
   normalizeTopicToCanonical,
   AttributedInsightSchema,
   synthesizeResearch
 };
-//# sourceMappingURL=chunk-ZSJG7EB2.js.map
+//# sourceMappingURL=chunk-HN6X3WJB.js.map