@mmerterden/multi-agent-pipeline 14.2.1 → 15.0.0

package/pipeline/scripts/test-gap-rules/android.json

@@ -0,0 +1,25 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "stack": "android",
+  "description": "Android / Jetpack Compose / Kotlin test gap rules. Sources in *.kt; tests under app/src/test/ or app/src/androidTest/.",
+  "sourceExtensions": [".kt", ".java"],
+  "testPathSuffixes": ["Test.kt", "Tests.kt", "Test.java"],
+  "testPathContains": ["/src/test/", "/src/androidTest/", "/test/", "/tests/"],
+  "excludePathGlobs": ["build/", ".gradle/", "generated/", "**/BuildConfig.java", "**/R.java"],
+  "publicApiPatterns": [
+    { "id": "open_class", "regex": "\\bopen\\s+class\\s+([A-Z][A-Za-z0-9_]*)" },
+    { "id": "open_fun", "regex": "\\bopen\\s+fun\\s+([a-z_][A-Za-z0-9_]*)" },
+    { "id": "public_fun", "regex": "^\\s*(?:public\\s+)?fun\\s+([a-z_][A-Za-z0-9_]*)" },
+    { "id": "public_class", "regex": "^\\s*(?:public\\s+)?class\\s+([A-Z][A-Za-z0-9_]*)" },
+    { "id": "jvmstatic", "regex": "@JvmStatic\\b" },
+    { "id": "interface", "regex": "^\\s*(?:public\\s+)?interface\\s+([A-Z][A-Za-z0-9_]*)" }
+  ],
+  "composablePatterns": [
+    {
+      "id": "composable_fun",
+      "regex": "@Composable\\s+(?:public\\s+|internal\\s+)?fun\\s+([A-Z][A-Za-z0-9_]*)"
+    }
+  ],
+  "expectedTestKindsForComposable": ["compose-ui-test"],
+  "hint": "Cover @Composable functions with createComposeRule() + onNodeWithText/Tag/ContentDescription assertions; ViewModels with runTest + Turbine."
+}

package/pipeline/scripts/test-gap-rules/ios.json

@@ -0,0 +1,34 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "stack": "ios",
+  "description": "iOS / SwiftUI / UIKit test gap rules. Source files in *.swift; tests in *Tests.swift. Snapshot/ViewInspector tests are also recognised when the source is a SwiftUI View.",
+  "sourceExtensions": [".swift"],
+  "testPathSuffixes": ["Tests.swift", "Test.swift"],
+  "testPathContains": ["/Tests/", "/UnitTests/", "/SnapshotTests/"],
+  "excludePathGlobs": [
+    "Pods/",
+    "Carthage/",
+    ".build/",
+    "DerivedData/",
+    "Generated/",
+    "Sourcery/",
+    "_Generated.swift",
+    "Tests/Fixtures/"
+  ],
+  "publicApiPatterns": [
+    { "id": "public_func", "regex": "\\bpublic\\s+func\\s+([A-Za-z_][A-Za-z0-9_]*)" },
+    { "id": "public_class", "regex": "\\bpublic\\s+(?:final\\s+)?class\\s+([A-Z][A-Za-z0-9_]*)" },
+    { "id": "public_struct", "regex": "\\bpublic\\s+struct\\s+([A-Z][A-Za-z0-9_]*)" },
+    { "id": "public_enum", "regex": "\\bpublic\\s+enum\\s+([A-Z][A-Za-z0-9_]*)" },
+    { "id": "public_proto", "regex": "\\bpublic\\s+protocol\\s+([A-Z][A-Za-z0-9_]*)" },
+    { "id": "public_init", "regex": "\\bpublic\\s+init\\b" },
+    { "id": "objc_export", "regex": "@objc(?:Members)?\\s+(?:public\\s+)?(?:func|class|var)" }
+  ],
+  "swiftUiViewPatterns": [
+    { "id": "view_struct", "regex": "struct\\s+([A-Z][A-Za-z0-9_]*)\\s*:\\s*View\\b" },
+    { "id": "config_struct", "regex": "struct\\s+([A-Z][A-Za-z0-9_]*Configuration)\\b" }
+  ],
+  "expectedTestKindsForView": ["snapshot", "viewinspector", "unit"],
+  "snapshotPathHints": ["SnapshotTests", "__Snapshots__"],
+  "hint": "Cover with a 3-layer test (structural ViewInspector + snapshot + unit) per swiftui-qa.md."
+}

package/pipeline/scripts/test-gap-rules/node.json

@@ -0,0 +1,29 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "stack": "node",
+  "description": "Node.js / TypeScript test gap rules. Sources in *.ts/*.tsx/*.js/*.mjs; tests in *.test.* / *.spec.* / __tests__/.",
+  "sourceExtensions": [".ts", ".tsx", ".js", ".mjs", ".cjs"],
+  "testPathSuffixes": [
+    ".test.ts",
+    ".test.tsx",
+    ".test.js",
+    ".test.mjs",
+    ".spec.ts",
+    ".spec.tsx",
+    ".spec.js",
+    ".spec.mjs"
+  ],
+  "testPathContains": ["/__tests__/", "/test/", "/tests/"],
+  "excludePathGlobs": ["node_modules/", "dist/", "build/", ".next/", "coverage/", "*.d.ts"],
+  "publicApiPatterns": [
+    {
+      "id": "named_export",
+      "regex": "^export\\s+(?:async\\s+)?(?:function|class|const|let|interface|type|enum)\\s+([A-Za-z_$][A-Za-z0-9_$]*)"
+    },
+    {
+      "id": "default_export",
+      "regex": "^export\\s+default\\s+(?:async\\s+)?(?:function|class)\\s+([A-Za-z_$][A-Za-z0-9_$]*)"
+    }
+  ],
+  "hint": "Cover named exports with vitest/jest test('<name>', ...). React components: React Testing Library (render + screen + userEvent)."
+}

package/pipeline/scripts/test-gap-rules/python.json

@@ -0,0 +1,25 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "stack": "python",
+  "description": "Python test gap rules. Sources in *.py; tests in test_*.py / *_test.py / tests/.",
+  "sourceExtensions": [".py"],
+  "testPathSuffixes": ["_test.py"],
+  "testPathPrefixes": ["test_"],
+  "testPathContains": ["/tests/", "/test/"],
+  "excludePathGlobs": [
+    "__pycache__/",
+    ".venv/",
+    "venv/",
+    ".tox/",
+    "build/",
+    "dist/",
+    "*.egg-info/",
+    "**/migrations/**"
+  ],
+  "publicApiPatterns": [
+    { "id": "top_def", "regex": "^def\\s+([a-z_][a-z0-9_]*)" },
+    { "id": "top_class", "regex": "^class\\s+([A-Z][A-Za-z0-9_]*)" },
+    { "id": "async_def", "regex": "^async\\s+def\\s+([a-z_][a-z0-9_]*)" }
+  ],
+  "hint": "Cover with pytest test_<symbol> style. Async with pytest-asyncio. Avoid name collision with private helpers (prefix _)."
+}

package/pipeline/scripts/test-gap-scan.mjs

@@ -141,6 +141,45 @@ function isExcluded(path) {
   return false;
 }
 
+// git quotes a `diff --git` path (core.quotePath, on by default) whenever it
+// has a non-ASCII byte or other unusual character - e.g. a Turkish filename
+// renders as `diff --git "a/\303\226deme.swift" "b/\303\226deme.swift"`, not
+// the bare a/...b/... form. The plain regex this replaced never matched that
+// line at all, so every non-ASCII-named file's added lines were silently
+// dropped from the test-gap scan.
+const DIFF_GIT_QUOTED_RE = /^diff --git "a\/((?:[^"\\]|\\.)*)" "b\/((?:[^"\\]|\\.)*)"$/;
+const DIFF_GIT_UNQUOTED_RE = /^diff --git a\/(.+?) b\/(.+)$/;
+
+function unquoteGitPath(s) {
+  const bytes = [];
+  for (let i = 0; i < s.length; i++) {
+    if (s[i] === "\\") {
+      const octal = s.slice(i + 1, i + 4);
+      if (/^[0-7]{3}$/.test(octal)) {
+        bytes.push(parseInt(octal, 8));
+        i += 3;
+        continue;
+      }
+      const simple = { "\\": 92, '"': 34, t: 9, n: 10, r: 13 };
+      const next = s[i + 1];
+      if (next in simple) {
+        bytes.push(simple[next]);
+        i += 1;
+        continue;
+      }
+    }
+    bytes.push(s.charCodeAt(i));
+  }
+  return Buffer.from(bytes).toString("utf-8");
+}
+
+function matchDiffGitHeader(line) {
+  const q = line.match(DIFF_GIT_QUOTED_RE);
+  if (q) return unquoteGitPath(q[2]);
+  const u = line.match(DIFF_GIT_UNQUOTED_RE);
+  return u ? u[2] : null;
+}
+
 function isTestPath(path) {
   if (Array.isArray(rules.testPathSuffixes) && rules.testPathSuffixes.some((s) => path.endsWith(s)))
     return true;
@@ -190,9 +229,9 @@ function parseDiffAddedLines(diffText) {
   const perFile = new Map();
   let cur = null;
   for (const line of diffText.split("\n")) {
-    const m = line.match(/^diff --git a\/(.+?) b\/(.+)$/);
-    if (m) {
-      cur = m[2];
+    const p = matchDiffGitHeader(line);
+    if (p !== null) {
+      cur = p;
       if (!perFile.has(cur)) perFile.set(cur, { lines: [], isNew: false });
       continue;
     }
@@ -300,9 +339,9 @@ function symbolMentionedInTest(diffText, symbol) {
   const lines = diffText.split("\n");
   let inTestFile = false;
   for (const line of lines) {
-    const fm = line.match(/^diff --git a\/(.+?) b\/(.+)$/);
-    if (fm) {
-      inTestFile = isTestPath(fm[2]);
+    const fm = matchDiffGitHeader(line);
+    if (fm !== null) {
+      inTestFile = isTestPath(fm);
       continue;
     }
     if (!inTestFile) continue;

package/pipeline/scripts/uninstall.mjs

@@ -35,9 +35,20 @@
  * @module pipeline/scripts/runtime/uninstall
  */
 
-import { existsSync, readdirSync, readFileSync, rmSync, writeFileSync } from "fs";
+import {
+  chmodSync,
+  existsSync,
+  lstatSync,
+  readdirSync,
+  readFileSync,
+  realpathSync,
+  renameSync,
+  rmSync,
+  statSync,
+  writeFileSync,
+} from "fs";
 import { execFileSync } from "child_process";
-import { join } from "path";
+import { join, dirname } from "path";
 import { homedir } from "os";
 import { pathToFileURL } from "url";
 import { createInterface } from "readline";
@@ -100,6 +111,43 @@ const adapterTarget = (() => {
   return raw ? raw.slice("--target=".length) : process.cwd();
 })();
 
+/**
+ * tmp + rename, preserving a symlinked target and the existing file mode.
+ *
+ * Duplicated from install/_common.mjs rather than imported: this script runs
+ * standalone from ~/.claude/scripts, where the install tree does not exist.
+ * A plain writeFileSync could leave the host's settings.json truncated on a
+ * crash; a naive rename would replace a dotfiles symlink with a regular file
+ * and reset a 0600 file to 0644.
+ *
+ * @param {string} path
+ * @param {string} content
+ */
+function atomicWrite(path, content) {
+  let target = path;
+  try {
+    if (lstatSync(path).isSymbolicLink()) target = realpathSync(path);
+  } catch {
+    // Missing file: nothing to preserve.
+  }
+  let mode;
+  try {
+    mode = statSync(target).mode & 0o777;
+  } catch {
+    mode = undefined;
+  }
+  const tmp = `${target}.tmp-${process.pid}`;
+  writeFileSync(tmp, content);
+  if (mode !== undefined) {
+    try {
+      chmodSync(tmp, mode);
+    } catch {
+      // Best effort: a failed chmod must not lose the write.
+    }
+  }
+  renameSync(tmp, target);
+}
+
 /**
  * Report a planned action. Always logged; in --dry-run mode, no side effects
  * are performed.
@@ -197,10 +245,7 @@ function deregisterCodexMcpServer() {
  */
 function deregisterClaudeMcpServer() {
   const localBin = join(homedir(), ".local", "bin", "claude");
-  deregisterMcpServer("claude", existsSync(localBin) ? localBin : undefined, [
-    "--scope",
-    "user",
-  ]);
+  deregisterMcpServer("claude", existsSync(localBin) ? localBin : undefined, ["--scope", "user"]);
 }
 
 /**
@@ -220,6 +265,104 @@ function deregisterCopilotMcpServer() {
  * @param {string} parent
  * @param {(name: string) => boolean} predicate
  */
+/**
+ * Remove the pipeline's command namespace while preserving user-authored
+ * local-only alias wrappers (frontmatter `local-only: true`). Those wrappers
+ * exist ONLY under the host dir - install/claude.mjs snapshots them across its
+ * wipe for the same reason - so removing the namespace wholesale would destroy
+ * content a reinstall can never bring back.
+ * @param {string} cmdDir - e.g. ~/.claude/commands/multi-agent
+ * @returns {number} preserved wrapper dirs
+ */
+function rmCommandsPreservingLocalOnly(cmdDir) {
+  // An install interrupted between its wipe and its restore leaves wrappers in
+  // a hidden stash beside the namespace. Adopt them back before deciding what
+  // to preserve, or the "local-only wrappers preserved" promise below strands
+  // them in a dot-directory the user never sees.
+  const stashDir = join(dirname(cmdDir), ".multi-agent-wrapper-stash");
+  if (existsSync(stashDir) && !dryRun) {
+    for (const name of readdirSync(stashDir)) {
+      const to = join(cmdDir, name);
+      if (existsSync(to)) continue;
+      try {
+        renameSync(join(stashDir, name), to);
+        console.log(`    recovered stashed wrapper from an interrupted install: ${name}`);
+      } catch {
+        /* best effort - a failed recovery must not block the uninstall */
+      }
+    }
+    rmIfExists(stashDir);
+  }
+  if (!existsSync(cmdDir)) return 0;
+  const isLocalOnly = (dir) => {
+    const skill = join(dir, "SKILL.md");
+    try {
+      return existsSync(skill) && /^local-only:\s*true\s*$/m.test(readFileSync(skill, "utf-8"));
+    } catch {
+      return false;
+    }
+  };
+  const preserved = readdirSync(cmdDir, { withFileTypes: true })
+    .filter((e) => e.isDirectory() && isLocalOnly(join(cmdDir, e.name)))
+    .map((e) => e.name);
+  if (preserved.length === 0) {
+    rmIfExists(cmdDir);
+    return 0;
+  }
+  for (const entry of readdirSync(cmdDir)) {
+    if (preserved.includes(entry)) continue;
+    rmIfExists(join(cmdDir, entry));
+  }
+  console.log(
+    `    preserved ${preserved.length} local-only alias wrapper(s): ${preserved.join(", ")}`,
+  );
+  return preserved.length;
+}
+
+/** Written by install/_platform-filter.mjs beside the skills it delivered. */
+const EXTERNAL_SKILLS_MANIFEST = ".external-skills-manifest.json";
+
+/**
+ * Remove the external skill catalog THIS install delivered, read from the
+ * manifest the installer wrote beside it.
+ *
+ * Deliberately not derived from `.skills-index.json`: that file is the shipped
+ * catalog copied verbatim, so it lists platform-filtered skills that were never
+ * installed, and it says nothing about which package version's tree is on disk.
+ * Either gap would delete a user-authored skill dir that happens to share a
+ * catalog name. Same contract as `.plugin-skills-manifest.json`.
+ *
+ * No manifest (a pre-manifest install) means ours and theirs are
+ * indistinguishable, so nothing is removed and the user is told why.
+ *
+ * @param {string} skillsDir
+ * @returns {number} dirs removed
+ */
+function rmExternalDeliveredSkills(skillsDir) {
+  if (!existsSync(skillsDir)) return 0;
+  const manifestPath = join(skillsDir, EXTERNAL_SKILLS_MANIFEST);
+  let names = null;
+  if (existsSync(manifestPath)) {
+    try {
+      const parsed = JSON.parse(readFileSync(manifestPath, "utf-8"));
+      if (Array.isArray(parsed)) names = new Set(parsed);
+    } catch {
+      names = null;
+    }
+  }
+  if (!names) {
+    console.log(
+      `    note: no ${EXTERNAL_SKILLS_MANIFEST} under ${skillsDir} - external skill dirs left in ` +
+        `place (cannot tell pipeline-delivered from user-authored; re-run install once, then uninstall)`,
+    );
+    return 0;
+  }
+  let n = rmMatchingDirs(skillsDir, (name) => names.has(name));
+  n += rmMatchingFiles(skillsDir, (name) => /^NOTICE-.*\.md$/.test(name));
+  rmIfExists(manifestPath);
+  return n;
+}
+
 function rmMatchingDirs(parent, predicate) {
   if (!existsSync(parent)) return 0;
   let count = 0;
@@ -248,6 +391,31 @@ function rmMatchingFiles(parent, predicate) {
   return count;
 }
 
+// Copilot CLI / Codex CLI have no plugin loader, so install/_plugin-skills.mjs
+// copies each stack plugin's authored skills straight into the flat skills/
+// dir (~100 dirs across a typical set of enabled plugins). None of those
+// names are in PIPELINE_CORE_SKILL_DIRS - the allowlist above only covers the
+// pipeline's OWN skills - so they were never removed on uninstall. The
+// installer now writes PLUGIN_SKILLS_MANIFEST listing exactly what it
+// delivered; read it back here rather than guessing plugin skill names.
+const PLUGIN_SKILLS_MANIFEST = ".plugin-skills-manifest.json";
+
+function rmPluginDeliveredSkills(skillsDir) {
+  const manifestPath = join(skillsDir, PLUGIN_SKILLS_MANIFEST);
+  if (!existsSync(manifestPath)) return 0;
+  let names;
+  try {
+    names = JSON.parse(readFileSync(manifestPath, "utf-8"));
+  } catch {
+    return 0;
+  }
+  if (!Array.isArray(names)) return 0;
+  const nameSet = new Set(names);
+  const count = rmMatchingDirs(skillsDir, (name) => nameSet.has(name));
+  rmIfExists(manifestPath);
+  return count;
+}
+
 // Explicit terminator install/copilot.mjs writes after the pipeline section
 // (v11.4.1+). Must stay in sync with INSTRUCTIONS_END_MARKER there.
 const COPILOT_END_MARKER = "<!-- multi-agent-pipeline:copilot-instructions:end -->";
@@ -339,7 +507,7 @@ function stripManagedBlock(filePath) {
           rmSync(filePath, { force: true });
           console.log(`    removed (was pipeline-only): ${filePath}`);
         } else {
-          writeFileSync(filePath, remaining + "\n");
+          atomicWrite(filePath, remaining + "\n");
           console.log(`    cleaned pipeline section: ${filePath}`);
         }
         return true;
@@ -356,7 +524,7 @@ function stripManagedBlock(filePath) {
     rmSync(filePath, { force: true });
     console.log(`    removed (was pipeline-only): ${filePath}`);
   } else {
-    writeFileSync(filePath, cleaned + "\n");
+    atomicWrite(filePath, cleaned + "\n");
     console.log(`    cleaned pipeline block from: ${filePath}`);
   }
   return true;
@@ -387,13 +555,21 @@ function cleanClaudeSettings(settingsPath) {
   if (settings.hooks?.PreToolUse?.length) {
     const before = settings.hooks.PreToolUse.length;
     // Match both the current matcher ("Bash") and the dead pre-v11.4.1 one
-    // ("Bash(git commit:*)"); the pre-commit-check.sh command identifies the
-    // entry as ours either way.
+    // ("Bash(git commit:*)"); the command identifies the entry as ours either
+    // way. install/claude.mjs registers TWO PreToolUse gates this way -
+    // pre-commit-check.sh AND agent-guard.sh - and only the first was ever
+    // stripped here. After ~/.claude/scripts/ is deleted below, the
+    // agent-guard.sh entry pointed at a script that no longer existed, so
+    // every subsequent Bash call fired a hook error.
     settings.hooks.PreToolUse = settings.hooks.PreToolUse.filter(
       (h) =>
         !(
           (h.matcher === "Bash" || h.matcher === "Bash(git commit:*)") &&
-          h.hooks?.some((sub) => sub.command?.includes("pre-commit-check.sh"))
+          h.hooks?.some(
+            (sub) =>
+              sub.command?.includes("pre-commit-check.sh") ||
+              sub.command?.includes("agent-guard.sh"),
+          )
         ),
     );
     if (settings.hooks.PreToolUse.length < before) touched = true;
@@ -405,7 +581,7 @@ function cleanClaudeSettings(settingsPath) {
     if (dryRun) {
       report("would update", settingsPath);
     } else {
-      writeFileSync(settingsPath, JSON.stringify(settings, null, 2) + "\n");
+      atomicWrite(settingsPath, JSON.stringify(settings, null, 2) + "\n");
       console.log(`    cleaned pipeline hook + env from: ${settingsPath}`);
     }
   }
@@ -465,6 +641,7 @@ export async function main() {
   );
   console.log("    - ~/.claude/CLAUDE.md (your customizations)");
   console.log("    - ~/.claude/rules/ (user-owned; installed write-if-missing, never overwritten)");
+  console.log("    - Local-only alias wrappers under commands/multi-agent/ (user-authored)");
   if (!allData) console.log("    - ~/.claude/multi-agent-preferences.json (your settings)");
   console.log("    - Your own content in copilot-instructions.md above the pipeline section");
   console.log("");
@@ -479,7 +656,7 @@ export async function main() {
     console.log("  [Claude Code] Removing...");
     deregisterClaudeMcpServer();
     const CLAUDE = join(HOME, ".claude");
-    rmIfExists(join(CLAUDE, "commands", "multi-agent"));
+    rmCommandsPreservingLocalOnly(join(CLAUDE, "commands", "multi-agent"));
     rmIfExists(join(CLAUDE, "scripts"));
     // Pipeline-managed trees the installer lays down alongside scripts/.
     rmIfExists(join(CLAUDE, "multi-agent-refs"));
@@ -506,6 +683,7 @@ export async function main() {
         name === "figma-to-component",
     );
     n += rmMatchingDirs(skills, (name) => PIPELINE_CORE_SKILL_DIRS.includes(name));
+    n += rmExternalDeliveredSkills(skills);
     if (n > 0) console.log(`    removed ${n} skill dir(s) under ${skills}`);
     rmIfExists(join(skills, ".skills-index.json"));
     rmIfExists(join(skills, "skills-index.md"));
@@ -540,10 +718,13 @@ export async function main() {
         name === "figma-to-component",
     );
     n += rmMatchingDirs(skills, (name) => PIPELINE_CORE_SKILL_DIRS.includes(name));
+    n += rmPluginDeliveredSkills(skills);
+    n += rmExternalDeliveredSkills(skills);
     if (n > 0) console.log(`    removed ${n} skill dir(s) under ${skills}`);
     rmIfExists(join(skills, ".skills-index.json"));
     rmIfExists(join(skills, "skills-index.md"));
     rmIfExists(join(skills, "README.md"));
+    rmIfExists(join(COP, "rules"));
     // Agent definitions are FILES; remove only the pipeline-shipped names so
     // user-authored agents survive.
     rmMatchingFiles(join(COP, "agents"), (name) => PIPELINE_AGENT_FILES.includes(name));
@@ -613,10 +794,11 @@ export async function main() {
     // Codex's own `.system` set plus user skills; `prompts/` and `agents/` hold
     // user-authored files.
     const skills = join(CODEX, "skills");
-    const n = rmMatchingDirs(
+    let n = rmMatchingDirs(
       skills,
       (name) => name === "multi-agent" || name.startsWith("multi-agent-"),
     );
+    n += rmPluginDeliveredSkills(skills);
     if (n > 0) console.log(`    removed ${n} skill dir(s) under ${skills}`);
     rmIfExists(join(CODEX, "prompts", "multi-agent.md"));
     removeGeneratedCodexAgents(join(CODEX, "agents"));

package/pipeline/scripts/update-issue-progress.sh

@@ -14,8 +14,8 @@
 #   update-issue-progress.sh <task-id>
 #
 # Inputs:
-#   $HOME/.claude/projects/{slug}/state/{taskId}/agent-state.json
-#     .issue.url, .issue.number, .repos.primary.org, .repos.primary.name
+#   $HOME/.claude/logs/multi-agent/{project}/{taskId}/agent-state.json
+#     .githubIssue.owner, .githubIssue.repo, .githubIssue.number
 #     .flags.implementation, .flags.testing, .flags.codeConnect, .flags.wiki
 #
 # Side effects:
@@ -86,11 +86,12 @@ if [ "$TASK_ID" = "--rewrite" ]; then
   exit 0
 fi
 
-# Resolve the project state directory (matches phase-tracker convention).
-STATE_GLOB="$HOME/.claude/projects/*"
+# Resolve agent-state.json. multi-repo-pipeline.sh writes it under a
+# per-project directory ($HOME/.claude/logs/multi-agent/{project}/{taskId}/)
+# - not the ~/.claude/projects/*/state/ path this used to glob, which no
+# writer in the pipeline ever populates.
 AGENT_STATE=""
-for dir in $STATE_GLOB; do
-  candidate="$dir/state/$TASK_ID/agent-state.json"
+for candidate in "$HOME"/.claude/logs/multi-agent/*/"$TASK_ID"/agent-state.json; do
   if [ -f "$candidate" ]; then
     AGENT_STATE="$candidate"
     break
@@ -102,18 +103,13 @@ if [ -z "$AGENT_STATE" ]; then
   exit 2
 fi
 
-ISSUE_URL=$(jq -r '.issue.url // empty' "$AGENT_STATE")
-ISSUE_NUM=$(jq -r '.issue.number // empty' "$AGENT_STATE")
-ORG_REPO=$(jq -r '.repos.primary.name // empty' "$AGENT_STATE")
-# Derive org/repo from URL if not present in state.
-if [ -z "$ORG_REPO" ] || ! [[ "$ORG_REPO" == */* ]]; then
-  if [[ "$ISSUE_URL" =~ github\.com/([^/]+/[^/]+)/issues/ ]]; then
-    ORG_REPO="${BASH_REMATCH[1]}"
-  fi
-fi
+# agent-state.schema.json has no `.issue`/`.repos` properties (additionalProperties
+# is false) - the real GitHub-issue coordinates live at `.githubIssue.{owner,repo,number}`.
+ISSUE_NUM=$(jq -r '.githubIssue.number // empty' "$AGENT_STATE")
+ORG_REPO=$(jq -r 'if .githubIssue then (.githubIssue.owner + "/" + .githubIssue.repo) else empty end' "$AGENT_STATE")
 
 if [ -z "$ORG_REPO" ] || [ -z "$ISSUE_NUM" ]; then
-  echo "update-issue-progress: cannot resolve org/repo or issue number from state" >&2
+  echo "update-issue-progress: no githubIssue in state for task=$TASK_ID (Jira-originated task, or issue not yet linked)" >&2
   exit 3
 fi