@astryxdesign/cli 0.7.2 → 0.7.3-canary.06872b4

package/foundation/agent-docs/agent-docs.mjs

@@ -3,26 +3,39 @@
 /**
  * @file agent-docs — Install/update agent docs for AI coding tools
  *
- * Generates a CLI cheat sheet from actual command metadata and injects
- * it into agent doc files. Supports multiple tools with auto-detection:
+ * Generates a CLI cheat sheet from actual command metadata and writes it, as
+ * one managed block, into the files AI coding tools read.
  *
- * - Claude Code: CLAUDE.md (root) or .claude/CLAUDE.md
- * - Cursor: .cursorrules
- * - Codex/generic: AGENTS.md
- * - Muse: AGENTS.md
- * - Hermes Agent: .hermes.md or HERMES.md (existing), else AGENTS.md
+ * Default (no --agent or --agent-docs-path): every agent reads the block, in a
+ * file the project commits.
  *
- * Auto-detect: discovers existing files and updates them in place.
- * Default (no existing files): creates AGENTS.md (the tool-agnostic standard).
+ * - AGENTS.md holds the block. Most agents read it; Claude Code reads it when
+ *   the folder has no CLAUDE.md or .claude/CLAUDE.md.
+ * - The Claude Code file the project already has holds a copy: root CLAUDE.md,
+ *   else .claude/CLAUDE.md, even when it imports AGENTS.md, because Claude Code
+ *   does not follow that import from a subfolder. Init creates no Claude file.
+ * - Gemini CLI reads only GEMINI.md: it gets a managed import, `@./AGENTS.md`,
+ *   created when missing, unless GEMINI.md already imports AGENTS.md. Project
+ *   settings that point Gemini at AGENTS.md don't replace it: Gemini loads them
+ *   only when it starts at the project root.
+ * - Existing Cursor (.cursorrules) and Hermes (.hermes.md, HERMES.md) files
+ *   keep a full block.
+ *
+ * No mode writes into the home folder, or into a settings folder in it outside a
+ * project: agents read the files there in every project. A project inside a
+ * settings folder, such as an agent worktree, is written normally.
  *
  * --agent <tool>: target a specific tool preset (claude, cursor, codex, hermes, muse, all)
  * --agent-docs-path <path>: explicit file path(s)
  */
 
+import {spawnSync} from 'node:child_process';
 import * as fs from 'node:fs';
+import * as os from 'node:os';
 import * as path from 'node:path';
 import {findCoreDir, CLI_ROOT} from '../fs/paths.mjs';
 import {assertWithin, PathSafetyError} from '../fs/path-safety.mjs';
+import {createFileProtectionResolver} from '../fs/file-protection.mjs';
 import {getCliInvocation} from '../env/package-manager.mjs';
 import {discoverComponents} from '../discovery/component-discovery.mjs';
 import {Project} from '../config/project.mjs';
@@ -31,9 +44,11 @@ import {humanLog} from '../response/json.mjs';
 import {ERROR_CODES} from '../response/error-codes.mjs';
 import {
   AGENTS_MD,
+  AGENT_DOC_PATHS,
   CLAUDE_MD,
   CLAUDE_DIR_MD,
   CURSOR_RULES,
+  GEMINI_MD,
   HERMES_DOT_MD,
   HERMES_MD,
   MARKER_START,
@@ -80,27 +95,26 @@ function validateIntegrationLabel(value) {
 }
 
 /**
- * Find tool-specific files that import another detected agent doc.
- *
- * Claude's `@path` directive is a real include, so injecting the full managed
- * block beside it duplicates the same instructions. Only an import whose
- * normalized target is another known agent doc counts; prose mentions and
- * standalone files keep the normal initialization behavior. Import cycles have
- * no canonical owner, so their members also stay standalone.
+ * The `@path` imports of other agent docs in each agent doc. Only an import
+ * whose normalized target is another known agent doc counts; prose mentions do
+ * not. Lines inside the managed block are Astryx's own (the default writes an
+ * import of AGENTS.md there), so they never count as the project's import.
  *
  * @param {string} targetDir
  * @param {string[]} agentDocs
- * @returns {Set<string>}
+ * @param {string[]} [extraTargets] Import targets that count even though they
+ *   do not exist yet (the default always writes AGENTS.md).
+ * @returns {Map<string, Set<string>>} each importing doc and the docs it imports.
  */
-function discoverAgentDocWrappers(targetDir, agentDocs) {
-  const known = new Set(agentDocs.map(p => path.normalize(p)));
+function readAgentDocImports(targetDir, agentDocs, extraTargets = []) {
+  const known = new Set([...agentDocs, ...extraTargets].map(p => path.normalize(p)));
   /** @type {Map<string, Set<string>>} */
   const imports = new Map();
 
   for (const rel of agentDocs) {
     let content;
     try {
-      content = fs.readFileSync(path.join(targetDir, rel), 'utf-8');
+      content = withoutManagedBlock(fs.readFileSync(path.join(targetDir, rel), 'utf-8'));
     } catch {
       continue;
     }
@@ -116,7 +130,21 @@ function discoverAgentDocWrappers(targetDir, agentDocs) {
     }
     if (targets.size > 0) imports.set(rel, targets);
   }
+  return imports;
+}
 
+/**
+ * Find tool-specific files that import another detected agent doc.
+ *
+ * Claude's `@path` directive is a real include, so injecting the full managed
+ * block beside it duplicates the same instructions. Standalone files keep the
+ * normal initialization behavior. Import cycles have no canonical owner, so
+ * their members also stay standalone.
+ *
+ * @param {Map<string, Set<string>>} imports From {@link readAgentDocImports}.
+ * @returns {Map<string, Set<string>>} each wrapper and the agent docs it imports.
+ */
+function findAgentDocWrappers(imports) {
   /** @param {string} start */
   const isCyclic = start => {
     /**
@@ -135,7 +163,7 @@ function discoverAgentDocWrappers(targetDir, agentDocs) {
     return visit(start, new Set([start]));
   };
 
-  return new Set([...imports.keys()].filter(rel => !isCyclic(rel)));
+  return new Map([...imports].filter(([rel]) => !isCyclic(rel)));
 }
 
 /**
@@ -177,6 +205,295 @@ function findManagedBlock(content) {
   return null;
 }
 
+/**
+ * `content` with its managed block cut out. A malformed block is left in
+ * place; the writers refuse it later.
+ * @param {string} content
+ * @returns {string}
+ */
+function withoutManagedBlock(content) {
+  try {
+    const block = findManagedBlock(content);
+    return block ? content.slice(0, block.start) + content.slice(block.end) : content;
+  } catch {
+    return content;
+  }
+}
+
+/**
+ * The managed one-line import of AGENTS.md that the default writes, keyed by
+ * file. Gemini CLI reads only GEMINI.md, and expands `@./AGENTS.md` there.
+ *
+ * @type {Readonly<Record<string, string>>}
+ */
+const AGENTS_IMPORTS = Object.freeze({
+  [GEMINI_MD]: '@./AGENTS.md',
+});
+
+/**
+ * Agent docs 0.7.0 already wrote. A path-safety refusal on one of them stays an
+ * error, as it was; a file only the current layout writes is skipped instead.
+ */
+const LEGACY_DOC_PATHS = AGENT_DOC_PATHS.filter(p => p !== GEMINI_MD);
+
+/**
+ * The managed block holding the import of AGENTS.md for `rel`.
+ * @param {string} rel A key of {@link AGENTS_IMPORTS}.
+ * @returns {string}
+ */
+function renderAgentsImportBlock(rel) {
+  return `${MARKER_START}\n${AGENTS_IMPORTS[rel]}\n${MARKER_END}`;
+}
+
+/**
+ * Whether the managed block in `content` holds only an import of the root
+ * AGENTS.md, resolved from the folder of `rel`. Such a block names no version,
+ * so it stays current while it points at AGENTS.md.
+ * @param {string} rel Project-relative path of the file `content` came from.
+ * @param {string} content
+ * @returns {boolean}
+ */
+function isAgentsImportBlock(rel, content) {
+  let block;
+  try {
+    block = findManagedBlock(content);
+  } catch {
+    return false;
+  }
+  if (block == null) return false;
+  const text = content.slice(block.start, block.end);
+  const inner = text.slice(text.indexOf('-->') + 3, text.lastIndexOf('<!--')).trim();
+  const match = /^@(\S+)$/.exec(inner);
+  if (match == null || path.isAbsolute(match[1])) return false;
+  return path.normalize(path.join(path.dirname(rel), match[1])) === AGENTS_MD;
+}
+
+/**
+ * The paths Gemini CLI imports from `content`, in order. Gemini reads `@path`
+ * where the `@` starts the text or follows whitespace, and the path runs to the
+ * next whitespace and starts with `.`, `/` or a letter. An `@` inside backticks
+ * (inline code or a fenced block) is not an import.
+ * @param {string} content
+ * @returns {string[]}
+ */
+function findGeminiImports(content) {
+  /** @type {Array<[number, number]>} */
+  const code = [];
+  for (const match of content.matchAll(/(`+)[\s\S]*?\1/g)) {
+    code.push([match.index, match.index + match[0].length]);
+  }
+  /** @type {string[]} */
+  const found = [];
+  for (const match of content.matchAll(/(?<=^|[ \t\r\n])@([^ \t\r\n]+)/g)) {
+    if (!/^[./A-Za-z]/.test(match[1])) continue;
+    if (code.some(([start, end]) => match.index >= start && match.index < end)) {
+      continue;
+    }
+    found.push(match[1]);
+  }
+  return found;
+}
+
+/**
+ * Whether GEMINI.md, outside Astryx's managed block, already has Gemini CLI
+ * import AGENTS.md, on a line of its own or inline in a sentence.
+ * @param {string} targetDir
+ * @returns {boolean}
+ */
+function geminiImportsAgentsMd(targetDir) {
+  let content;
+  try {
+    content = fs.readFileSync(path.join(targetDir, GEMINI_MD), 'utf-8');
+  } catch {
+    return false;
+  }
+  const agents = path.resolve(targetDir, AGENTS_MD);
+  return findGeminiImports(withoutManagedBlock(content)).some(
+    rel => path.resolve(targetDir, rel) === agents,
+  );
+}
+
+/**
+ * Thrown when agent docs would be written into the home folder, or into a
+ * settings folder in it such as `~/.gemini` outside a project. Agents read the
+ * files there (for example `~/.claude/CLAUDE.md` or `~/.gemini/GEMINI.md`) in
+ * every project, so a project's version-pinned block never goes there. Removal
+ * stays allowed.
+ */
+export class AgentDocsHomeError extends Error {
+  /** @param {string} dir */
+  constructor(dir) {
+    super(
+      `Agent docs are not written into the home folder, or into a settings folder in it outside a project (${dir}): agents read the files there in every project. Run init inside a project folder.`,
+    );
+    this.name = 'AgentDocsHomeError';
+    /** The refused folder. */
+    this.dir = dir;
+  }
+}
+
+/**
+ * `p` resolved, through symlinks when it exists.
+ * @param {string} p
+ * @returns {string}
+ */
+function realDir(p) {
+  try {
+    return fs.realpathSync(path.resolve(p));
+  } catch {
+    return path.resolve(p);
+  }
+}
+
+/**
+ * `dir` relative to the home folder, compared without symlinks (and without
+ * case on Windows). null when there is no home folder.
+ * @param {string} dir
+ * @returns {string | null}
+ */
+function relativeToHome(dir) {
+  let home;
+  try {
+    home = os.homedir();
+  } catch {
+    return null;
+  }
+  if (!home) return null;
+  /** @param {string} p */
+  const fold = p => (process.platform === 'win32' ? p.toLowerCase() : p);
+  return path.relative(fold(realDir(home)), fold(realDir(dir)));
+}
+
+/**
+ * Whether `dir` is the home folder.
+ * @param {string} dir
+ * @returns {boolean}
+ */
+function isHomeFolder(dir) {
+  return relativeToHome(dir) === '';
+}
+
+/**
+ * Whether agent docs stay out of `dir`: the home folder, or a folder in a
+ * settings folder of it (a folder of the home folder whose name starts with a
+ * dot, such as `~/.gemini` or `~/.claude`) that belongs to no project there.
+ * Agents read the files at the top of a settings folder in every project, so
+ * the settings folder itself is never a project, even with a package.json. A
+ * folder below it with a package.json at or above it is a project, such as an
+ * agent worktree in `~/.codex/worktrees/<id>/<repo>`.
+ * @param {string} dir
+ * @returns {boolean}
+ */
+function isHomeOrSettingsFolder(dir) {
+  const rel = relativeToHome(dir);
+  if (rel == null) return false;
+  if (rel === '') return true;
+  if (rel === '..' || rel.startsWith(`..${path.sep}`) || path.isAbsolute(rel)) {
+    return false;
+  }
+  const parts = rel.split(path.sep);
+  if (!parts[0].startsWith('.')) return false;
+  // Look for a package.json from `dir` up to, not including, the settings folder.
+  let current = realDir(dir);
+  for (let depth = parts.length; depth > 1; depth--) {
+    if (fs.existsSync(path.join(current, 'package.json'))) return false;
+    current = path.dirname(current);
+  }
+  return true;
+}
+
+/**
+ * Throw {@link AgentDocsHomeError} when `targetDir` is the home folder, or a
+ * settings folder in it outside a project.
+ * @param {string} targetDir
+ */
+export function assertAgentDocsTarget(targetDir) {
+  if (isHomeOrSettingsFolder(targetDir)) throw new AgentDocsHomeError(realDir(targetDir));
+}
+
+/** Folders that mark a repository root; the project search stops there. */
+const REPOSITORY_MARKERS = ['.git', '.hg', '.sl'];
+
+/** Dependency fields where a project declares the Astryx packages it uses. */
+const DEPENDENCY_FIELDS = [
+  'dependencies',
+  'devDependencies',
+  'peerDependencies',
+  'optionalDependencies',
+];
+
+/**
+ * The package.json in `dir`: its parsed content, `null` when it exists but
+ * does not parse, or `undefined` when there is none.
+ * @param {string} dir
+ * @returns {Record<string, unknown> | null | undefined}
+ */
+function readPackageJson(dir) {
+  const file = path.join(dir, 'package.json');
+  if (!fs.existsSync(file)) return undefined;
+  try {
+    const parsed = JSON.parse(fs.readFileSync(file, 'utf-8'));
+    return parsed && typeof parsed === 'object' ? parsed : null;
+  } catch {
+    return null;
+  }
+}
+
+/**
+ * Whether a parsed package.json declares an `@astryxdesign` package.
+ * @param {Record<string, unknown> | null} manifest
+ * @returns {boolean}
+ */
+function declaresAstryx(manifest) {
+  return DEPENDENCY_FIELDS.some(field => {
+    const deps = manifest?.[field];
+    return (
+      deps != null &&
+      typeof deps === 'object' &&
+      Object.keys(deps).some(name => name.startsWith('@astryxdesign/'))
+    );
+  });
+}
+
+/**
+ * The folder a run started in `cwd` writes agent docs to: the nearest folder at
+ * or above it whose package.json declares an `@astryxdesign` package, else the
+ * nearest folder with any package.json. The search stops at a repository root
+ * and never reaches the home folder, so a stray `~/package.json` cannot pull
+ * the docs there.
+ * @param {string} cwd
+ * @returns {string | null} null when no folder it searches has a package.json;
+ *   init then writes where it runs, as before.
+ */
+export function resolveAgentDocsRoot(cwd) {
+  let dir = path.resolve(cwd);
+  /** @type {string | null} */
+  let nearest = null;
+  for (let i = 0; i < 50 && !isHomeFolder(dir); i++) {
+    const manifest = readPackageJson(dir);
+    if (manifest !== undefined) {
+      if (declaresAstryx(manifest)) return dir;
+      nearest ??= dir;
+    }
+    if (REPOSITORY_MARKERS.some(marker => fs.existsSync(path.join(dir, marker)))) break;
+    const parent = path.dirname(dir);
+    if (parent === dir) break;
+    dir = parent;
+  }
+  return nearest;
+}
+
+/**
+ * The folder `init` run in `cwd` writes the agent docs to: the project root
+ * {@link resolveAgentDocsRoot} finds, else `cwd` itself. The one definition
+ * that init, its removal, and the per-command setup nudge all use.
+ * @param {string} cwd
+ * @returns {string}
+ */
+export function agentDocsTargetDir(cwd) {
+  return resolveAgentDocsRoot(cwd) ?? cwd;
+}
+
 /**
  * Agent tool presets — maps tool names to their file search paths.
  * Order matters: first existing file wins, last entry is the default (created if none exist).
@@ -215,6 +532,8 @@ export function parseBlockVersion(content) {
  * - `current` — every managed block already matches the installed version.
  * And the project is `missing` when no managed block exists anywhere (the repo
  * has agent-doc files without our markers, or none at all — i.e. never `init`ed).
+ * A managed import of AGENTS.md is not a block here: it names no version and
+ * stays current while AGENTS.md holds the block.
  *
  * @param {string} targetDir
  * @param {string} [installedVersion] Defaults to the installed core version.
@@ -244,6 +563,8 @@ export function inspectAgentDocs(targetDir, installedVersion, expectedBlock) {
     const hasNew = content.includes(MARKER_START);
     const hasLegacy = content.includes(LEGACY_MARKER_START);
     if (!hasNew && !hasLegacy) continue; // Not a block we manage.
+    // An import of AGENTS.md names no version and never needs a refresh.
+    if (isAgentsImportBlock(rel, content)) continue;
 
     const legacy = !hasNew && hasLegacy;
     const blockVersion = parseBlockVersion(content);
@@ -291,8 +612,11 @@ export function inspectAgentDocs(targetDir, installedVersion, expectedBlock) {
  */
 export function resolveAgentPaths(targetDir, agent) {
   if (agent === 'all') {
-    // Inject into all existing files, create defaults for each tool
-    const existing = discoverAgentDocs(targetDir);
+    // Every existing agent doc gets the block, except GEMINI.md, which keeps
+    // the one-line import of AGENTS.md the default writes. When CLAUDE.md is
+    // among them, installAgentDocs then removes the block from
+    // .claude/CLAUDE.md, unless the project ignores CLAUDE.md (INV31).
+    const existing = discoverAgentDocs(targetDir).filter(p => p !== GEMINI_MD);
     if (existing.length > 0) {
       return {inject: existing, create: []};
     }
@@ -700,14 +1024,16 @@ export function injectClaudeMd(targetDir, version) {
 }
 
 /**
- * Remove Astryx section from a file.
- * If the file becomes empty (only boilerplate header remains), deletes it.
+ * Remove the Astryx-managed block, between its markers, from a file, leaving
+ * every other line as it is. With `deleteIfEmpty`, the file is deleted when
+ * nothing is left but whitespace or the exact heading init writes into a file
+ * it creates; with `deleteIfBlank`, only when nothing but whitespace is left.
  *
  * @param {string} filePath
- * @param {{deleteIfEmpty?: boolean}} [options]
+ * @param {{deleteIfEmpty?: boolean, deleteIfBlank?: boolean}} [options]
  * @returns {boolean} Whether the Astryx section was found and removed
  */
-export function removeXdsBlock(filePath, {deleteIfEmpty = false} = {}) {
+export function removeXdsBlock(filePath, {deleteIfEmpty = false, deleteIfBlank = false} = {}) {
   if (!fs.existsSync(filePath)) return false;
 
   let content = fs.readFileSync(filePath, 'utf-8');
@@ -719,18 +1045,198 @@ export function removeXdsBlock(filePath, {deleteIfEmpty = false} = {}) {
   const after = content.slice(block.end).trimStart();
   content = before + (after ? '\n\n' + after : '') + '\n';
 
-  if (deleteIfEmpty) {
-    const stripped = content.replace(/^#.*\n+.*guidance.*\n*/m, '').trim();
-    if (!stripped) {
-      fs.unlinkSync(filePath);
-      return true;
-    }
+  const rest = content.trim();
+  if (
+    (deleteIfBlank && rest === '') ||
+    (deleteIfEmpty && (rest === '' || CREATED_HEADING.test(rest)))
+  ) {
+    fs.unlinkSync(filePath);
+    return true;
   }
 
   fs.writeFileSync(filePath, content);
   return true;
 }
 
+/**
+ * The whole of a file init created, once its block is gone: the heading init
+ * writes, `# <name>` and its one line, and nothing else.
+ */
+const CREATED_HEADING =
+  /^# [^\n]+\n\nProject-specific guidance for AI coding agents\.$/u;
+
+/**
+ * Whether the project's ignore rules exclude root CLAUDE.md, read with the
+ * working-tree ignore reader upgrade uses, from the repository root down to
+ * the project root. It decides only where the copy
+ * goes (a fresh clone lacks an ignored file); the managed block is written
+ * whatever the ignore rules say (INV31). An ignore file that cannot be read
+ * counts as excluding root CLAUDE.md, so the copy in .claude/CLAUDE.md stays.
+ * @param {string} targetDir
+ * @returns {boolean}
+ */
+function rootClaudeIgnored(targetDir) {
+  return uncommittedHere(targetDir, CLAUDE_MD, true);
+}
+
+/**
+ * Whether a fresh clone lacks `rel` in `targetDir`: it is untracked and
+ * ignored. Inside a repository the repository answers, with every ignore
+ * source it reads (its ignore files, its local exclude file and configured
+ * excludes), and a tracked file is committed whatever they say, as git and
+ * Mercurial ignore only untracked files. Outside one, the project's ignore
+ * files answer. `unreadable` is the answer when the repository, or an ignore
+ * file, cannot answer.
+ * @param {string} targetDir
+ * @param {string} rel
+ * @param {boolean} unreadable
+ * @returns {boolean}
+ */
+function uncommittedHere(targetDir, rel, unreadable) {
+  const root = repositoryRootOf(targetDir);
+  if (!root) return ignoredHere(targetDir, rel, unreadable);
+  return untrackedIgnored(root, targetDir, rel) ?? unreadable;
+}
+
+/**
+ * How each repository kind lists `rel` when it is untracked and ignored:
+ * `git check-ignore` exits 0 for such a file and 1 otherwise (it never
+ * reports a tracked file); `status -i -n` prints it, or nothing.
+ */
+const IGNORED_QUERIES = [
+  {marker: '.git', command: 'git', args: ['check-ignore', '-q', '--'], by: 'exit'},
+  {marker: '.sl', command: 'sl', args: ['status', '-i', '-n', '--'], by: 'output'},
+  {marker: '.hg', command: 'hg', args: ['status', '-i', '-n', '--'], by: 'output'},
+];
+
+/**
+ * Whether the repository at `root` holds `rel` in `targetDir` as untracked
+ * and ignored; null, which keeps the copy, when it cannot answer: its tool is
+ * not installed or cannot start, runs past the time limit, or exits with a
+ * code other than its documented answers.
+ * @param {string} root
+ * @param {string} targetDir
+ * @param {string} rel
+ * @returns {boolean | null}
+ */
+function untrackedIgnored(root, targetDir, rel) {
+  const query = IGNORED_QUERIES.find(q => fs.existsSync(path.join(root, q.marker)));
+  if (!query) return null;
+  const result = spawnSync(query.command, [...query.args, rel], {
+    cwd: targetDir,
+    encoding: 'utf-8',
+    stdio: ['ignore', 'pipe', 'ignore'],
+    timeout: 10_000,
+    windowsHide: true,
+    shell: false,
+  });
+  if (result.error) return null;
+  if (query.by === 'exit') {
+    if (result.status === 0) return true;
+    if (result.status === 1) return false;
+    return null;
+  }
+  if (result.status !== 0) return null;
+  return result.stdout.trim() !== '';
+}
+
+/**
+ * Whether the ignore files in `targetDir` exclude `rel`, read with the
+ * working-tree ignore reader upgrade uses; for a folder outside any
+ * repository. `unreadable` when an ignore file cannot be read.
+ * @param {string} targetDir
+ * @param {string} rel
+ * @param {boolean} unreadable
+ * @returns {boolean}
+ */
+function ignoredHere(targetDir, rel, unreadable) {
+  try {
+    return createFileProtectionResolver(targetDir)
+      .classify(path.join(targetDir, rel))
+      .some(item => item.reason === 'ignored');
+  } catch {
+    return unreadable;
+  }
+}
+
+/**
+ * The repository root at or above `dir`: the nearest folder holding `.git`,
+ * `.hg`, or `.sl`. Null outside a repository.
+ * @param {string} dir
+ * @returns {string | null}
+ */
+function repositoryRootOf(dir) {
+  for (let current = path.resolve(dir); ; ) {
+    if (REPOSITORY_MARKERS.some(marker => fs.existsSync(path.join(current, marker)))) {
+      return current;
+    }
+    const parent = path.dirname(current);
+    if (parent === current) return null;
+    current = parent;
+  }
+}
+
+/**
+ * Whether .claude/CLAUDE.md keeps a copy beside root CLAUDE.md (INV31): while
+ * a fresh clone lacks root CLAUDE.md (the project ignores it and does not
+ * track it), a .claude/CLAUDE.md the project commits (tracked, or not
+ * ignored) gets the copy too (DEC-2: an extra copy beats none). One the
+ * project ignores and does not track follows the usual rule: its block goes
+ * once root CLAUDE.md holds one. An ignore file, or tracking, that cannot be
+ * read keeps the copy.
+ * @param {string} targetDir
+ * @returns {boolean}
+ */
+function claudeDirKeepsCopy(targetDir) {
+  if (!rootClaudeIgnored(targetDir)) return false;
+  return !uncommittedHere(targetDir, CLAUDE_DIR_MD, false);
+}
+
+/**
+ * `rels` without the files that resolve outside `targetDir`, each reported
+ * through `onSkipped`.
+ * @param {string} targetDir
+ * @param {readonly string[]} rels
+ * @param {((rel: string, reason: string) => void) | undefined} onSkipped
+ * @returns {Set<string>} the files skipped
+ */
+function skipEscaping(targetDir, rels, onSkipped) {
+  /** @type {Set<string>} */
+  const skipped = new Set();
+  for (const p of rels) {
+    try {
+      assertWithin(p, targetDir, {label: 'agent docs path'});
+    } catch (err) {
+      if (!(err instanceof PathSafetyError)) throw err;
+      skipped.add(p);
+      onSkipped?.(p, err.message);
+    }
+  }
+  return skipped;
+}
+
+/**
+ * Whether root CLAUDE.md holds `block` as its managed block, so a copy in
+ * .claude/CLAUDE.md may go.
+ * @param {string} targetDir
+ * @param {string} block
+ * @returns {boolean}
+ */
+function rootClaudeHolds(targetDir, block) {
+  // A root CLAUDE.md the project ignores is not in a fresh clone, so it never
+  // stands in for a committed copy in .claude/CLAUDE.md (an extra copy beats
+  // none, DEC-2). An ignored .claude/CLAUDE.md is not in one either, so the
+  // usual rule holds for it.
+  if (claudeDirKeepsCopy(targetDir)) return false;
+  try {
+    const content = fs.readFileSync(path.join(targetDir, CLAUDE_MD), 'utf-8');
+    const found = findManagedBlock(content);
+    return found != null && content.slice(found.start, found.end) === block.trim();
+  } catch {
+    return false;
+  }
+}
+
 /**
  * Whether an agent-doc file already carries a managed-block marker.
  * @param {string} filePath
@@ -773,24 +1279,40 @@ function assertTargetsWithin(targetDir, relPaths) {
 }
 
 /**
- * Remove Astryx section from all known agent doc files.
+ * Throw `ERR_PATH_TRAVERSAL` when an agent doc in `targetDir` that holds a
+ * managed block resolves outside `targetDir`.
  * @param {string} targetDir
- * @returns {string[]} the project-relative files a block was removed from.
- * @throws {PathSafetyError} `ERR_PATH_TRAVERSAL` when a file it would change
- *   resolves outside `targetDir`; nothing is changed.
  */
-export function removeAgentDocs(targetDir) {
+function assertRemovableWithin(targetDir, skip = new Set()) {
   const allPaths = discoverAgentDocs(targetDir);
   try {
     assertTargetsWithin(
       targetDir,
-      allPaths.filter(p => hasRemovableBlock(path.join(targetDir, p))),
+      allPaths.filter(
+        p => !skip.has(p) && hasRemovableBlock(path.join(targetDir, p)),
+      ),
     );
   } catch (err) {
     // The code reaches the error envelope as is, so it must be registered.
     if (!(err instanceof PathSafetyError)) throw err;
     throw new PathSafetyError(err.message, ERROR_CODES.ERR_PATH_TRAVERSAL);
   }
+}
+
+/**
+ * Remove Astryx section from all known agent doc files.
+ * @param {string} targetDir
+ * @param {object} [options]
+ * @param {string} [options.shownFrom] - Folder the logged paths are shown
+ *   relative to; defaults to `targetDir`.
+ * @param {Set<string>} [options.skip] - Files left as they are.
+ * @returns {string[]} the project-relative files a block was removed from.
+ * @throws {PathSafetyError} `ERR_PATH_TRAVERSAL` when a file it would change
+ *   resolves outside `targetDir`; nothing is changed.
+ */
+export function removeAgentDocs(targetDir, {shownFrom = targetDir, skip = new Set()} = {}) {
+  assertRemovableWithin(targetDir, skip);
+  const allPaths = discoverAgentDocs(targetDir).filter(p => !skip.has(p));
 
   /** @type {string[]} */
   const removedFrom = [];
@@ -799,27 +1321,374 @@ export function removeAgentDocs(targetDir) {
     // Delete if empty for files we created (AGENTS.md, .claude/CLAUDE.md)
     const deleteIfEmpty = p === AGENTS_MD || p === CLAUDE_DIR_MD;
     if (removeXdsBlock(filePath, {deleteIfEmpty})) {
+      // The default creates GEMINI.md holding only the import of AGENTS.md.
+      if (p === GEMINI_MD && fs.readFileSync(filePath, 'utf-8').trim() === '') {
+        fs.unlinkSync(filePath);
+      }
       removedFrom.push(p);
+      const shown = path.relative(shownFrom, filePath).split(path.sep).join('/') || p;
       if (!fs.existsSync(filePath)) {
-        humanLog(`[ok] Removed empty ${p}`);
+        humanLog(`[ok] Removed empty ${shown}`);
       } else {
-        humanLog(`[ok] Removed design system section from ${p}`);
+        humanLog(`[ok] Removed design system section from ${shown}`);
       }
     }
   }
   return removedFrom;
 }
 
+/**
+ * Remove the managed block where init writes it, the project root (see
+ * {@link resolveAgentDocsRoot}), and in `cwd`, so a block an earlier version
+ * wrote in that folder goes too. Each folder is checked before anything is
+ * changed. Run below the project root, a project-root agent file holding a
+ * block that resolves outside the project is left as it is and reported to
+ * `onSkipped`, as install does there; 0.7.x touched only `cwd`. A file in
+ * `cwd`, or at the root when run there, that resolves outside refuses the run.
+ *
+ * @param {string} cwd
+ * @param {{onSkipped?: (rel: string, reason: string) => void}} [options]
+ * @returns {string[]} the files a block was removed from, relative to `cwd`
+ * @throws {PathSafetyError} `ERR_PATH_TRAVERSAL`; nothing is changed
+ */
+export function removeProjectAgentDocs(cwd, {onSkipped} = {}) {
+  const root = agentDocsTargetDir(cwd);
+  const below = realDir(root) !== realDir(cwd);
+  /** @type {Set<string>} */
+  const rootSkip = below
+    ? skipEscaping(
+        root,
+        discoverAgentDocs(root).filter(p => hasRemovableBlock(path.join(root, p))),
+        (rel, reason) =>
+          onSkipped?.(path.relative(cwd, path.join(root, rel)).split(path.sep).join('/'), reason),
+      )
+    : new Set();
+  const dirs = below ? [root, cwd] : [cwd];
+  for (const dir of dirs) assertRemovableWithin(dir, dir === root ? rootSkip : undefined);
+  return dirs.flatMap(dir =>
+    removeAgentDocs(dir, {shownFrom: cwd, skip: dir === root ? rootSkip : undefined}).map(rel =>
+      path.relative(cwd, path.join(dir, rel)).split(path.sep).join('/'),
+    ),
+  );
+}
+
+/**
+ * Write the block into each standalone agent doc and remove a managed block
+ * from each import wrapper. A refresh (`onlyReplace`) skips files without a
+ * block and leaves a managed import of AGENTS.md as it is.
+ *
+ * @param {string} targetDir
+ * @param {string[]} existing
+ * @param {Map<string, Set<string>>} givenWrappers
+ * @param {string} compressedIndex
+ * @param {boolean} onlyReplace
+ * @param {((rel: string, reason: string) => void) | undefined} onSkipped
+ * @param {boolean} [refuseEscapes] whether a file 0.7.1 wrote that escapes
+ *   `targetDir` refuses the run
+ * @returns {string[]} files written
+ */
+function writeEachAgentDoc(targetDir, existing, givenWrappers, compressedIndex, onlyReplace, onSkipped, refuseEscapes = true) {
+  /** @param {string} p */
+  const marked = p => hasManagedMarker(path.join(targetDir, p));
+  // A committed .claude/CLAUDE.md beside an ignored root CLAUDE.md keeps a
+  // copy (INV31): one that already holds a block is refreshed where it is,
+  // even when it imports another agent file, rather than left stale.
+  const keptCopy =
+    givenWrappers.has(CLAUDE_DIR_MD) && marked(CLAUDE_DIR_MD) && claudeDirKeepsCopy(targetDir);
+  const wrappers = new Map(givenWrappers);
+  if (keptCopy) wrappers.delete(CLAUDE_DIR_MD);
+  /** @param {string} p */
+  const isImport = p => {
+    try {
+      return isAgentsImportBlock(p, fs.readFileSync(path.join(targetDir, p), 'utf-8'));
+    } catch {
+      return false;
+    }
+  };
+  // Every agent file that imports no other agent file holds a copy, GEMINI.md
+  // included (INV31); a managed import of AGENTS.md is left as it is.
+  const targets = existing.filter(p => !wrappers.has(p) && !isImport(p));
+  const writes = targets.filter(p => !onlyReplace || marked(p));
+  const strips = [...wrappers.keys()].filter(marked);
+  // A file 0.7.1 did not write here (GEMINI.md, or any file when init runs
+  // below the project root) that resolves outside the project is skipped and
+  // reported, as in the default layout, and the rest is written. A path of a
+  // file 0.7.1 wrote that escapes the project refuses the run, as in 0.7.1.
+  const skipped = skipEscaping(
+    targetDir,
+    // A kept copy here already holds a block, which 0.7.x wrote, so its
+    // escape refuses the run like any file 0.7.x wrote.
+    [...writes, ...strips].filter(p => !refuseEscapes || p === GEMINI_MD),
+    onSkipped,
+  );
+  assertTargetsWithin(
+    targetDir,
+    [...writes, ...strips].filter(p => !skipped.has(p)),
+  );
+  // A refresh skips unmarked files and a wrapper is only written when it
+  // carries a block, so only the files this run writes are checked.
+  /** @type {string[]} */
+  const written = [];
+  for (const p of targets) {
+    if (skipped.has(p)) continue;
+    const didWrite = injectXdsBlock(path.join(targetDir, p), compressedIndex, {onlyReplace});
+    if (didWrite) written.push(p);
+  }
+  for (const p of wrappers.keys()) {
+    if (skipped.has(p)) continue;
+    // The copy in .claude/CLAUDE.md goes only once root CLAUDE.md holds it.
+    if (
+      p === CLAUDE_DIR_MD &&
+      (skipped.has(CLAUDE_MD) || !rootClaudeHolds(targetDir, compressedIndex))
+    ) {
+      continue;
+    }
+    if (stripManagedBlock(path.join(targetDir, p), compressedIndex)) written.push(p);
+  }
+  return written;
+}
+
+/**
+ * The Claude Code file that holds the copy of the block: root CLAUDE.md, which
+ * projects commit even when they ignore .claude/, else .claude/CLAUDE.md. It
+ * holds the copy even when it imports AGENTS.md: Claude Code does not follow an
+ * import of a file above the folder it starts in, so a session started in a
+ * subfolder reads only the copy.
+ *
+ * @param {Set<string>} present Existing agent docs that are not AGENTS.md under
+ *   another name.
+ * @param {Set<string>} aliases Files that are AGENTS.md under another name.
+ * @returns {string | null} null when the project has no Claude file, or when
+ *   root CLAUDE.md is AGENTS.md under another name and so holds the block.
+ */
+function claudeCopyFile(present, aliases) {
+  if (aliases.has(CLAUDE_MD)) return null;
+  return [CLAUDE_MD, CLAUDE_DIR_MD].find(p => present.has(p)) ?? null;
+}
+
+/**
+ * Plan the default layout. AGENTS.md holds the block. The Claude Code file the
+ * project already has holds a copy (see {@link claudeCopyFile}), so the block
+ * sits in a file the project commits; init creates no Claude file. GEMINI.md
+ * imports AGENTS.md unless it already does. Every other wrapper here imports
+ * AGENTS.md, so it already reaches the block.
+ *
+ * @param {string} targetDir
+ * @param {string[]} existing
+ * @param {Map<string, Set<string>>} wrappers
+ * @param {Set<string>} aliases Files that are AGENTS.md under another name;
+ *   they are never written.
+ * @returns {Map<string, 'block' | 'import' | 'strip'>}
+ */
+function planDefaultAgentDocs(targetDir, existing, wrappers, aliases) {
+  const present = new Set(existing.filter(p => !aliases.has(p)));
+  /** @type {Map<string, 'block' | 'import' | 'strip'>} */
+  const plan = new Map([[AGENTS_MD, 'block']]);
+
+  // Claude Code reads CLAUDE.md and .claude/CLAUDE.md, and skips AGENTS.md
+  // when either exists. One Claude file holds the copy, so Claude Code reads
+  // it once in a subfolder and at most twice at the root, where it also
+  // follows that file's import of AGENTS.md.
+  const claudeCopy = claudeCopyFile(present, aliases);
+  for (const p of [CLAUDE_MD, CLAUDE_DIR_MD]) {
+    if (present.has(p)) plan.set(p, p === claudeCopy ? 'block' : 'strip');
+  }
+
+  // Gemini CLI reads GEMINI.md. Project settings can point it at AGENTS.md
+  // too, but Gemini loads them only when it starts at the project root, so the
+  // import is written anyway: two copies at the root beat none in a subfolder.
+  // An import GEMINI.md already has, even inline, is enough.
+  if (!aliases.has(GEMINI_MD)) {
+    if (geminiImportsAgentsMd(targetDir)) {
+      if (present.has(GEMINI_MD)) plan.set(GEMINI_MD, 'strip');
+    } else {
+      plan.set(GEMINI_MD, 'import');
+    }
+  }
+
+  // Every other file: a full block when standalone, none in a wrapper.
+  for (const p of present) {
+    if (!plan.has(p)) plan.set(p, wrappers.has(p) ? 'strip' : 'block');
+  }
+  return plan;
+}
+
+/**
+ * Write the default layout (see {@link planDefaultAgentDocs}).
+ *
+ * Path safety follows 0.7.0: an agent doc it would have written that resolves
+ * outside `targetDir` refuses the whole run before any write. A file only this
+ * layout writes, such as GEMINI.md, is skipped instead, reported through
+ * `onSkipped`, and the rest is written.
+ *
+ * @param {string} targetDir
+ * @param {string[]} existing
+ * @param {Map<string, Set<string>>} wrappers
+ * @param {Set<string>} aliases
+ * @param {string} compressedIndex
+ * @param {((rel: string, reason: string) => void) | undefined} onSkipped
+ * @param {boolean} [refuseEscapes] whether a file 0.7.1 wrote that escapes
+ *   `targetDir` refuses the run
+ * @returns {string[]} files written, in {@link AGENT_DOC_PATHS} order
+ */
+function writeDefaultAgentDocs(targetDir, existing, wrappers, aliases, compressedIndex, onSkipped, refuseEscapes = true) {
+  const plan = planDefaultAgentDocs(targetDir, existing, wrappers, aliases);
+  // While root CLAUDE.md is one the project ignores, .claude/CLAUDE.md gets
+  // the copy too, first run included: a fresh clone has only that file.
+  if (plan.get(CLAUDE_DIR_MD) === 'strip' && claudeDirKeepsCopy(targetDir)) {
+    plan.set(CLAUDE_DIR_MD, 'block');
+  }
+  // 0.7.x left a block-less import of an existing AGENTS.md alone, so a Claude
+  // file of that shape that now gets the copy and resolves outside the project
+  // is skipped and reported. Any other agent file 0.7.x wrote, so its escape
+  // still refuses the run.
+  /** @param {string} p */
+  const leftAlone = p =>
+    existing.includes(AGENTS_MD) &&
+    wrappers.get(p)?.has(AGENTS_MD) === true &&
+    !hasManagedMarker(path.join(targetDir, p));
+  const foundLegacy = existing.filter(p => LEGACY_DOC_PATHS.includes(p));
+  /** @param {string} p */
+  const legacy = p =>
+    !leftAlone(p) &&
+    (foundLegacy.includes(p) || (p === AGENTS_MD && foundLegacy.length === 0));
+
+  /** @type {Set<string>} */
+  const escaped = new Set();
+  for (const [p, action] of [...plan]) {
+    // A strip writes only a file that carries a block.
+    if (action === 'strip' && !hasManagedMarker(path.join(targetDir, p))) {
+      plan.delete(p);
+      continue;
+    }
+    try {
+      assertWithin(p, targetDir, {label: 'agent docs path'});
+    } catch (err) {
+      if (!(err instanceof PathSafetyError) || (refuseEscapes && legacy(p))) throw err;
+      plan.delete(p);
+      escaped.add(p);
+      onSkipped?.(p, err.message);
+    }
+  }
+  // An import of an AGENTS.md left as it is would point at no block, so the
+  // GEMINI.md import is not written either.
+  if (escaped.has(AGENTS_MD) && plan.get(GEMINI_MD) === 'import') {
+    plan.delete(GEMINI_MD);
+    onSkipped?.(GEMINI_MD, 'its import of AGENTS.md would point at a file left as it is');
+  }
+
+  /** @type {string[]} */
+  const written = [];
+  for (const p of AGENT_DOC_PATHS) {
+    const action = plan.get(p);
+    if (action == null) continue;
+    const filePath = path.join(targetDir, p);
+    if (action === 'strip') {
+      // The copy in .claude/CLAUDE.md goes only once root CLAUDE.md holds it.
+      if (
+        p === CLAUDE_DIR_MD &&
+        (escaped.has(CLAUDE_MD) || !rootClaudeHolds(targetDir, compressedIndex))
+      ) {
+        continue;
+      }
+      if (stripManagedBlock(filePath, compressedIndex)) written.push(p);
+      continue;
+    }
+    fs.mkdirSync(path.dirname(filePath), {recursive: true});
+    injectXdsBlock(
+      filePath,
+      action === 'block' ? compressedIndex : renderAgentsImportBlock(p),
+      {createIfMissing: true, header: CREATED_HEADERS[p] ?? ''},
+    );
+    written.push(p);
+  }
+  return written;
+}
+
+/**
+ * Heading of the AGENTS.md the default creates; the same text the presets
+ * write, so `--remove-agents` recognizes and deletes it.
+ * @type {Readonly<Record<string, string>>}
+ */
+const CREATED_HEADERS = Object.freeze({
+  [AGENTS_MD]: '# AGENTS.md\n\nProject-specific guidance for AI coding agents.',
+});
+
+/**
+ * Agent docs that are one file under several names (symlinks), resolved inside
+ * or outside the project.
+ * @param {string} targetDir
+ * @param {string[]} existing
+ * @returns {{agentsAliases: Set<string>, otherShared: boolean}} the files that
+ *   are AGENTS.md under another name, and whether any other two docs share a
+ *   file.
+ */
+function findSharedAgentDocs(targetDir, existing) {
+  /** @type {Map<string, string[]>} */
+  const byFile = new Map();
+  for (const p of existing) {
+    let real;
+    try {
+      real = fs.realpathSync(path.join(targetDir, p));
+    } catch {
+      real = path.resolve(targetDir, p);
+    }
+    byFile.set(real, [...(byFile.get(real) ?? []), p]);
+  }
+  /** @type {Set<string>} */
+  const agentsAliases = new Set();
+  let otherShared = false;
+  for (const names of byFile.values()) {
+    if (names.length < 2) continue;
+    if (!names.includes(AGENTS_MD)) {
+      otherShared = true;
+      continue;
+    }
+    for (const name of names) if (name !== AGENTS_MD) agentsAliases.add(name);
+  }
+  return {agentsAliases, otherShared};
+}
+
+/**
+ * Remove the managed block from a file that should not carry one, leaving the
+ * rest of the file as it is. A malformed block is refused (throws) rather than
+ * guessed at. `.claude/CLAUDE.md` is deleted when nothing but whitespace is
+ * left.
+ * @param {string} filePath
+ * @param {string} compressedIndex
+ * @returns {boolean} whether the file changed
+ */
+function stripManagedBlock(filePath, compressedIndex) {
+  const deleteIfBlank =
+    path.basename(filePath) === path.basename(CLAUDE_DIR_MD) &&
+    path.basename(path.dirname(filePath)) === path.dirname(CLAUDE_DIR_MD);
+  if (removeXdsBlock(filePath, {deleteIfBlank})) return true;
+  if (hasManagedMarker(filePath)) {
+    // Preserve the existing fail-closed behavior for malformed blocks.
+    injectXdsBlock(filePath, compressedIndex, {onlyReplace: true});
+  }
+  return false;
+}
+
 /**
  * Programmatic entry point for installing agent docs.
  * Used by the init command, upgrade command, and agent-docs command.
  *
- * Strategy (when no agent/paths specified):
- * - Discover all existing agent doc files.
- * - Leave `@path` import wrappers untouched; if an older run expanded a block
- *   into one, remove that duplicate block.
- * - Initialize or refresh every standalone file.
- * - If nothing exists, create AGENTS.md as the tool-agnostic default.
+ * Default strategy (no agent/paths specified), so every agent reads the block:
+ * - Write the block to AGENTS.md (created when missing).
+ * - Write the block to the project's Claude Code file: root CLAUDE.md when it
+ *   exists, else an existing .claude/CLAUDE.md, even when it imports AGENTS.md.
+ *   Remove a block from the other one. Create no Claude file.
+ * - Write a managed import of AGENTS.md to GEMINI.md (created when missing),
+ *   unless GEMINI.md already imports AGENTS.md.
+ * - Keep a full block in every other existing standalone file.
+ * - Leave every other `@path` import wrapper untouched; if an older run
+ *   expanded a block into one, remove that duplicate block. When a wrapper
+ *   imports a file other than AGENTS.md, the project keeps its own layout:
+ *   every standalone file gets the block.
+ * A refresh (`onlyReplace`) rewrites existing blocks in place, the Claude
+ * file's copy included, leaves imports of AGENTS.md as they are, and creates
+ * nothing.
  *
  * @param {string} targetDir
  * @param {object} [options]
@@ -833,9 +1702,19 @@ export function removeAgentDocs(targetDir) {
  *   so an integration's topics reach the agent.
  * @param {string} [options.renderedBlock] - Fully rendered expected block. Init
  *   and upgrade pass one shared block to every target.
+ * @param {(rel: string, reason: string) => void} [options.onSkipped] - Called
+ *   for each file skipped because it resolves outside `targetDir` and 0.7.1
+ *   never wrote it: GEMINI.md, or any file when `refuseEscapes` is false.
+ * @param {boolean} [options.refuseEscapes] - Whether a file 0.7.1 wrote that
+ *   resolves outside `targetDir` refuses the run (default). Init passes false
+ *   when it runs below the project root, where 0.7.1 wrote in the folder it
+ *   ran in instead.
  * @returns {string[]} List of files written
  * @throws {import('../fs/path-safety.mjs').PathSafetyError} when a file it would
  *   write resolves outside `targetDir`; nothing is written.
+ * @throws {AgentDocsHomeError} when `targetDir` is the home folder, or a settings
+ *   folder in it outside a project, or, with `paths`, when a file's own folder
+ *   is; nothing is written.
  */
 export function installAgentDocs(
   targetDir,
@@ -847,8 +1726,14 @@ export function installAgentDocs(
     onlyReplace = false,
     topics,
     renderedBlock,
+    onSkipped,
+    refuseEscapes = true,
   } = {},
 ) {
+  const explicit = paths != null && paths.length > 0;
+  // Explicit paths are checked file by file below: each file's own folder
+  // is what agents would read in every project.
+  if (!explicit) assertAgentDocsTarget(targetDir);
   const coreDir = findCoreDir(targetDir);
   const version = getXdsVersion(coreDir);
   const invocation = getCliInvocation(targetDir);
@@ -867,13 +1752,20 @@ export function installAgentDocs(
   const written = [];
 
   // Explicit paths override everything
-  if (paths && paths.length > 0) {
+  if (explicit) {
     // Path-safety: each --agent-docs-path entry must resolve inside the
     // target directory. Reject absolute paths (silent re-rooting via
     // path.join hides intent) and `..` traversal.
     for (const p of paths) {
       assertWithin(p, targetDir, {label: 'agent docs path'});
     }
+    // A file directly in the home folder, or at the top of a settings folder
+    // in it, is refused, as 0.7.x never wrote there unasked; a file in a
+    // plain folder of the home folder, such as ~/notes/AI.md, is written.
+    // Every path is checked before anything is written.
+    for (const p of paths) {
+      assertAgentDocsTarget(path.dirname(path.join(targetDir, p)));
+    }
     for (const p of paths) {
       const filePath = path.join(targetDir, p);
       const dir = path.dirname(filePath);
@@ -892,12 +1784,43 @@ export function installAgentDocs(
   // Agent preset
   if (agent) {
     const {inject, create} = resolveAgentPaths(targetDir, agent);
-    assertTargetsWithin(targetDir, [...inject, ...create]);
-    for (const p of inject) {
+    // Claude Code reads CLAUDE.md and .claude/CLAUDE.md together: when the
+    // block goes in CLAUDE.md, .claude/CLAUDE.md gets none, and a block there
+    // is removed.
+    const claudeRoot = inject.includes(CLAUDE_MD);
+    // While root CLAUDE.md is ignored, a committed .claude/CLAUDE.md holds a
+    // copy too, with `claude` and `all` alike (INV31), first run included.
+    const keepDirCopy = claudeRoot && claudeDirKeepsCopy(targetDir);
+    const injectAll = !claudeRoot
+      ? inject
+      : keepDirCopy
+        ? [...new Set([...inject, CLAUDE_DIR_MD])].filter(p =>
+            p !== CLAUDE_DIR_MD || fs.existsSync(path.join(targetDir, CLAUDE_DIR_MD)),
+          )
+        : inject.filter(p => p !== CLAUDE_DIR_MD);
+    const dirHasBlock = hasManagedMarker(path.join(targetDir, CLAUDE_DIR_MD));
+    const strip = claudeRoot && !keepDirCopy && dirHasBlock ? [CLAUDE_DIR_MD] : [];
+    // A path that escapes the project refuses the run, as in 0.7.0; below the
+    // project root, where 0.7.1 wrote nothing, it is skipped and reported. A
+    // .claude/CLAUDE.md the preset adds beside an ignored root, which 0.7.1
+    // did not write, is skipped and reported wherever init runs.
+    // So is removing a block from .claude/CLAUDE.md with `claude`, whose
+    // 0.7.1 preset wrote only root CLAUDE.md there; `all` wrote both, so its
+    // escape still refuses.
+    const added = injectAll.filter(p => !inject.includes(p));
+    const unrefused = agent === 'claude' ? [...added, ...strip] : added;
+    const escaping = refuseEscapes
+      ? skipEscaping(targetDir, unrefused, onSkipped)
+      : skipEscaping(targetDir, [...injectAll, ...create, ...strip], onSkipped);
+    const injectHere = injectAll.filter(p => !escaping.has(p));
+    const createHere = create.filter(p => !escaping.has(p));
+    const stripHere = escaping.has(CLAUDE_MD) ? [] : strip.filter(p => !escaping.has(p));
+    assertTargetsWithin(targetDir, [...injectHere, ...createHere, ...stripHere]);
+    for (const p of injectHere) {
       injectXdsBlock(path.join(targetDir, p), compressedIndex);
       written.push(p);
     }
-    for (const p of create) {
+    for (const p of createHere) {
       const filePath = path.join(targetDir, p);
       const dir = path.dirname(filePath);
       if (dir !== targetDir) {
@@ -909,57 +1832,45 @@ export function installAgentDocs(
       });
       written.push(p);
     }
+    for (const p of stripHere) {
+      if (!rootClaudeHolds(targetDir, compressedIndex)) continue;
+      if (stripManagedBlock(path.join(targetDir, p), compressedIndex)) written.push(p);
+    }
     return written;
   }
 
-  // Auto-detect: initialize standalone files, but do not expand the managed
-  // block beside an `@path` import of another agent doc. Remove a block from a
-  // wrapper if an older run already duplicated it there.
+  // Auto-detect. A refresh rewrites each existing block where it is.
   const existing = discoverAgentDocs(targetDir);
-
-  if (existing.length > 0) {
-    const wrappers = discoverAgentDocWrappers(targetDir, existing);
-    const targets = existing.filter(p => !wrappers.has(p));
-    // A refresh skips unmarked files and a wrapper is only written when it
-    // carries a block, so only the files this run writes are checked.
-    /** @param {string} p */
-    const marked = p => hasManagedMarker(path.join(targetDir, p));
-    assertTargetsWithin(targetDir, [
-      ...targets.filter(p => !onlyReplace || marked(p)),
-      ...[...wrappers].filter(marked),
-    ]);
-
-    for (const p of targets) {
-      const didWrite = injectXdsBlock(path.join(targetDir, p), compressedIndex, {onlyReplace});
-      if (didWrite) written.push(p);
-    }
-    for (const p of wrappers) {
-      const filePath = path.join(targetDir, p);
-      if (removeXdsBlock(filePath)) {
-        written.push(p);
-      } else {
-        const content = fs.readFileSync(filePath, 'utf-8');
-        if (content.includes(MARKER_START) || content.includes(LEGACY_MARKER_START)) {
-          // Preserve the existing fail-closed behavior for malformed blocks.
-          injectXdsBlock(filePath, compressedIndex, {onlyReplace: true});
-        }
-      }
-    }
-    return written;
+  if (onlyReplace) {
+    const wrappers = findAgentDocWrappers(readAgentDocImports(targetDir, existing));
+    // The Claude file keeps its copy even when it imports AGENTS.md, so a
+    // refresh rewrites that block rather than removing it.
+    const {agentsAliases} = findSharedAgentDocs(targetDir, existing);
+    const claudeCopy = claudeCopyFile(
+      new Set(existing.filter(p => !agentsAliases.has(p))),
+      agentsAliases,
+    );
+    if (claudeCopy != null) wrappers.delete(claudeCopy);
+    // A committed .claude/CLAUDE.md kept beside an ignored root CLAUDE.md is
+    // refreshed even when it imports AGENTS.md (writeEachAgentDoc).
+    return writeEachAgentDoc(targetDir, existing, wrappers, compressedIndex, true, onSkipped, refuseEscapes);
   }
-
-  // Nothing exists — create root AGENTS.md as the default (skip if onlyReplace).
-  // AGENTS.md is the tool-agnostic standard (Codex/Copilot, Cursor, Muse, and
-  // most agents read it), so it's the safe default. Claude-specific output is
-  // opt-in via `--agent claude` (→ .claude/CLAUDE.md); `--agent all` writes both.
-  if (onlyReplace) return written;
-
-  const defaultPath = AGENTS_MD;
-  assertTargetsWithin(targetDir, [defaultPath]);
-  injectXdsBlock(path.join(targetDir, defaultPath), compressedIndex, {
-    createIfMissing: true,
-    header: `# AGENTS.md\n\nProject-specific guidance for AI coding agents.`,
-  });
-  written.push(defaultPath);
-  return written;
+  // A wrapper that imports something other than AGENTS.md, or two agent docs
+  // that are one file, mean the project chose its own layout: keep the
+  // per-file layout then. AGENTS.md under another name is fine.
+  const wrappers = findAgentDocWrappers(readAgentDocImports(targetDir, existing, [AGENTS_MD]));
+  const {agentsAliases, otherShared} = findSharedAgentDocs(targetDir, existing);
+  if (otherShared || [...wrappers.values()].some(targets => !targets.has(AGENTS_MD))) {
+    const ownWrappers = findAgentDocWrappers(readAgentDocImports(targetDir, existing));
+    return writeEachAgentDoc(targetDir, existing, ownWrappers, compressedIndex, false, onSkipped, refuseEscapes);
+  }
+  return writeDefaultAgentDocs(
+    targetDir,
+    existing,
+    wrappers,
+    agentsAliases,
+    compressedIndex,
+    onSkipped,
+    refuseEscapes,
+  );
 }