agentsmesh 0.35.0 → 0.37.0

package/dist/engine.js

@@ -1,13 +1,13 @@
 import { z } from 'zod';
 import { parse, stringify, parseDocument, isMap, Document, isSeq, isScalar, Scalar, Pair, YAMLSeq } from 'yaml';
 import { existsSync, readFileSync, constants, readdirSync, realpathSync, statSync } from 'fs';
-import { basename, join, dirname, relative, win32, posix, sep, resolve, extname } from 'path';
-import { readFile, rm, mkdir, readdir, lstat, unlink, writeFile, rename, chmod, access, stat, realpath, mkdtemp, cp } from 'fs/promises';
+import { basename, join, dirname, relative, extname, win32, posix, sep, resolve } from 'path';
+import { readFile, rm, mkdir, readdir, lstat, open, access, stat, realpath, rename, writeFile, mkdtemp, cp } from 'fs/promises';
 import { setTimeout } from 'timers/promises';
+import { randomUUID, createHash } from 'crypto';
 import { parse as parse$1, stringify as stringify$1 } from 'smol-toml';
 import { Buffer } from 'buffer';
 import { homedir, tmpdir } from 'os';
-import { createHash } from 'crypto';
 import { execFile } from 'child_process';
 import { fileURLToPath, pathToFileURL, URL as URL$1 } from 'url';
 import { promisify } from 'util';
@@ -845,6 +845,12 @@ function shouldNormalizeLineEndings(path) {
   const base = basename(path).toLowerCase();
   return TEXT_DOTFILES.has(base);
 }
+function isBinaryPayloadPath(path) {
+  return BINARY_EXTENSIONS.has(extname(path).toLowerCase());
+}
+function payloadEncodingFor(path) {
+  return isBinaryPayloadPath(path) ? "latin1" : "utf-8";
+}
 function normalizeLineEndings(content) {
   return content.replace(/\r\n?/g, "\n");
 }
@@ -856,7 +862,7 @@ function normalizeTextPayload(path, content) {
   const withoutBom = content.startsWith(UTF8_BOM) ? content.slice(UTF8_BOM.length) : content;
   return normalizeLineEndings(withoutBom);
 }
-var UTF8_BOM, TEXT_EXTENSIONS, TEXT_DOTFILES, EXECUTABLE_SCRIPT_EXTENSIONS;
+var UTF8_BOM, TEXT_EXTENSIONS, TEXT_DOTFILES, BINARY_EXTENSIONS, EXECUTABLE_SCRIPT_EXTENSIONS;
 var init_fs_text_encoding = __esm({
   "src/utils/filesystem/fs-text-encoding.ts"() {
     UTF8_BOM = "\uFEFF";
@@ -901,9 +907,109 @@ var init_fs_text_encoding = __esm({
       ".rooignore",
       ".antigravityignore"
     ]);
+    BINARY_EXTENSIONS = /* @__PURE__ */ new Set([
+      ".png",
+      ".jpg",
+      ".jpeg",
+      ".gif",
+      ".bmp",
+      ".ico",
+      ".webp",
+      ".avif",
+      ".tiff",
+      ".pdf",
+      ".zip",
+      ".gz",
+      ".tgz",
+      ".bz2",
+      ".xz",
+      ".7z",
+      ".rar",
+      ".jar",
+      ".woff",
+      ".woff2",
+      ".ttf",
+      ".otf",
+      ".eot",
+      ".mp3",
+      ".mp4",
+      ".wav",
+      ".ogg",
+      ".webm",
+      ".mov",
+      ".wasm",
+      ".bin",
+      ".dat",
+      ".db",
+      ".sqlite",
+      ".so",
+      ".dylib",
+      ".dll",
+      ".exe",
+      ".class",
+      ".pyc",
+      // Office and design documents are zip or proprietary containers.
+      ".xlsx",
+      ".xls",
+      ".docx",
+      ".doc",
+      ".pptx",
+      ".ppt",
+      ".odt",
+      ".ods",
+      ".psd",
+      ".ai",
+      ".sketch",
+      ".fig",
+      ".heic",
+      ".heif",
+      // Archives, columnar data, models and compressed payloads.
+      ".tar",
+      ".zst",
+      ".br",
+      ".lz4",
+      ".parquet",
+      ".avro",
+      ".orc",
+      ".pkl",
+      ".npy",
+      ".npz",
+      ".onnx",
+      ".pt",
+      ".safetensors",
+      ".gguf",
+      ".sqlite3",
+      ".avi",
+      ".mkv",
+      ".flac",
+      ".aac",
+      ".m4a",
+      ".ttc"
+    ]);
     EXECUTABLE_SCRIPT_EXTENSIONS = /* @__PURE__ */ new Set([".sh", ".bash", ".zsh"]);
   }
 });
+async function renameWithRetry(from, to, options = {}) {
+  const attempts = options.attempts ?? 5;
+  const delayMs = options.delayMs ?? 50;
+  for (let attempt = 0; ; attempt++) {
+    try {
+      await rename(from, to);
+      return;
+    } catch (err) {
+      const code = err.code;
+      const transient = code !== void 0 && TRANSIENT_RENAME_CODES.has(code);
+      if (!transient || attempt >= attempts - 1) throw err;
+      await setTimeout(delayMs * 2 ** attempt);
+    }
+  }
+}
+var TRANSIENT_RENAME_CODES;
+var init_rename_retry = __esm({
+  "src/utils/filesystem/rename-retry.ts"() {
+    TRANSIENT_RENAME_CODES = /* @__PURE__ */ new Set(["EPERM", "EACCES", "EBUSY", "ENOTEMPTY", "EEXIST"]);
+  }
+});
 function shouldSkipRecursiveBranch(segments) {
   if (segments.length > MAX_RECURSIVE_DEPTH) return true;
   const counts = /* @__PURE__ */ new Map();
@@ -994,30 +1100,10 @@ var init_fs_traverse = __esm({
     MAX_SEGMENT_REPETITIONS = 3;
   }
 });
-async function renameWithRetry(from, to, options = {}) {
-  const attempts = options.attempts ?? 5;
-  const delayMs = options.delayMs ?? 50;
-  for (let attempt = 0; ; attempt++) {
-    try {
-      await rename(from, to);
-      return;
-    } catch (err) {
-      const code = err.code;
-      const transient = code !== void 0 && TRANSIENT_RENAME_CODES.has(code);
-      if (!transient || attempt >= attempts - 1) throw err;
-      await setTimeout(delayMs * 2 ** attempt);
-    }
-  }
-}
-var TRANSIENT_RENAME_CODES;
-var init_rename_retry = __esm({
-  "src/utils/filesystem/rename-retry.ts"() {
-    TRANSIENT_RENAME_CODES = /* @__PURE__ */ new Set(["EPERM", "EACCES", "EBUSY", "ENOTEMPTY", "EEXIST"]);
-  }
-});
 async function readFileSafe(path) {
   try {
-    const data = await readFile(path, "utf-8");
+    const data = await readFile(path, payloadEncodingFor(path));
+    if (isBinaryPayloadPath(path)) return data;
     return data.startsWith(UTF8_BOM) ? data.slice(UTF8_BOM.length) : data;
   } catch (err) {
     const e = err;
@@ -1041,40 +1127,28 @@ async function writeFileAtomic(path, content, options) {
         { errnoCode: "EISDIR" }
       );
     }
-    if (info.isSymbolicLink()) {
-      await unlink(path).catch((e) => {
-        if (e.code !== "ENOENT") throw e;
-      });
-    }
   } catch (err) {
     if (err instanceof FileSystemError) throw err;
     const e = err;
     if (e.code !== "ENOENT") throw err;
   }
-  const tmpPath = `${path}.tmp`;
+  const tmpPath = `${path}.tmp-${randomUUID()}`;
   const payload = shouldNormalizeLineEndings(path) ? normalizeLineEndings(content) : content;
   const mode = executableModeFor(path);
+  let handle;
+  let ownsTemporaryFile = false;
   try {
-    try {
-      const tmpInfo = await lstat(tmpPath);
-      if (tmpInfo.isSymbolicLink()) {
-        await unlink(tmpPath);
-      }
-    } catch (tmpErr) {
-      if (tmpErr.code !== "ENOENT") throw tmpErr;
-    }
-    const writeOpts = {
-      encoding: "utf-8",
-      flag: "w"
-    };
-    if (mode !== void 0) writeOpts.mode = mode;
-    await writeFile(tmpPath, payload, writeOpts);
-    await rename(tmpPath, path);
-    if (mode !== void 0) {
-      await chmod(path, mode);
-    }
+    handle = await open(tmpPath, "wx", mode);
+    ownsTemporaryFile = true;
+    await handle.writeFile(payload, payloadEncodingFor(path));
+    if (mode !== void 0) await handle.chmod(mode);
+    await handle.close();
+    handle = void 0;
+    await renameWithRetry(tmpPath, path);
   } catch (err) {
-    await rm(tmpPath, { force: true }).catch(() => {
+    await handle?.close().catch(() => {
+    });
+    if (ownsTemporaryFile) await rm(tmpPath, { force: true }).catch(() => {
     });
     const e = err;
     throw new FileSystemError(
@@ -1099,6 +1173,7 @@ var init_fs = __esm({
   "src/utils/filesystem/fs.ts"() {
     init_errors();
     init_fs_text_encoding();
+    init_rename_retry();
     init_fs_traverse();
     init_fs_text_encoding();
     init_rename_retry();
@@ -2251,43 +2326,92 @@ function isGlobAdjacent(content, start, end) {
   const next = end < content.length ? content.at(end) : "";
   return prev === "*" || next === "*";
 }
+var NON_REWRITABLE_BARE_FILES, PATH_TOKEN, LINE_NUMBER_SUFFIX;
+var init_link_rebaser_helpers = __esm({
+  "src/core/reference/link-rebaser-helpers.ts"() {
+    init_path_helpers();
+    init_link_format_registry();
+    NON_REWRITABLE_BARE_FILES = /* @__PURE__ */ new Set([
+      "AGENTS.md",
+      "CLAUDE.md",
+      "GEMINI.md",
+      "codex.md",
+      ".windsurfrules",
+      ".cursorrules"
+    ]);
+    PATH_TOKEN = /(?:\.\.[\\/]|\.\/|\.\\|\/[A-Za-z0-9._-]|[A-Za-z]:[\\/][A-Za-z0-9._-]|\.agentsmesh[\\/]|\.claude[\\/]|\.cursor[\\/]|\.github[\\/]|\.continue[\\/]|\.junie[\\/]|\.kiro[\\/]|\.gemini[\\/]|\.clinerules[\\/]|\.cline[\\/]|\.codex[\\/]|\.agents[\\/]|\.windsurf[\\/]|\.roo[\\/]|(?:[A-Za-z0-9._-]+[\\/])+|[A-Za-z0-9._-]+\.[A-Za-z0-9._-]+)[A-Za-z0-9._@%+~:\\/-]*/g;
+    LINE_NUMBER_SUFFIX = /(?::(\d+)){1,2}$/;
+  }
+});
+
+// src/core/reference/protected-ranges.ts
+function inlineCodeRanges(content) {
+  const ranges = [];
+  let openStart = -1;
+  let openLength = 0;
+  for (const match of content.matchAll(/`+/g)) {
+    const start = match.index;
+    const length = match[0].length;
+    if (openStart === -1) {
+      openStart = start;
+      openLength = length;
+      continue;
+    }
+    if (length === openLength) {
+      ranges.push([openStart, start + length]);
+      openStart = -1;
+      openLength = 0;
+    }
+  }
+  return ranges;
+}
+function extendAcrossBalancedParens(content, end) {
+  let cursor = end;
+  while (content[cursor] === "(") {
+    let depth = 0;
+    let scan = cursor;
+    while (scan < content.length) {
+      const ch = content[scan];
+      if (ch === "(") depth += 1;
+      else if (ch === ")") {
+        depth -= 1;
+        if (depth === 0) break;
+      } else if (ch === void 0 || /\s/.test(ch)) return cursor;
+      scan += 1;
+    }
+    if (depth !== 0) return cursor;
+    cursor = scan + 1;
+    while (cursor < content.length && !/[\s<>()\]]/.test(content.charAt(cursor))) cursor += 1;
+  }
+  return cursor;
+}
 function protectedRanges(content) {
   const ranges = [];
   for (const pattern of getLinkFormatRegistry().protectedSchemes) {
     const globalPattern = pattern.flags.includes("g") ? pattern : new RegExp(pattern.source, `${pattern.flags}g`);
     for (const match of content.matchAll(globalPattern)) {
-      ranges.push([match.index ?? 0, (match.index ?? 0) + match[0].length]);
+      const start = match.index;
+      ranges.push([start, extendAcrossBalancedParens(content, start + match[0].length)]);
     }
   }
   for (const match of content.matchAll(FENCED_CODE_BLOCK)) {
-    ranges.push([match.index ?? 0, (match.index ?? 0) + match[0].length]);
+    ranges.push([match.index, match.index + match[0].length]);
   }
   for (const match of content.matchAll(ROOT_GENERATION_CONTRACT_BLOCK)) {
-    ranges.push([match.index ?? 0, (match.index ?? 0) + match[0].length]);
+    ranges.push([match.index, match.index + match[0].length]);
   }
   for (const match of content.matchAll(EMBEDDED_RULES_BLOCK)) {
-    ranges.push([match.index ?? 0, (match.index ?? 0) + match[0].length]);
+    ranges.push([match.index, match.index + match[0].length]);
   }
   return ranges;
 }
-var NON_REWRITABLE_BARE_FILES, FENCED_CODE_BLOCK, ROOT_GENERATION_CONTRACT_BLOCK, EMBEDDED_RULES_BLOCK, PATH_TOKEN, LINE_NUMBER_SUFFIX;
-var init_link_rebaser_helpers = __esm({
-  "src/core/reference/link-rebaser-helpers.ts"() {
-    init_path_helpers();
+var FENCED_CODE_BLOCK, ROOT_GENERATION_CONTRACT_BLOCK, EMBEDDED_RULES_BLOCK;
+var init_protected_ranges = __esm({
+  "src/core/reference/protected-ranges.ts"() {
     init_link_format_registry();
-    NON_REWRITABLE_BARE_FILES = /* @__PURE__ */ new Set([
-      "AGENTS.md",
-      "CLAUDE.md",
-      "GEMINI.md",
-      "codex.md",
-      ".windsurfrules",
-      ".cursorrules"
-    ]);
     FENCED_CODE_BLOCK = /^(?:```|~~~)[^\n]*\n[\s\S]*?^(?:```|~~~)/gm;
     ROOT_GENERATION_CONTRACT_BLOCK = /<!-- agentsmesh:root-generation-contract:start -->[\s\S]*?<!-- agentsmesh:root-generation-contract:end -->/g;
     EMBEDDED_RULES_BLOCK = /<!-- agentsmesh:embedded-rules:start -->[\s\S]*?<!-- agentsmesh:embedded-rules:end -->/g;
-    PATH_TOKEN = /(?:\.\.[\\/]|\.\/|\.\\|\/[A-Za-z0-9._-]|[A-Za-z]:[\\/][A-Za-z0-9._-]|\.agentsmesh[\\/]|\.claude[\\/]|\.cursor[\\/]|\.github[\\/]|\.continue[\\/]|\.junie[\\/]|\.kiro[\\/]|\.gemini[\\/]|\.clinerules[\\/]|\.cline[\\/]|\.codex[\\/]|\.agents[\\/]|\.windsurf[\\/]|\.roo[\\/]|(?:[A-Za-z0-9._-]+[\\/])+|[A-Za-z0-9._-]+\.[A-Za-z0-9._-]+)[A-Za-z0-9._@%+~:\\/-]*/g;
-    LINE_NUMBER_SUFFIX = /(?::(\d+)){1,2}$/;
   }
 });
 
@@ -2780,6 +2904,7 @@ var init_link_rebaser = __esm({
   "src/core/reference/link-rebaser.ts"() {
     init_path_helpers();
     init_link_rebaser_helpers();
+    init_protected_ranges();
     init_link_rebaser_output();
     init_link_rebaser_resolution();
     init_link_uri_encoding();
@@ -7203,6 +7328,60 @@ var init_embedded_rules = __esm({
   }
 });
 
+// src/utils/text/json-comments.ts
+function stripJsonComments(text) {
+  let result2 = "";
+  let i = 0;
+  const len = text.length;
+  while (i < len) {
+    const ch = text[i];
+    if (ch === '"') {
+      result2 += ch;
+      i++;
+      while (i < len) {
+        const sc = text[i];
+        result2 += sc;
+        if (sc === "\\") {
+          i++;
+          if (i < len) {
+            result2 += text[i];
+          }
+        } else if (sc === '"') {
+          break;
+        }
+        i++;
+      }
+      i++;
+      continue;
+    }
+    if (ch === "/" && text[i + 1] === "*") {
+      i += 2;
+      while (i < len) {
+        if (text[i] === "*" && text[i + 1] === "/") {
+          i += 2;
+          break;
+        }
+        i++;
+      }
+      continue;
+    }
+    if (ch === "/" && text[i + 1] === "/") {
+      i += 2;
+      while (i < len && text[i] !== "\n") {
+        i++;
+      }
+      continue;
+    }
+    result2 += ch;
+    i++;
+  }
+  return result2;
+}
+var init_json_comments = __esm({
+  "src/utils/text/json-comments.ts"() {
+  }
+});
+
 // src/canonical/features/syntax-error.ts
 function failSyntax(filePath2, cause, onParseError) {
   const error = new CanonicalParseError(filePath2, cause);
@@ -7252,54 +7431,6 @@ function parseServer(raw) {
     env
   };
 }
-function stripJsonComments(text) {
-  let result2 = "";
-  let i = 0;
-  const len = text.length;
-  while (i < len) {
-    const ch = text[i];
-    if (ch === '"') {
-      result2 += ch;
-      i++;
-      while (i < len) {
-        const sc = text[i];
-        result2 += sc;
-        if (sc === "\\") {
-          i++;
-          if (i < len) {
-            result2 += text[i];
-          }
-        } else if (sc === '"') {
-          break;
-        }
-        i++;
-      }
-      i++;
-      continue;
-    }
-    if (ch === "/" && text[i + 1] === "*") {
-      i += 2;
-      while (i < len) {
-        if (text[i] === "*" && text[i + 1] === "/") {
-          i += 2;
-          break;
-        }
-        i++;
-      }
-      continue;
-    }
-    if (ch === "/" && text[i + 1] === "/") {
-      i += 2;
-      while (i < len && text[i] !== "\n") {
-        i++;
-      }
-      continue;
-    }
-    result2 += ch;
-    i++;
-  }
-  return result2;
-}
 async function parseMcp(mcpPath, onParseError) {
   const content = await readFileSafe(mcpPath);
   if (!content) return null;
@@ -7322,6 +7453,7 @@ async function parseMcp(mcpPath, onParseError) {
 }
 var init_mcp = __esm({
   "src/canonical/features/mcp.ts"() {
+    init_json_comments();
     init_syntax_error();
     init_fs();
   }
@@ -8653,7 +8785,7 @@ ${rawBody}`;
   });
 }
 function generateMcp3(canonical) {
-  if (!canonical.mcp || Object.keys(canonical.mcp.mcpServers).length === 0) return [];
+  if (!canonical.mcp) return [];
   const content = JSON.stringify({ mcpServers: canonical.mcp.mcpServers }, null, 2);
   return [{ path: CLAUDE_MCP_JSON, content }];
 }
@@ -8688,14 +8820,12 @@ function generatePermissions4(canonical) {
   if (!canonical.permissions) return [];
   const { allow, deny } = canonical.permissions;
   const ask = canonical.permissions.ask ?? [];
-  if (allow.length === 0 && deny.length === 0 && ask.length === 0) return [];
   const content = JSON.stringify({ permissions: { allow, deny, ask } }, null, 2);
   return [{ path: CLAUDE_SETTINGS, content }];
 }
 function generateHooks3(canonical) {
-  if (!canonical.hooks || Object.keys(canonical.hooks).length === 0) return [];
+  if (!canonical.hooks) return [];
   const claudeHooks = buildClaudeHooksObjectFromCanonical(canonical);
-  if (Object.keys(claudeHooks).length === 0) return [];
   const content = JSON.stringify({ hooks: claudeHooks }, null, 2);
   return [{ path: CLAUDE_SETTINGS, content }];
 }
@@ -20513,9 +20643,9 @@ var init_config_toml = __esm({
 function isValidKimiPermissionPattern(pattern) {
   const trimmed = pattern.trim();
   if (trimmed.length === 0) return false;
-  const open = trimmed.indexOf("(");
-  if (open === -1) return true;
-  return trimmed.endsWith(")") && open > 0;
+  const open2 = trimmed.indexOf("(");
+  if (open2 === -1) return true;
+  return trimmed.endsWith(")") && open2 > 0;
 }
 function listOf(permissions, key) {
   return permissions[key] ?? [];
@@ -29705,6 +29835,7 @@ function rewriteGeneratedReferences(results, canonical, config, projectRoot, sco
 // src/core/reference/validate-generated-markdown-links.ts
 init_path_helpers();
 init_link_rebaser_helpers();
+init_protected_ranges();
 
 // src/utils/output/color.ts
 function noColorRequested() {
@@ -29787,7 +29918,7 @@ var logger = {
 
 // src/core/reference/validate-generated-markdown-links.ts
 var INLINE_MD_LINK = /!?\[[^\]]*\]\(([^)]+)\)/g;
-var REF_LINK_DEF = /^\s*\[[^\]\n]+\]:\s*(?:<([^>\n]*)>|(\S+))/gm;
+var REF_LINK_DEF = /^\s*\[(?!\^)[^\]\n]+\]:\s*(?:<([^>\n]*)>|(\S+))/gm;
 function isMarkdownLikeOutput(relativePath) {
   return relativePath.endsWith(".md") || relativePath.endsWith(".mdc");
 }
@@ -29920,7 +30051,7 @@ function findBrokenMarkdownLinks(results, projectRoot) {
       projectRoot,
       pathApi(projectRoot).join(projectRoot, result2.path)
     );
-    const protectedR = protectedRanges(result2.content);
+    const protectedR = [...protectedRanges(result2.content), ...inlineCodeRanges(result2.content)];
     const visitDestination = (raw, matchIndex) => {
       if (isOffsetInRanges(matchIndex, protectedR)) return;
       const checked = resolveMarkdownLinkTargets(raw, projectRoot, destinationAbs);
@@ -30014,28 +30145,10 @@ function ruleNameFromSource(source) {
 
 // src/core/generate/collision.ts
 init_fs_text_encoding();
+
+// src/core/generate/collision-agents.ts
 init_target_ids();
 var AGENTS_SUFFIX = "AGENTS.md";
-function statusRank(status) {
-  switch (status) {
-    case "created":
-      return 3;
-    case "updated":
-      return 2;
-    case "unchanged":
-      return 1;
-    case "skipped":
-      return 0;
-  }
-}
-function mergeDuplicateMetadata(preferred, other) {
-  if (statusRank(other.status) <= statusRank(preferred.status)) return preferred;
-  return {
-    ...preferred,
-    status: other.status,
-    currentContent: other.currentContent ?? preferred.currentContent
-  };
-}
 function trimmedContent(content) {
   return content.trim();
 }
@@ -30069,15 +30182,82 @@ function richerAgentsResult(left, right) {
   }
   return null;
 }
+function contentLines(content) {
+  const lines = /* @__PURE__ */ new Set();
+  for (const line of content.split("\n")) {
+    const trimmed = line.trim();
+    if (trimmed !== "") lines.add(trimmed);
+  }
+  return lines;
+}
+function covers(outer, inner) {
+  for (const line of inner) {
+    if (!outer.has(line)) return false;
+  }
+  return true;
+}
+var EMBEDDED_RULES_BLOCK2 = /(<!-- agentsmesh:embedded-rules:start -->)([\s\S]*?)(<!-- agentsmesh:embedded-rules:end -->)/;
+var EMBEDDED_RULE_UNIT = /<!-- agentsmesh:embedded-rule:start [\s\S]*?<!-- agentsmesh:embedded-rule:end -->/g;
+function embeddedRuleUnits(block) {
+  return [...block.matchAll(EMBEDDED_RULE_UNIT)].map((m) => m[0]);
+}
+function mergedEmbeddedRulesResult(left, right) {
+  if (!left.path.endsWith(AGENTS_SUFFIX) || left.path !== right.path) return null;
+  if (normalizeAgentsContent(left.content) !== normalizeAgentsContent(right.content)) return null;
+  const leftBlock = EMBEDDED_RULES_BLOCK2.exec(left.content);
+  const rightBlock = EMBEDDED_RULES_BLOCK2.exec(right.content);
+  if (!leftBlock?.[2] || !rightBlock?.[2]) return null;
+  const leftUnits = embeddedRuleUnits(leftBlock[2]);
+  const rightUnits = embeddedRuleUnits(rightBlock[2]);
+  if (leftUnits.length === 0 && rightUnits.length === 0) return null;
+  const added = rightUnits.filter((unit) => !leftUnits.includes(unit));
+  if (added.length === 0) return left;
+  const merged = [...leftUnits, ...added].join("\n\n");
+  const content = left.content.replace(
+    EMBEDDED_RULES_BLOCK2,
+    (_full, start, _inner, end) => `${start}
+
+${merged}
+
+${end}`
+  );
+  logger.warn(
+    `${left.path} is shared by ${left.target} and ${right.target}, so their target-scoped rules were combined into one file \u2014 every target reading it sees all of them.`
+  );
+  return { ...left, content };
+}
 function richerCodexAgentsResult(left, right) {
   if (!left.path.endsWith(AGENTS_SUFFIX) || left.path !== right.path) return null;
   const codex = left.target === CODEX_CLI_TARGET_ID ? left : right.target === CODEX_CLI_TARGET_ID ? right : null;
   const other = codex === left ? right : left;
   if (!codex) return null;
-  const codexLen = trimmedContent(codex.content).length;
-  const otherLen = trimmedContent(other.content).length;
-  if (codexLen === otherLen) return null;
-  return codexLen > otherLen ? codex : other;
+  const codexLines = contentLines(codex.content);
+  const otherLines = contentLines(other.content);
+  if (covers(codexLines, otherLines)) return codex;
+  if (covers(otherLines, codexLines)) return other;
+  return null;
+}
+
+// src/core/generate/collision.ts
+function statusRank(status) {
+  switch (status) {
+    case "created":
+      return 3;
+    case "updated":
+      return 2;
+    case "unchanged":
+      return 1;
+    case "skipped":
+      return 0;
+  }
+}
+function mergeDuplicateMetadata(preferred, other) {
+  if (statusRank(other.status) <= statusRank(preferred.status)) return preferred;
+  return {
+    ...preferred,
+    status: other.status,
+    currentContent: other.currentContent ?? preferred.currentContent
+  };
 }
 function resolveOutputCollisions(results) {
   const deduped = [];
@@ -30094,6 +30274,11 @@ function resolveOutputCollisions(results) {
         deduped[existingIdx] = richer;
         continue;
       }
+      const mergedRules = mergedEmbeddedRulesResult(existing, result2);
+      if (mergedRules) {
+        deduped[existingIdx] = refreshResultStatus(mergedRules);
+        continue;
+      }
       const richerCodex = richerCodexAgentsResult(existing, result2);
       if (richerCodex) {
         deduped[existingIdx] = richerCodex;
@@ -30659,6 +30844,14 @@ function redactUrlSecrets(message) {
     }
   );
 }
+function stripUrlCredentials(url) {
+  return url.replace(
+    URL_WITH_CREDENTIALS,
+    (_full, scheme, _userinfo, rest) => {
+      return `${scheme}${rest}`;
+    }
+  );
+}
 function gitProtocolOptIns() {
   const on = (v) => v === "1" || v === "true";
   return {
@@ -31057,6 +31250,7 @@ async function sweepStaleCache(cacheDir, maxAgeMs) {
 var MAX_CACHE_KEY_LENGTH = 80;
 var CACHE_KEY_HASH_LENGTH = 12;
 function buildCacheKey(provider, identifier, ref) {
+  identifier = stripUrlCredentials(identifier);
   const safe = (value) => value.replace(/[^a-zA-Z0-9_.-]/g, "_").replace(/^\.+/, "_");
   const [org, repo] = provider === "github" ? identifier.split("/", 2) : [];
   const readable = org && repo ? `${safe(org)}--${safe(repo)}--${safe(ref)}` : `${safe(provider)}__${safe(identifier)}__${safe(ref)}`;
@@ -34329,8 +34523,59 @@ async function diffOutputChecksums(rootBase, lockOutputs) {
 
 // src/core/generate/stale-cleanup.ts
 init_fs();
+async function canonicalizePath(path) {
+  try {
+    return await realpath(path);
+  } catch (error) {
+    if (error.code !== "ENOENT") throw error;
+    const parent = dirname(path);
+    if (parent === path) return resolve(path);
+    return join(await canonicalizePath(parent), basename(path));
+  }
+}
+function isPathInside(target34, root) {
+  return target34 === root || target34.startsWith(root.endsWith(sep) ? root : `${root}${sep}`);
+}
+var display = (path) => path.replaceAll("\\", "/");
+async function assertPathInsideRoot(root, target34) {
+  const rootAbs = resolve(root);
+  const targetAbs = resolve(target34);
+  if (!isPathInside(targetAbs, rootAbs)) {
+    throw new Error(`Unsafe filesystem path: ${display(target34)} is outside ${display(rootAbs)}`);
+  }
+  let realTarget;
+  let realRoot;
+  try {
+    [realTarget, realRoot] = await Promise.all([
+      canonicalizePath(targetAbs),
+      canonicalizePath(rootAbs)
+    ]);
+  } catch (cause) {
+    const detail = cause instanceof Error ? cause.message : String(cause);
+    throw new Error(
+      `Unsafe filesystem path: ${display(target34)} could not be resolved (${detail})`,
+      { cause }
+    );
+  }
+  if (isPathInside(realTarget, realRoot)) return;
+  throw new Error(
+    `Unsafe filesystem path: ${display(target34)} resolves to ${display(realTarget)} outside ${display(realRoot)}`
+  );
+}
+
+// src/core/generate/stale-cleanup.ts
 init_builtin_targets();
 init_registry();
+init_builtin_targets();
+function retainedDirs(inactiveTargets, scope) {
+  const dirs = /* @__PURE__ */ new Set();
+  for (const target34 of inactiveTargets) {
+    for (const dir of getTargetManagedOutputs(target34, scope)?.dirs ?? []) dirs.add(dir);
+  }
+  return dirs;
+}
+
+// src/core/generate/stale-cleanup.ts
 async function listFiles2(root, base = root) {
   const entries = await readdir(root, { withFileTypes: true });
   const files = [];
@@ -34344,13 +34589,6 @@ async function listFiles2(root, base = root) {
   }
   return files;
 }
-function retainedDirs(inactiveTargets, scope) {
-  const dirs = /* @__PURE__ */ new Set();
-  for (const target34 of inactiveTargets) {
-    for (const dir of getTargetManagedOutputs(target34, scope)?.dirs ?? []) dirs.add(dir);
-  }
-  return dirs;
-}
 function primaryEmitted(target34, scope, expected) {
   const descriptor34 = getBuiltinTargetDefinition(target34) ?? getDescriptor(target34);
   const primary = getTargetLayout(target34, scope)?.rootInstructionPath ?? descriptor34?.generators.primaryRootInstructionPath;
@@ -34377,6 +34615,7 @@ async function findStaleGeneratedOutputs(args) {
     for (const dir of managed.dirs) {
       if (retained.has(dir)) continue;
       const absDir = join(args.projectRoot, dir);
+      await assertPathInsideRoot(args.projectRoot, absDir);
       if (!await exists(absDir)) continue;
       for (const file of await listFiles2(absDir)) {
         const relPath = `${dir}/${file}`.replace(/\/+/g, "/");
@@ -34388,6 +34627,7 @@ async function findStaleGeneratedOutputs(args) {
   const found = [];
   for (const relPath of stale) {
     if (expected.has(relPath) || coOwned.has(relPath)) continue;
+    await assertPathInsideRoot(args.projectRoot, dirname(join(args.projectRoot, relPath)));
     if (await exists(join(args.projectRoot, relPath))) found.push(relPath);
   }
   return found.sort();
@@ -34401,6 +34641,7 @@ async function findUntrackedManagedDirFiles(args) {
     for (const dir of getTargetManagedOutputs(target34, scope)?.dirs ?? []) {
       if (retained.has(dir)) continue;
       const absDir = join(args.projectRoot, dir);
+      await assertPathInsideRoot(args.projectRoot, absDir);
       if (!await exists(absDir)) continue;
       for (const file of await listFiles2(absDir)) {
         const relPath = `${dir}/${file}`.replace(/\/+/g, "/");