@iowarp/clio-coder 0.3.0 → 0.3.1

package/dist/{chunk-UWIJNAOB.js → chunk-M5T5VO65.js}

@@ -1,9 +1,10 @@
+import { createRequire as __clioCreateRequire } from "node:module"; const require = __clioCreateRequire(import.meta.url);
 import {
   renderCodewikiDigest
-} from "./chunk-X3BR7HWV.js";
+} from "./chunk-5WIGXA4T.js";
 import {
   loadMemoryRecordsSync
-} from "./chunk-VOO7NYPP.js";
+} from "./chunk-PFEFKVGL.js";
 import {
   WIKI_INDEX,
   WIKI_PLAN_FILE,
@@ -31,7 +32,7 @@ import {
   wikiStaleness,
   writeWikiMeta,
   writeWikiPlanFile
-} from "./chunk-GNGDQYDU.js";
+} from "./chunk-7SS2CTV2.js";
 import {
   computeFingerprint,
   computeFingerprintAsync,
@@ -40,7 +41,7 @@ import {
   readClioState,
   statePath,
   writeClioState
-} from "./chunk-RQDWMVRB.js";
+} from "./chunk-BSU2YIWB.js";
 import {
   buildCodewiki,
   codewikiNeedsBackfill,
@@ -54,30 +55,45 @@ import {
   syncCodewiki,
   updateCodewikiPaths,
   writeCodewiki
-} from "./chunk-TPOCL34A.js";
+} from "./chunk-N6F52NLF.js";
 import {
   classifyProjectPreload
-} from "./chunk-KBR4MZZR.js";
+} from "./chunk-K5XEMXTI.js";
 import {
   ceilChars
-} from "./chunk-TKHQ4DGZ.js";
+} from "./chunk-H6F6BYOH.js";
+import {
+  INTEROP_AGENT_KINDS
+} from "./chunk-IHXBNWMM.js";
 import {
   BusChannels
-} from "./chunk-D5YD55AR.js";
+} from "./chunk-Q5WJOSJ7.js";
+import {
+  require_dist
+} from "./chunk-GB6QRBXN.js";
 import {
   clioDataDir,
   resolveClioDirs
-} from "./chunk-X3NE4WVW.js";
+} from "./chunk-BNAZZHFG.js";
 import {
   resolvePackageRoot
-} from "./chunk-DXQNI4PC.js";
+} from "./chunk-IWHMRKLL.js";
+import {
+  __toESM,
+  init_esm_shims
+} from "./chunk-3R73A4XB.js";
+
+// src/domains/context/index.ts
+init_esm_shims();
 
 // src/domains/context/extension.ts
+init_esm_shims();
 import { createHash as createHash2 } from "node:crypto";
 import { existsSync as existsSync7, readFileSync as readFileSync7 } from "node:fs";
 import { isAbsolute, relative as relative3 } from "node:path";
 
 // src/domains/context/adoption.ts
+init_esm_shims();
 import { createHash } from "node:crypto";
 import { existsSync, lstatSync, readdirSync, readFileSync, statSync } from "node:fs";
 import { homedir } from "node:os";
@@ -125,6 +141,13 @@ var GENERATED_OR_SECRET_DIRS = /* @__PURE__ */ new Set([
   "state",
   "projects"
 ]);
+var NESTED_INSTRUCTION_PROVIDERS = new Map(
+  INTEROP_AGENT_KINDS.flatMap((kind) => {
+    const provider = kind.adoptionProvider;
+    if (provider === void 0) return [];
+    return kind.instructionFiles.filter((file) => !file.includes("/")).map((file) => [file, provider]);
+  })
+);
 var UNSAFE_FILE_NAME_RE = /(^\.env(?:\.|$)|secret|credential|token|password|history|cache|session|\.log$|state\.json$)/i;
 var RULE_KEYWORDS = /\b(always|never|must|should|prefer|avoid|do not|don't|use|run|keep|write|allow|allows|deny|denies|enable|enables|define|defines)\b/i;
 var SECRET_LINE_PATTERNS = [
@@ -234,31 +257,26 @@ function discoverCandidateSpecs(cwd, home, includeGlobal) {
   const addProjectDir = (relPath, provider, kind, maxDepth, accept) => {
     for (const filePath of collectFiles(join(cwd, relPath), maxDepth, accept)) add(filePath, "project", provider, kind);
   };
-  addProject("CLAUDE.md", "claude-code", "instructions");
-  addProject(join(".claude", "CLAUDE.md"), "claude-code", "instructions");
-  addProject("AGENTS.md", "codex", "instructions");
-  addProject("CODEX.md", "codex", "instructions");
-  addProject(join(".codex", "AGENTS.md"), "codex", "instructions");
-  addProject("GEMINI.md", "gemini", "instructions");
-  addProject(join(".gemini", "GEMINI.md"), "gemini", "instructions");
-  addProject(join(".github", "copilot-instructions.md"), "copilot", "instructions");
+  for (const kind of INTEROP_AGENT_KINDS) {
+    if (kind.adoptionProvider === void 0) continue;
+    for (const file of kind.instructionFiles) addProject(file, kind.adoptionProvider, "instructions");
+  }
   const visibleWorkspaceFiles = enumerateWorkspaceFiles(cwd);
   for (const relPath of visibleWorkspaceFiles) {
     const parts = relPath.split("/");
     if (parts.length - 1 > 6) continue;
     const name2 = parts.at(-1);
-    if (name2 !== "CLAUDE.md" && name2 !== "AGENTS.md" && name2 !== "CODEX.md" && name2 !== "GEMINI.md") continue;
-    const filePath = join(cwd, relPath);
-    const provider = name2 === "CLAUDE.md" ? "claude-code" : name2 === "GEMINI.md" ? "gemini" : "codex";
-    add(filePath, "project", provider, "instructions");
+    const provider = name2 === void 0 ? void 0 : NESTED_INSTRUCTION_PROVIDERS.get(name2);
+    if (provider === void 0) continue;
+    add(join(cwd, relPath), "project", provider, "instructions");
   }
   addProject(join(".claude", "settings.json"), "claude-code", "settings");
   addProjectDir(join(".claude", "commands"), "claude-code", "command", 3, markdownLike);
   addProjectDir(join(".claude", "agents"), "claude-code", "agent", 2, markdownLike);
-  addProjectDir(join(".claude", "skills"), "claude-code", "skill", 4, markdownLike);
-  addProjectDir(join(".agents", "skills"), "agents", "skill", 4, markdownLike);
-  addProjectDir(join(".codex", "skills"), "codex", "skill", 4, markdownLike);
-  addProjectDir(join(".opencode", "skills"), "opencode", "skill", 4, markdownLike);
+  for (const kind of INTEROP_AGENT_KINDS) {
+    if (kind.adoptionProvider === void 0 || kind.projectSkillRoot === void 0) continue;
+    addProjectDir(kind.projectSkillRoot, kind.adoptionProvider, "skill", 4, markdownLike);
+  }
   addProject(join(".gemini", "settings.json"), "gemini", "settings");
   addProject(join(".gemini", "config.json"), "gemini", "settings");
   addProjectDir(
@@ -276,7 +294,6 @@ function discoverCandidateSpecs(cwd, home, includeGlobal) {
     (filePath) => markdownLike(filePath) || jsonLike(filePath)
   );
   addProjectDir(join(".cursor", "rules"), "cursor", "rule", 0, markdownLike);
-  addProjectDir(join(".github", "skills"), "copilot", "skill", 4, markdownLike);
   if (includeGlobal) add(join(home, ".codex", "AGENTS.md"), "global", "codex", "instructions");
   return specs.filter((spec) => existsSync(spec.path));
 }
@@ -736,11 +753,13 @@ function adoptionSourcesChanged(snapshots, options = {}) {
 }
 
 // src/domains/context/bootstrap.ts
+init_esm_shims();
 import { execFileSync } from "node:child_process";
 import { existsSync as existsSync4, mkdirSync, readFileSync as readFileSync4, writeFileSync } from "node:fs";
 import { dirname as dirname2, join as join4, parse } from "node:path";
 
 // src/domains/context/clio-md.ts
+init_esm_shims();
 import { existsSync as existsSync2, readFileSync as readFileSync2 } from "node:fs";
 import { join as join2 } from "node:path";
 var FOOTER_RE = /<!--\s*clio:fingerprint v1\s*\n([\s\S]*?)\n\s*-->/;
@@ -988,9 +1007,10 @@ function tryReadClioMd(cwd) {
 }
 
 // src/domains/context/project-metadata.ts
+init_esm_shims();
+var import_yaml = __toESM(require_dist(), 1);
 import { existsSync as existsSync3, readdirSync as readdirSync2, readFileSync as readFileSync3 } from "node:fs";
 import { join as join3 } from "node:path";
-import { parse as parseYaml } from "yaml";
 var MAX_DESCRIPTION_CHARS = 400;
 var MAX_NAME_CHARS = 80;
 function readText(cwd, relative6) {
@@ -1073,7 +1093,7 @@ function yamlRecord(cwd, relative6) {
   const raw = readText(cwd, relative6);
   if (raw === null) return null;
   try {
-    const parsed = parseYaml(raw);
+    const parsed = (0, import_yaml.parse)(raw);
     return typeof parsed === "object" && parsed !== null && !Array.isArray(parsed) ? parsed : null;
   } catch {
     return null;
@@ -1329,6 +1349,7 @@ function readProjectMetadata(cwd) {
 }
 
 // src/domains/context/prompt-context.ts
+init_esm_shims();
 function renderPromptContext(cwd) {
   const projectType = detectProjectType(cwd);
   const pieces = [renderProjectTypeFragment(projectType)];
@@ -1440,7 +1461,7 @@ function resolveDefaultIdentity(cwd, projectType, files) {
   if (/Clio owns the agent loop/i.test(context) && /pi-(?:ai|SDK)/i.test(context)) {
     return {
       text: [
-        "Clio Coder is IOWarp's orchestrator coding agent, named for the Greek muse of history and developed by the Gnosis Research Center at Illinois Tech under PI @akougkas. CLIO stands for Context Layer for Input/Output.",
+        "Clio Coder is IOWarp's orchestrator coding agent, named for the Greek muse of history and developed by the Gnosis Research Center at Illinois Tech (github.com/grc-iit, @grc-iit) and the IOWarp team. CLIO stands for Context Layer for Input/Output.",
         "pi-ai is accessed through the engine boundary.",
         "Clio owns the agent loop, TUI, session format, tool registry, and identity."
       ].join(" "),
@@ -1483,14 +1504,35 @@ function harvestSiblingBullets(files) {
   }
   return out3;
 }
-function inferConventions(cwd, projectType, files) {
+function localImportExtension(codewiki) {
+  const counts = /* @__PURE__ */ new Map();
+  let total = 0;
+  for (const file of codewiki.files) {
+    for (const specifier of file.imports) {
+      if (!specifier.startsWith(".")) continue;
+      total += 1;
+      const extension = /\.([A-Za-z0-9]+)$/.exec(specifier)?.[1];
+      const key = extension === void 0 ? "" : `.${extension}`;
+      counts.set(key, (counts.get(key) ?? 0) + 1);
+    }
+  }
+  if (total < 4) return null;
+  for (const [extension, count] of counts) {
+    if (extension.length > 0 && count / total >= 0.8) return extension;
+  }
+  return null;
+}
+function inferConventions(cwd, files, codewiki) {
   const conventions = [];
   const context = allContextText(files);
   const pkg = readJsonFile(join4(cwd, "package.json"));
   const packageText = typeof pkg === "object" && pkg !== null ? JSON.stringify(pkg) : "";
-  if (/Local imports end in `?\.js`?/i.test(context) || projectType === "typescript" && existsSync4(join4(cwd, "tsconfig.json"))) {
-    pushUnique(conventions, "Local imports end in `.js`. Tests use `node:test`. Avoid `any` without a tracking issue.");
-  } else if (/node:test/i.test(context) || /node --import tsx --test|node --test/.test(packageText)) {
+  const declaredJs = /Local imports end in `?\.js`?/i.test(context);
+  const importExtension = declaredJs ? ".js" : localImportExtension(codewiki);
+  if (importExtension !== null) {
+    pushUnique(conventions, `Local imports end in \`${importExtension}\`.`);
+  }
+  if (/node:test/i.test(context) || /node --import tsx --test|node --test/.test(packageText)) {
     pushUnique(conventions, "Tests use `node:test`.");
   }
   if (/No em-dash|em-dash/i.test(context)) {
@@ -1610,9 +1652,25 @@ function createModelGroundingCorpus(input) {
   return { lower: evidence.toLowerCase(), indexedPaths };
 }
 var CODE_TOKEN_RE = /`([^`\n]+)`/g;
-function groundedToken(token, evidence) {
+var CITED_LOCATION_RE = /^(.*[^:]):(\d+)(?:[-:]\d+)?$/;
+var CITED_CALL_RE = /^(.+?)\(\s*\)$/;
+function groundedName(token, evidence) {
   return evidence.lower.includes(token.toLowerCase()) || evidence.indexedPaths.has(token.replace(/^\.\//, ""));
 }
+function citedNames(token) {
+  const names = [];
+  let current = token;
+  for (let round = 0; round < 2; round += 1) {
+    const next = (CITED_CALL_RE.exec(current)?.[1] ?? CITED_LOCATION_RE.exec(current)?.[1])?.trim();
+    if (next === void 0 || next.length === 0 || next === current) break;
+    names.push(next);
+    current = next;
+  }
+  return names;
+}
+function groundedToken(token, evidence) {
+  return groundedName(token, evidence) || citedNames(token).some((name2) => groundedName(name2, evidence));
+}
 function groundedModelBody(body, evidence) {
   const kept = [];
   let inFence = false;
@@ -1650,7 +1708,7 @@ function stabilizeGeneratedOutput(input, base, onModelSectionRetained, groundMod
   const existing = input.existingClioMd;
   const conventions = [];
   for (const convention of existing?.conventions ?? []) pushUnique(conventions, convention);
-  for (const convention of inferConventions(input.cwd, input.projectType, input.siblingFiles)) {
+  for (const convention of inferConventions(input.cwd, input.siblingFiles, input.codewiki)) {
     pushUnique(conventions, convention);
   }
   const invariants = [];
@@ -1731,7 +1789,7 @@ function heuristicBootstrapOutputSync(input) {
   return stabilizeGeneratedOutput(input, {
     projectName: projectName(input.cwd),
     identity: resolveDefaultIdentity(input.cwd, input.projectType, input.siblingFiles).text,
-    conventions: inferConventions(input.cwd, input.projectType, input.siblingFiles),
+    conventions: inferConventions(input.cwd, input.siblingFiles, input.codewiki),
     invariants: inferInvariants(input.siblingFiles),
     sections: inferHeuristicSections(input)
   });
@@ -2272,6 +2330,7 @@ async function runBootstrap(input = {}) {
 }
 
 // src/domains/context/clear.ts
+init_esm_shims();
 import { existsSync as existsSync5, rmSync } from "node:fs";
 import { join as join5 } from "node:path";
 var ACCUMULATED_CONTEXT_PATHS = [
@@ -2328,10 +2387,12 @@ async function runContextClear(input = {}) {
 }
 
 // src/domains/context/refresh.ts
+init_esm_shims();
 import { writeFileSync as writeFileSync3 } from "node:fs";
 import { join as join8 } from "node:path";
 
 // src/domains/context/wiki/generate.ts
+init_esm_shims();
 import {
   closeSync,
   copyFileSync,
@@ -2349,6 +2410,7 @@ import {
 import { dirname as dirname4, join as join7 } from "node:path";
 
 // src/domains/context/wiki/assemble.ts
+init_esm_shims();
 import { mkdirSync as mkdirSync2, readFileSync as readFileSync5, rmSync as rmSync2, writeFileSync as writeFileSync2 } from "node:fs";
 import { basename as basename2, dirname as dirname3, join as join6, normalize, posix, relative as relative2 } from "node:path";
 var SOURCE_CITATION = /`((?:src|tests?|scripts|benchmarks|docs|packages|apps|lib|config|\.github)\/[^`\s:#]+)(?::(\d+)(?:-\d+)?)?(?::[A-Za-z_$][\w$.-]*)?`/g;
@@ -2537,6 +2599,7 @@ function normalizeRepoPath(sourceRoot, candidate) {
 }
 
 // src/domains/context/wiki/plan.ts
+init_esm_shims();
 var WIKI_DEPTH_STRATEGY = {
   simple: { areaDepth: 1, areaShare: 0.08, minAreaLines: 400 },
   medium: { areaDepth: 2, areaShare: 0.03, minAreaLines: 250 },
@@ -3424,16 +3487,18 @@ function createContextBundle(_context, options = {}) {
 }
 
 // src/domains/context/manifest.ts
+init_esm_shims();
 var ContextManifest = {
   name: "context",
   dependsOn: ["resources"]
 };
 
 // src/domains/context/operator-profile.ts
+init_esm_shims();
+var import_yaml2 = __toESM(require_dist(), 1);
 import { createHash as createHash3 } from "node:crypto";
 import { existsSync as existsSync8, readFileSync as readFileSync8 } from "node:fs";
 import { join as join9 } from "node:path";
-import { parse as parseYaml2 } from "yaml";
 var RESPONSE_POSTURES = ["concise", "balanced", "thorough"];
 var VALIDATION_PREFERENCES = ["tests-first", "manual", "trust"];
 var COMMIT_MESSAGE_STYLES = ["conventional", "descriptive", "terse"];
@@ -3473,7 +3538,7 @@ function readProfileBlob(value, issues) {
 function readProfileFile(path, issues) {
   if (!existsSync8(path)) return { profile: {}, present: false };
   try {
-    return { profile: readProfileBlob(parseYaml2(readFileSync8(path, "utf8")), issues), present: true };
+    return { profile: readProfileBlob((0, import_yaml2.parse)(readFileSync8(path, "utf8")), issues), present: true };
   } catch (err) {
     issues.push(`${path}: invalid YAML: ${err instanceof Error ? err.message : String(err)}`);
     return { profile: {}, present: false };
@@ -3518,10 +3583,11 @@ ${lines.join("\n")}`;
 }
 
 // src/domains/context/project-rules.ts
+init_esm_shims();
+var import_yaml3 = __toESM(require_dist(), 1);
 import { createHash as createHash4 } from "node:crypto";
 import { readdirSync as readdirSync4, readFileSync as readFileSync9 } from "node:fs";
 import { join as join10, relative as relative4, sep as sep2 } from "node:path";
-import { parse as parseYaml3 } from "yaml";
 var FRONTMATTER_RE = /^---\n([\s\S]*?)\n---\n?/;
 function isRecord3(value) {
   return value !== null && typeof value === "object" && !Array.isArray(value);
@@ -3584,7 +3650,7 @@ function parseRule(filePath, root, issues) {
   if (match) {
     body = text.slice(match[0].length);
     try {
-      const front = parseYaml3(match[1] ?? "");
+      const front = (0, import_yaml3.parse)(match[1] ?? "");
       if (isRecord3(front)) {
         if (Object.hasOwn(front, "paths")) {
           const parsedPaths = validateGlobArray(front.paths, "paths", id, issues);
@@ -3676,6 +3742,7 @@ function selectActiveRules(rules, workingContextPaths) {
 }
 
 // src/domains/context/wiki/prompts.ts
+init_esm_shims();
 import { execFileSync as execFileSync2 } from "node:child_process";
 import { existsSync as existsSync9, readFileSync as readFileSync10, realpathSync, statSync as statSync3 } from "node:fs";
 import { isAbsolute as isAbsolute2, join as join11, relative as relative5 } from "node:path";
@@ -3903,4 +3970,4 @@ export {
   ContextDomainModule,
   createContextDomainModule
 };
-//# sourceMappingURL=chunk-UWIJNAOB.js.map
+//# sourceMappingURL=chunk-M5T5VO65.js.map

package/dist/{chunk-JPOWPFCU.js → chunk-MAR7Y6HW.js}

@@ -1,6 +1,7 @@
+import { createRequire as __clioCreateRequire } from "node:module"; const require = __clioCreateRequire(import.meta.url);
 import {
   assertAgentIdNamespace
-} from "./chunk-527KG6XR.js";
+} from "./chunk-Q3RUPKEJ.js";
 import {
   CONFIRMED_SCOPE,
   READONLY_SCOPE,
@@ -11,10 +12,7 @@ import {
   observe,
   parseFrontmatter,
   parseResultContract
-} from "./chunk-XV4ZJ6ZM.js";
-import {
-  loadSkills
-} from "./chunk-26BZQOAD.js";
+} from "./chunk-GEP36Y4X.js";
 import {
   assertAgentSpecPolicy,
   classify,
@@ -26,28 +24,40 @@ import {
   isAgentProjectContextTier,
   isShadowAgent,
   normalizeAgentSpec
-} from "./chunk-WD6AJM35.js";
+} from "./chunk-OLBBMFRD.js";
+import {
+  loadSkills
+} from "./chunk-474KN5II.js";
 import {
   BusChannels,
   isRunAbortedPayload
-} from "./chunk-D5YD55AR.js";
+} from "./chunk-Q5WJOSJ7.js";
 import {
   clioConfigDir,
   clioStateDir,
   stateRootRemoved
-} from "./chunk-X3NE4WVW.js";
+} from "./chunk-BNAZZHFG.js";
 import {
   resolvePackageRoot
-} from "./chunk-DXQNI4PC.js";
+} from "./chunk-IWHMRKLL.js";
+import {
+  init_esm_shims
+} from "./chunk-3R73A4XB.js";
+
+// src/domains/agents/index.ts
+init_esm_shims();
 
 // src/domains/agents/extension.ts
+init_esm_shims();
 import path3 from "node:path";
 
 // src/domains/agents/registry.ts
+init_esm_shims();
 import { existsSync, readdirSync, readFileSync } from "node:fs";
 import path2 from "node:path";
 
 // src/domains/agents/recipe.ts
+init_esm_shims();
 import path from "node:path";
 var AGENT_BUDGET_KEYS = ["toolCalls", "readReserve", "synthesis"];
 function parseAgentBudget(value, sourcePath) {
@@ -101,6 +111,7 @@ function recipeIdFromPath(absPath, rootDir) {
 }
 
 // src/domains/agents/recipe-schema.ts
+init_esm_shims();
 var RECIPE_KEYS = [
   "version",
   "name",
@@ -425,6 +436,7 @@ function createAgentsBundle(_context) {
 }
 
 // src/domains/agents/manifest.ts
+init_esm_shims();
 var AgentsManifest = {
   name: "agents",
   dependsOn: ["config"]
@@ -436,19 +448,28 @@ var AgentsDomainModule = {
   createExtension: createAgentsBundle
 };
 
+// src/domains/safety/index.ts
+init_esm_shims();
+
+// src/domains/safety/extension.ts
+init_esm_shims();
+
 // src/domains/safety/audit.ts
+init_esm_shims();
 import { randomBytes } from "node:crypto";
 import { closeSync, fsyncSync, mkdirSync, openSync, writeSync } from "node:fs";
 import { join } from "node:path";
 var REDACT_KEY_RE = /(password|token|secret|key|auth|credential)/i;
 var MAX_STRING_LEN = 200;
+var DATE_OPTIONS = { year: "numeric", month: "2-digit", day: "2-digit" };
+var dateFormatterZone = process.env.TZ;
+var dateFormatter = new Intl.DateTimeFormat("en-CA", DATE_OPTIONS);
 function localDateString(d) {
-  const fmt = new Intl.DateTimeFormat("en-CA", {
-    year: "numeric",
-    month: "2-digit",
-    day: "2-digit"
-  });
-  return fmt.format(d);
+  if (process.env.TZ !== dateFormatterZone) {
+    dateFormatterZone = process.env.TZ;
+    dateFormatter = new Intl.DateTimeFormat("en-CA", DATE_OPTIONS);
+  }
+  return dateFormatter.format(d);
 }
 function newCorrelationId() {
   const n = BigInt(`0x${randomBytes(8).toString("hex")}`);
@@ -992,6 +1013,7 @@ function fallbackRejection(policy) {
 }
 
 // src/domains/safety/manifest.ts
+init_esm_shims();
 var SafetyManifest = {
   name: "safety",
   dependsOn: ["config"]
@@ -1007,4 +1029,4 @@ export {
   AgentsDomainModule,
   SafetyDomainModule
 };
-//# sourceMappingURL=chunk-JPOWPFCU.js.map
+//# sourceMappingURL=chunk-MAR7Y6HW.js.map