@open-agent-toolkit/cli 0.3.24 → 0.3.26

package/dist/commands/config/index.js

@@ -12,7 +12,7 @@ import { normalizeDispatchMatrix, validateDispatchRouteTarget, walkDispatchMatri
 import { formatDispatchNotices, terminalReviewerNoticesForMatrix, } from '../../config/dispatch-notices.js';
 import { dispatchPolicyModeDescription, dispatchPolicyPolicyDescription, managedDispatchPolicyValueList, } from '../../config/dispatch-policy-options.js';
 import { parseJsonConfig } from '../../config/json.js';
-import { DEFAULT_INSTRUCTION_SYNC_STRATEGY, INSTRUCTION_SYNC_STRATEGIES, VALID_DISPATCH_POLICY_MODES, VALID_MANAGED_DISPATCH_POLICIES, MAX_GATE_TIMEOUT_MS, MIN_GATE_TIMEOUT_MS, isValidGateTimeoutMs, isValidProjectLogDigestBound, normalizeWorkflowPostImplementSequence, normalizeDocumentationGuidance, readOatConfig, readOatConfigForDefaultScopeRepair, readOatConfigForDocumentationExcludesRepair, readOatConfigForInstructionPointerExcludesRepair, readOatConfigForInstructionSyncStrategyRepair, readOatConfigWithWarnings, readOatLocalConfig, readUserConfig, writeOatConfig, writeOatLocalConfig, writeUserConfig, VALID_POST_IMPLEMENT_LEGACY_SEQUENCES, } from '../../config/oat-config.js';
+import { DEFAULT_INSTRUCTION_SYNC_STRATEGY, INSTRUCTION_SYNC_STRATEGIES, VALID_DISPATCH_POLICY_MODES, VALID_MANAGED_DISPATCH_POLICIES, MAX_GATE_TIMEOUT_MS, MIN_GATE_TIMEOUT_MS, isValidGateTimeoutMs, isValidProjectLogDigestBound, normalizeWorkflowPostImplementSequence, normalizeDocumentationGuidance, normalizeDocumentationIa, normalizeDocumentationNavOwner, readOatConfig, readOatConfigForDefaultScopeRepair, readOatConfigForDocumentationExcludesRepair, readOatConfigForInstructionPointerExcludesRepair, readOatConfigForInstructionSyncStrategyRepair, readOatConfigWithWarnings, readOatLocalConfig, readUserConfig, writeOatConfig, writeOatLocalConfig, writeUserConfig, VALID_POST_IMPLEMENT_LEGACY_SEQUENCES, } from '../../config/oat-config.js';
 import { getOwnKey, setOwnKey } from '../../config/own-keys.js';
 import { resolveEffectiveConfig, resolveEnvOverride, } from '../../config/resolve.js';
 import { resolveAssetsRoot } from '../../fs/assets.js';
@@ -67,6 +67,9 @@ const KEY_ORDER = [
     'archive.awsRegion',
     'autoReviewAtCheckpoints',
     'lastPausedProject',
+    'documentation.ia',
+    'documentation.nonReaderPaths',
+    'documentation.navOwner',
     'documentation.guidance',
     'documentation.root',
     'documentation.tooling',
@@ -239,6 +242,28 @@ const CONFIG_CATALOG = [
         description: 'Deprecated compatibility alias for workflow.autoReviewAtHillCheckpoints. Prefer `oat config set workflow.autoReviewAtHillCheckpoints <true|false>`.',
         deprecated: { supersededBy: 'workflow.autoReviewAtHillCheckpoints' },
     },
+    {
+        key: 'documentation.ia',
+        group: 'Shared Repo (.oat/config.json)',
+        scope: 'shared repo',
+        file: '.oat/config.json',
+        type: 'JSON object',
+        defaultValue: 'null (no recorded IA)',
+        mutability: 'read/write',
+        owningCommand: 'oat config set documentation.ia <JSON>',
+        description: 'Repository mirror of authored IA: preset, repo-relative decision, optional tracks [{path, principle}] and verification (triad|agent-only|none). Authored records remain authoritative.',
+    },
+    {
+        key: 'documentation.navOwner',
+        group: 'Shared Repo (.oat/config.json)',
+        scope: 'shared repo',
+        file: '.oat/config.json',
+        type: 'nav-sync | hand-authored',
+        defaultValue: 'null (undeclared)',
+        mutability: 'read/write',
+        owningCommand: 'oat config set documentation.navOwner <value>',
+        description: 'Sidebar owner for framework docs only. Unset is undeclared and authorizes no automatic navigation generation. Markdown ignores this key.',
+    },
     {
         key: 'documentation.guidance',
         group: 'Documentation Guidance (shared > user)',
@@ -283,6 +308,17 @@ const CONFIG_CATALOG = [
         owningCommand: 'oat config set documentation.config <value>',
         description: 'Repository-relative path to the primary documentation tool config file.',
     },
+    {
+        key: 'documentation.nonReaderPaths',
+        group: 'Shared Repo (.oat/config.json)',
+        file: '.oat/config.json',
+        scope: 'shared repo',
+        type: 'string[]',
+        defaultValue: 'unset',
+        mutability: 'read/write',
+        owningCommand: 'oat config set documentation.nonReaderPaths <glob[,glob...]>',
+        description: 'Content-root-relative globs excluded from reader navigation, manifest and supported framework rendering. Empty clears the key.',
+    },
     {
         key: 'documentation.excludes',
         group: 'Shared Repo (.oat/config.json)',
@@ -1784,17 +1820,36 @@ async function listConfigKeys(repoRoot, userConfigDir, dependencies) {
 async function setConfigValue(repoRoot, userConfigDir, key, rawValue, surface, dependencies, warn) {
     validateSurfaceForKey(key, surface);
     const effectiveSurface = surface === 'auto' ? defaultSurfaceForKey(key) : surface;
-    if (key === 'documentation.guidance') {
+    if (key === 'documentation.nonReaderPaths' ||
+        key === 'documentation.guidance' ||
+        key === 'documentation.ia' ||
+        key === 'documentation.navOwner') {
         const configPath = effectiveSurface === 'user'
             ? join(userConfigDir, 'config.json')
             : join(repoRoot, '.oat', 'config.json');
+        const field = key.slice('documentation.'.length);
         const trimmed = rawValue.trim();
-        let guidance;
+        let value;
         try {
-            guidance = normalizeDocumentationGuidance(trimmed.startsWith('[') ? JSON.parse(trimmed) : trimmed, configPath, effectiveSurface === 'user' ? 'user' : 'shared');
+            if (key === 'documentation.nonReaderPaths') {
+                const paths = parseDocumentationExcludes(rawValue);
+                value = paths.length > 0 ? paths : undefined;
+            }
+            else if (key === 'documentation.ia') {
+                const parsed = JSON.parse(trimmed);
+                if (parsed === null)
+                    throw new Error('Expected an IA JSON object.');
+                value = normalizeDocumentationIa(parsed, configPath);
+            }
+            else {
+                value =
+                    key === 'documentation.navOwner'
+                        ? normalizeDocumentationNavOwner(trimmed, configPath)
+                        : normalizeDocumentationGuidance(trimmed.startsWith('[') ? JSON.parse(trimmed) : trimmed, configPath, effectiveSurface === 'user' ? 'user' : 'shared');
+            }
         }
         catch {
-            throw new Error('Invalid documentation.guidance value: expected a non-empty path/URL string or ordered non-empty string array.');
+            throw new Error(`Invalid ${key} value: ${key === 'documentation.ia' ? 'expected IA JSON with preset, repo-relative decision, optional tracks and verification' : key === 'documentation.navOwner' ? 'expected nav-sync or hand-authored' : 'expected a non-empty path/URL string or ordered non-empty string array'}.`);
         }
         let raw = { version: 1 };
         try {
@@ -1818,18 +1873,18 @@ async function setConfigValue(repoRoot, userConfigDir, key, rawValue, surface, d
             throw new Error(`Expected a documentation object in ${configPath}`);
         }
         // Patch only the declared input; do not normalize away unrelated or future fields.
-        if (!isDeepStrictEqual(documentation?.guidance, guidance)) {
+        if (!isDeepStrictEqual(documentation?.[field], value)) {
             await dependencies.atomicWriteJson(configPath, {
                 ...raw,
                 documentation: {
                     ...documentation,
-                    guidance,
+                    [field]: value,
                 },
             });
         }
         return {
             key,
-            value: guidance ?? null,
+            value: value ?? null,
             source: effectiveSurface,
         };
     }
@@ -2393,7 +2448,10 @@ async function unsetConfigValue(repoRoot, userConfigDir, key, surface, dependenc
  * runs only when the normalized pass found nothing to remove.
  */
 async function removeFromSurface(repoRoot, userConfigDir, key, effectiveSurface, path, dependencies) {
-    if (key === 'documentation.guidance') {
+    if (key === 'documentation.nonReaderPaths' ||
+        key === 'documentation.guidance' ||
+        key === 'documentation.ia' ||
+        key === 'documentation.navOwner') {
         const configPath = effectiveSurface === 'user'
             ? join(userConfigDir, 'config.json')
             : join(repoRoot, '.oat', 'config.json');

package/dist/commands/docs/index-generate/generator.d.ts

@@ -1,8 +1,12 @@
+export { createExclusionMatcher } from '../../docs/shared/exclusions.js';
+export type { ExclusionMatcher } from '../../docs/shared/exclusions.js';
 export interface IndexEntry {
     title: string;
     description?: string;
     path: string;
     children?: IndexEntry[];
+    /** Present Contents did not list this direct reader entry. */
+    unlisted?: boolean;
 }
 export interface GenerateIndexOptions {
     /**
@@ -12,40 +16,6 @@ export interface GenerateIndexOptions {
      */
     excludes?: string[];
 }
-/**
- * A compiled exclusion list.
- *
- * Files and directories are asked separately so a trailing-slash pattern can
- * mean "directories only" while every other pattern applies to both.
- */
-export interface ExclusionMatcher {
-    excludesFile: (relativePath: string) => boolean;
-    excludesDirectory: (relativePath: string) => boolean;
-}
-/**
- * Compile exclusion globs matched against **docs-root-relative POSIX paths**
- * (`api/auth.md`, `api/nested`), never against absolute or CWD-relative ones.
- *
- * Grammar, defined once and documented in
- * `apps/oat-docs/docs/reference/oat-directory-structure.md`:
- *
- * - `*` matches any run of characters inside a single path segment.
- * - `**` spans `/` only as a whole segment, where it covers zero or more
- *   segments: `**\/CLAUDE.md` matches `CLAUDE.md` and `api/CLAUDE.md`. Inside a
- *   segment (`a**b`) it is an ordinary single-segment wildcard.
- * - Patterns are anchored at both ends against the whole relative path, so a
- *   bare `CLAUDE.md` matches only the root-level file. Use `**\/CLAUDE.md` for
- *   every depth.
- * - A trailing `/` restricts a pattern to directories: `drafts/` prunes the
- *   `drafts` directory and everything beneath it, and never matches a file.
- *   Without it, a pattern that matches a directory path prunes it too.
- * - Matching is case-sensitive, `/` is the separator on every platform, and
- *   `*` is the only metacharacter — `.`, `+`, and friends are literal.
- *
- * Entries are trimmed; a leading `./` or `/` is stripped so both spellings
- * anchor at the docs root. Blank entries are ignored.
- */
-export declare function createExclusionMatcher(patterns: readonly string[]): ExclusionMatcher;
 export declare function generateIndex(docsDir: string, options?: GenerateIndexOptions): Promise<IndexEntry[]>;
 export declare function renderIndex(entries: IndexEntry[]): string;
 //# sourceMappingURL=generator.d.ts.map

package/dist/commands/docs/index-generate/generator.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"generator.d.ts","sourceRoot":"","sources":["../../../../src/commands/docs/index-generate/generator.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,UAAU;IACzB,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,CAAC,EAAE,UAAU,EAAE,CAAC;CACzB;AAED,MAAM,WAAW,oBAAoB;IACnC;;;;OAIG;IACH,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;CACrB;AAED;;;;;GAKG;AACH,MAAM,WAAW,gBAAgB;IAC/B,YAAY,EAAE,CAAC,YAAY,EAAE,MAAM,KAAK,OAAO,CAAC;IAChD,iBAAiB,EAAE,CAAC,YAAY,EAAE,MAAM,KAAK,OAAO,CAAC;CACtD;AAmHD;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,SAAS,MAAM,EAAE,GAC1B,gBAAgB,CAwClB;AAqID,wBAAsB,aAAa,CACjC,OAAO,EAAE,MAAM,EACf,OAAO,GAAE,oBAAyB,GACjC,OAAO,CAAC,UAAU,EAAE,CAAC,CAMvB;AAmBD,wBAAgB,WAAW,CAAC,OAAO,EAAE,UAAU,EAAE,GAAG,MAAM,CAMzD"}
+{"version":3,"file":"generator.d.ts","sourceRoot":"","sources":["../../../../src/commands/docs/index-generate/generator.ts"],"names":[],"mappings":"AAYA,OAAO,EAAE,sBAAsB,EAAE,MAAM,kCAAkC,CAAC;AAC1E,YAAY,EAAE,gBAAgB,EAAE,MAAM,kCAAkC,CAAC;AAEzE,MAAM,WAAW,UAAU;IACzB,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,CAAC,EAAE,UAAU,EAAE,CAAC;IACxB,8DAA8D;IAC9D,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAED,MAAM,WAAW,oBAAoB;IACnC;;;;OAIG;IACH,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;CACrB;AAgLD,wBAAsB,aAAa,CACjC,OAAO,EAAE,MAAM,EACf,OAAO,GAAE,oBAAyB,GACjC,OAAO,CAAC,UAAU,EAAE,CAAC,CAMvB;AAuBD,wBAAgB,WAAW,CAAC,OAAO,EAAE,UAAU,EAAE,GAAG,MAAM,CAMzD"}

package/dist/commands/docs/index-generate/generator.js

@@ -1,155 +1,9 @@
 import { readdir, readFile } from 'node:fs/promises';
-import { join } from 'node:path';
-const NO_EXCLUSIONS = {
-    excludesFile: () => false,
-    excludesDirectory: () => false,
-};
-/**
- * Match one path segment against one pattern segment, where `*` is the only
- * metacharacter and never crosses `/`.
- *
- * This is the classic greedy two-pointer wildcard match, deliberately not a
- * compiled regular expression: a pattern like `*a*a*a...` translates to
- * nested-quantifier alternatives that backtrack exponentially, and exclusion
- * patterns come from config and flags where a typo should not hang generation.
- * Restarting from the last `*` instead bounds the work at O(pattern x text).
- */
-function matchSegment(pattern, text) {
-    let patternIndex = 0;
-    let textIndex = 0;
-    let starPatternIndex = -1;
-    let starTextIndex = 0;
-    while (textIndex < text.length) {
-        if (pattern[patternIndex] === '*') {
-            // Collapse a run of stars: within a segment they are all equivalent.
-            while (pattern[patternIndex] === '*') {
-                patternIndex += 1;
-            }
-            if (patternIndex === pattern.length) {
-                return true;
-            }
-            starPatternIndex = patternIndex;
-            starTextIndex = textIndex;
-            continue;
-        }
-        if (patternIndex < pattern.length &&
-            pattern[patternIndex] === text[textIndex]) {
-            patternIndex += 1;
-            textIndex += 1;
-            continue;
-        }
-        if (starPatternIndex === -1) {
-            return false;
-        }
-        // Give the last star one more character and retry from just after it.
-        starTextIndex += 1;
-        patternIndex = starPatternIndex;
-        textIndex = starTextIndex;
-    }
-    while (pattern[patternIndex] === '*') {
-        patternIndex += 1;
-    }
-    return patternIndex === pattern.length;
-}
-/**
- * Match a docs-root-relative path against a pattern, segment by segment, where
- * a whole-segment `**` spans zero or more path segments.
- *
- * Same greedy-restart shape as {@link matchSegment}, one level up, so a pattern
- * full of `**` segments stays bounded too.
- */
-function matchPath(patternSegments, pathSegments) {
-    let patternIndex = 0;
-    let pathIndex = 0;
-    let starPatternIndex = -1;
-    let starPathIndex = 0;
-    while (pathIndex < pathSegments.length) {
-        if (patternSegments[patternIndex] === '**') {
-            while (patternSegments[patternIndex] === '**') {
-                patternIndex += 1;
-            }
-            if (patternIndex === patternSegments.length) {
-                return true;
-            }
-            starPatternIndex = patternIndex;
-            starPathIndex = pathIndex;
-            continue;
-        }
-        if (patternIndex < patternSegments.length &&
-            matchSegment(patternSegments[patternIndex], pathSegments[pathIndex])) {
-            patternIndex += 1;
-            pathIndex += 1;
-            continue;
-        }
-        if (starPatternIndex === -1) {
-            return false;
-        }
-        starPathIndex += 1;
-        patternIndex = starPatternIndex;
-        pathIndex = starPathIndex;
-    }
-    while (patternSegments[patternIndex] === '**') {
-        patternIndex += 1;
-    }
-    return patternIndex === patternSegments.length;
-}
-/**
- * Compile exclusion globs matched against **docs-root-relative POSIX paths**
- * (`api/auth.md`, `api/nested`), never against absolute or CWD-relative ones.
- *
- * Grammar, defined once and documented in
- * `apps/oat-docs/docs/reference/oat-directory-structure.md`:
- *
- * - `*` matches any run of characters inside a single path segment.
- * - `**` spans `/` only as a whole segment, where it covers zero or more
- *   segments: `**\/CLAUDE.md` matches `CLAUDE.md` and `api/CLAUDE.md`. Inside a
- *   segment (`a**b`) it is an ordinary single-segment wildcard.
- * - Patterns are anchored at both ends against the whole relative path, so a
- *   bare `CLAUDE.md` matches only the root-level file. Use `**\/CLAUDE.md` for
- *   every depth.
- * - A trailing `/` restricts a pattern to directories: `drafts/` prunes the
- *   `drafts` directory and everything beneath it, and never matches a file.
- *   Without it, a pattern that matches a directory path prunes it too.
- * - Matching is case-sensitive, `/` is the separator on every platform, and
- *   `*` is the only metacharacter — `.`, `+`, and friends are literal.
- *
- * Entries are trimmed; a leading `./` or `/` is stripped so both spellings
- * anchor at the docs root. Blank entries are ignored.
- */
-export function createExclusionMatcher(patterns) {
-    const filePatterns = [];
-    const directoryPatterns = [];
-    for (const rawPattern of patterns) {
-        const trimmedPattern = rawPattern.trim();
-        if (!trimmedPattern) {
-            continue;
-        }
-        const directoryOnly = trimmedPattern.endsWith('/');
-        const normalized = trimmedPattern
-            .replace(/\/+$/, '')
-            .replace(/^\.\//, '')
-            .replace(/^\/+/, '');
-        if (!normalized) {
-            continue;
-        }
-        const segments = normalized.split('/');
-        directoryPatterns.push(segments);
-        if (!directoryOnly) {
-            filePatterns.push(segments);
-        }
-    }
-    if (directoryPatterns.length === 0) {
-        return NO_EXCLUSIONS;
-    }
-    const matches = (compiled, relativePath) => {
-        const pathSegments = relativePath.split('/');
-        return compiled.some((segments) => matchPath(segments, pathSegments));
-    };
-    return {
-        excludesFile: (relativePath) => matches(filePatterns, relativePath),
-        excludesDirectory: (relativePath) => matches(directoryPatterns, relativePath),
-    };
-}
+import { join, relative, resolve } from 'node:path';
+import { hasIndexContents, parseIndexContents, } from '../../docs/nav/contents.js';
+import { resolveFolderTitle } from '../../docs/nav/fumadocs.js';
+import { createExclusionMatcher, } from '../../docs/shared/exclusions.js';
+export { createExclusionMatcher } from '../../docs/shared/exclusions.js';
 const FRONTMATTER_RE = /^---\n([\s\S]*?)\n---/;
 const HEADING_RE = /^#\s+(.+)$/m;
 function fileNameToTitle(fileName) {
@@ -206,17 +60,18 @@ function sortEntries(entries) {
 function prefixEntryPath(entry, prefix) {
     return {
         ...entry,
-        path: join(prefix, entry.path),
+        path: relativeKey(prefix, entry.path),
         children: entry.children?.map((child) => prefixEntryPath(child, prefix)),
     };
 }
-/** Docs-root-relative POSIX path used for matching, never for reading files. */
+/** Relative POSIX path used for matching and manifests, never for file IO. */
 function relativeKey(base, name) {
     return base ? `${base}/${name}` : name;
 }
 async function collectEntries(docsDir, relativeBase, matcher) {
     const entries = [];
     const subdirs = [];
+    let indexMarkdown;
     const dirEntries = await readdir(docsDir, { withFileTypes: true });
     for (const entry of dirEntries) {
         const relativePath = relativeKey(relativeBase, entry.name);
@@ -231,6 +86,8 @@ async function collectEntries(docsDir, relativeBase, matcher) {
             }
             const filePath = join(docsDir, entry.name);
             const content = await readFile(filePath, 'utf8');
+            if (entry.name === 'index.md')
+                indexMarkdown = content;
             const { title, description } = resolveTitle(content, entry.name);
             entries.push({
                 title,
@@ -246,13 +103,50 @@ async function collectEntries(docsDir, relativeBase, matcher) {
         // them, and it composes upward through the recursion.
         if (children.length > 0) {
             entries.push({
-                title: fileNameToTitle(subdir),
+                title: children.find((child) => child.path === 'index.md')
+                    ? (resolveFolderTitle(await readFile(join(docsDir, subdir, 'index.md'), 'utf8')) ?? fileNameToTitle(subdir))
+                    : fileNameToTitle(subdir),
                 path: subdir,
                 children: children.map((child) => prefixEntryPath(child, subdir)),
             });
         }
     }
-    return sortEntries(entries);
+    const fallback = sortEntries(entries);
+    if (indexMarkdown === undefined || !hasIndexContents(indexMarkdown))
+        return fallback;
+    const contents = parseIndexContents(indexMarkdown, join(docsDir, 'index.md'), {
+        allowEmpty: true,
+    });
+    // Contents only orders surviving inventory. Looking up captured paths avoids
+    // probing missing, excluded or outside-root targets with nav's strict resolver.
+    const inventory = new Map();
+    const recordPaths = (entry, direct) => {
+        inventory.set(entry.path, direct);
+        for (const child of entry.children ?? [])
+            recordPaths(child, direct);
+    };
+    for (const entry of entries)
+        recordPaths(entry, entry);
+    const ordered = [];
+    const add = (entry) => {
+        if (entry && !ordered.includes(entry))
+            ordered.push(entry);
+    };
+    add(entries.find((entry) => entry.path === 'index.md'));
+    for (const entry of contents) {
+        const href = entry.href.split('#', 1)[0]?.trim() ?? '';
+        if (!href || /^[a-z][a-z0-9+.-]*:/i.test(href) || href.startsWith('//'))
+            continue;
+        const local = relative(docsDir, resolve(docsDir, href)).replaceAll('\\', '/');
+        if (local === '..' || local.startsWith('../'))
+            continue;
+        add(inventory.get(local));
+    }
+    for (const entry of fallback) {
+        if (!ordered.includes(entry))
+            ordered.push({ ...entry, unlisted: true });
+    }
+    return ordered;
 }
 export async function generateIndex(docsDir, options = {}) {
     return collectEntries(docsDir, '', createExclusionMatcher(options.excludes ?? []));
@@ -262,12 +156,12 @@ function renderEntries(entries, indent) {
     const prefix = '  '.repeat(indent);
     for (const entry of entries) {
         if (entry.children) {
-            lines.push(`${prefix}- ${entry.title}`);
+            lines.push(`${prefix}- ${entry.title}${entry.unlisted ? ' [unlisted in Contents]' : ''}`);
             lines.push(...renderEntries(entry.children, indent + 1));
         }
         else {
             const desc = entry.description ? ` — ${entry.description}` : '';
-            lines.push(`${prefix}- [${entry.title}](${entry.path})${desc}`);
+            lines.push(`${prefix}- [${entry.title}](${entry.path})${desc}${entry.unlisted ? ' [unlisted in Contents]' : ''}`);
         }
     }
     return lines;

package/dist/commands/docs/index-generate/index.d.ts

@@ -1,7 +1,7 @@
 import { type CommandContext, type GlobalOptions } from '../../../app/command-context.js';
 import { type OatConfig } from '../../../config/oat-config.js';
 import { Command } from 'commander';
-export declare const GENERATED_INDEX_WARNING = "<!-- AUTOGENERATED by `oat docs generate-index`. Do not hand-edit; changes are clobbered on every `predev` / `prebuild`. -->";
+export declare const GENERATED_INDEX_WARNING = "<!-- AUTOGENERATED by `oat docs generate-index`. Do not hand-edit; run `oat docs generate-index` to regenerate. -->";
 interface IndexGenerateFileDependencies {
     generateIndex: (docsDir: string, options: import('./generator.js').GenerateIndexOptions) => Promise<import('./generator.js').IndexEntry[]>;
     renderIndex: (entries: import('./generator.js').IndexEntry[]) => string;

package/dist/commands/docs/index-generate/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/docs/index-generate/index.ts"],"names":[],"mappings":"AAWA,OAAO,EAEL,KAAK,cAAc,EACnB,KAAK,aAAa,EACnB,MAAM,sBAAsB,CAAC;AAE9B,OAAO,EACL,KAAK,SAAS,EAGf,MAAM,oBAAoB,CAAC;AAI5B,OAAO,EAAE,OAAO,EAAU,MAAM,WAAW,CAAC;AAI5C,eAAO,MAAM,uBAAuB,iIAC4F,CAAC;AAuBjI,UAAU,6BAA6B;IACrC,aAAa,EAAE,CACb,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,OAAO,aAAa,EAAE,oBAAoB,KAChD,OAAO,CAAC,OAAO,aAAa,EAAE,UAAU,EAAE,CAAC,CAAC;IACjD,WAAW,EAAE,CAAC,OAAO,EAAE,OAAO,aAAa,EAAE,UAAU,EAAE,KAAK,MAAM,CAAC;IACrE,SAAS,EAAE,CACT,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,MAAM,EACf,QAAQ,EAAE,cAAc,KACrB,OAAO,CAAC,IAAI,CAAC,CAAC;IACnB,aAAa,EAAE,CAAC,QAAQ,EAAE,MAAM,KAAK,OAAO,CAAC,SAAS,CAAC,CAAC;IACxD,cAAc,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,SAAS,KAAK,OAAO,CAAC,IAAI,CAAC,CAAC;IACvE,eAAe,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC;IAClD,SAAS,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;IAC9C,iBAAiB,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC;IAC5D,QAAQ,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC;IAC5C,iBAAiB,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC;CAC7D;AAED,UAAU,yBAAyB;IACjC,mBAAmB,EAAE,CAAC,OAAO,EAAE,aAAa,KAAK,cAAc,CAAC;IAChE,QAAQ,EAAE,6BAA6B,CAAC;CACzC;AAspBD,wBAAgB,8BAA8B,CAC5C,SAAS,GAAE,OAAO,CAAC,yBAAyB,CAAM,GACjD,OAAO,CAgCT"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/docs/index-generate/index.ts"],"names":[],"mappings":"AAWA,OAAO,EAEL,KAAK,cAAc,EACnB,KAAK,aAAa,EACnB,MAAM,sBAAsB,CAAC;AAE9B,OAAO,EACL,KAAK,SAAS,EAGf,MAAM,oBAAoB,CAAC;AAI5B,OAAO,EAAE,OAAO,EAAU,MAAM,WAAW,CAAC;AAI5C,eAAO,MAAM,uBAAuB,wHACmF,CAAC;AA2BxH,UAAU,6BAA6B;IACrC,aAAa,EAAE,CACb,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,OAAO,aAAa,EAAE,oBAAoB,KAChD,OAAO,CAAC,OAAO,aAAa,EAAE,UAAU,EAAE,CAAC,CAAC;IACjD,WAAW,EAAE,CAAC,OAAO,EAAE,OAAO,aAAa,EAAE,UAAU,EAAE,KAAK,MAAM,CAAC;IACrE,SAAS,EAAE,CACT,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,MAAM,EACf,QAAQ,EAAE,cAAc,KACrB,OAAO,CAAC,IAAI,CAAC,CAAC;IACnB,aAAa,EAAE,CAAC,QAAQ,EAAE,MAAM,KAAK,OAAO,CAAC,SAAS,CAAC,CAAC;IACxD,cAAc,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,SAAS,KAAK,OAAO,CAAC,IAAI,CAAC,CAAC;IACvE,eAAe,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC;IAClD,SAAS,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;IAC9C,iBAAiB,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC;IAC5D,QAAQ,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC;IAC5C,iBAAiB,EAAE,CAAC,IAAI,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC;CAC7D;AAED,UAAU,yBAAyB;IACjC,mBAAmB,EAAE,CAAC,OAAO,EAAE,aAAa,KAAK,cAAc,CAAC;IAChE,QAAQ,EAAE,6BAA6B,CAAC;CACzC;AAmrBD,wBAAgB,8BAA8B,CAC5C,SAAS,GAAE,OAAO,CAAC,yBAAyB,CAAM,GACjD,OAAO,CAgCT"}

package/dist/commands/docs/index-generate/index.js

@@ -8,7 +8,9 @@ import { dirExists } from '../../../fs/io.js';
 import { normalizeToPosixPath, resolveProjectRoot } from '../../../fs/paths.js';
 import { Command, Option } from 'commander';
 import { generateIndex, renderIndex } from './generator.js';
-export const GENERATED_INDEX_WARNING = '<!-- AUTOGENERATED by `oat docs generate-index`. Do not hand-edit; changes are clobbered on every `predev` / `prebuild`. -->';
+export const GENERATED_INDEX_WARNING = '<!-- AUTOGENERATED by `oat docs generate-index`. Do not hand-edit; run `oat docs generate-index` to regenerate. -->';
+// Released before the tooling-aware regeneration instructions were introduced.
+const LEGACY_GENERATED_INDEX_WARNING = '<!-- AUTOGENERATED by `oat docs generate-index`. Do not hand-edit; changes are clobbered on every `predev` / `prebuild`. -->';
 const YAML_EXTENSIONS = ['.yml', '.yaml'];
 /**
  * Exit codes, per the `packages/cli/AGENTS.md` taxonomy.
@@ -59,11 +61,19 @@ const DEFAULT_DEPENDENCIES = {
     buildCommandContext,
     fileDeps: DEFAULT_FILE_DEPS,
 };
-function buildGeneratedIndexOutput(content) {
+function buildGeneratedIndexOutput(content, tooling) {
+    const regeneration = tooling === 'markdown'
+        ? 'Markdown has no automatic manifest hooks; regenerate explicitly after source changes.'
+        : tooling === 'fumadocs'
+            ? 'Fresh Fumadocs apps regenerate this manifest in predev/prebuild.'
+            : tooling === 'mkdocs'
+                ? 'MkDocs manifests are optional; regenerate explicitly or configure a build hook.'
+                : 'Regenerate after source changes, or configure a dev/build hook.';
+    const header = `${GENERATED_INDEX_WARNING}\n<!-- ${regeneration} -->`;
     if (!content) {
-        return GENERATED_INDEX_WARNING;
+        return header;
     }
-    return `${GENERATED_INDEX_WARNING}\n\n${content}`;
+    return `${header}\n\n${content}`;
 }
 /**
  * True when the relative path escapes its base. A bare `startsWith('..')` test
@@ -171,10 +181,11 @@ function collectExclude(value, previous) {
  * repository deliberately excluded. Entries are trimmed, blanks are dropped,
  * and duplicates collapse while preserving first-seen order.
  */
-function resolveExcludes(config, flagValues) {
+function resolveExcludes(config, flagValues, nonReaderPaths = []) {
     const merged = [];
     for (const value of [
         ...(config.documentation?.excludes ?? []),
+        ...nonReaderPaths,
         ...(flagValues ?? []),
     ]) {
         const entry = value.trim();
@@ -252,7 +263,13 @@ async function resolveIndexGeneratePaths(context, options, deps) {
         docsDirSource,
         outputPath,
         outputIsExplicit,
-        excludes: resolveExcludes(config, options.exclude),
+        excludes: resolveExcludes(config, options.exclude, configuredRoot &&
+            docsDir ===
+                (!isMarkdown && (await deps.dirExists(join(configuredRoot, 'docs')))
+                    ? join(configuredRoot, 'docs')
+                    : configuredRoot)
+            ? config.documentation?.nonReaderPaths
+            : []),
     };
 }
 /** `canonicalize`, but an unresolvable path yields null instead of throwing. */
@@ -359,7 +376,8 @@ async function assertOutputIsSafe(resolved, canonical, deps) {
         return;
     }
     const existing = await deps.readFileIfPresent(outputPath);
-    if (existing !== null && !existing.includes(GENERATED_INDEX_WARNING)) {
+    if (existing !== null &&
+        ![GENERATED_INDEX_WARNING, LEGACY_GENERATED_INDEX_WARNING].some((marker) => existing.includes(marker))) {
         throw new CliError(`Refusing to overwrite ${outputPath}: the file exists and is not a generated index ` +
             '(it has no `oat docs generate-index` AUTOGENERATED header). ' +
             'Move or delete it, or pass --output to name it explicitly.', REFUSAL_EXIT_CODE);
@@ -412,7 +430,7 @@ async function runIndexGenerate(context, options, deps) {
     const entries = await deps.generateIndex(docsDir, {
         excludes: resolved.excludes,
     });
-    const content = buildGeneratedIndexOutput(deps.renderIndex(entries));
+    const content = buildGeneratedIndexOutput(deps.renderIndex(entries), resolved.config.documentation?.tooling);
     await deps.writeFile(outputPath, content, 'utf8');
     if (isFumadocsManifestTransition(resolved, canonical)) {
         const indexPath = buildDocumentationIndexValue(resolved, canonical);

package/dist/commands/docs/init/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/commands/docs/init/index.ts"],"names":[],"mappings":"AAGA,OAAO,EAEL,KAAK,cAAc,EACnB,KAAK,aAAa,EACnB,MAAM,sBAAsB,CAAC;AAE9B,OAAO,EACL,KAAK,mBAAmB,EAGxB,sBAAsB,EAEvB,MAAM,4BAA4B,CAAC;AACpC,OAAO,EAGL,KAAK,aAAa,EAClB,KAAK,YAAY,EAElB,MAAM,iCAAiC,CAAC;AAEzC,OAAO,EACL,KAAK,SAAS,EAGf,MAAM,oBAAoB,CAAC;AAG5B,OAAO,EAAE,OAAO,EAAU,MAAM,WAAW,CAAC;AAU5C,OAAO,EAIL,KAAK,uBAAuB,EAK7B,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EAEL,KAAK,sBAAsB,EAC5B,MAAM,gBAAgB,CAAC;AAgBxB,UAAU,uBAAuB;IAC/B,YAAY,EAAE,MAAM,EAAE,CAAC;IACvB,OAAO,EAAE,MAAM,CAAC;IAChB,gBAAgB,CAAC,EAAE,sBAAsB,CAAC;IAC1C,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;IAC1B,eAAe,CAAC,EAAE,MAAM,EAAE,CAAC;IAC3B,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB,OAAO,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,EAAE,CAAC;QAAC,MAAM,EAAE,OAAO,CAAA;KAAE,CAAC;IAC/C,YAAY,CAAC,EACT,SAAS,GACT,SAAS,GACT,WAAW,GACX,QAAQ,GACR,eAAe,CAAC;IACpB,OAAO,CAAC,EAAE;QAAE,KAAK,EAAE,UAAU,GAAG,QAAQ,CAAC;QAAC,OAAO,EAAE,MAAM,CAAA;KAAE,CAAC;CAC7D;AAED,UAAU,oBAAoB;IAC5B,mBAAmB,EAAE,CAAC,OAAO,EAAE,aAAa,KAAK,cAAc,CAAC;IAChE,iBAAiB,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,CAAC;IACzC,eAAe,EAAE,CAAC,QAAQ,EAAE,MAAM,KAAK,OAAO,CAAC,UAAU,GAAG,gBAAgB,CAAC,CAAC;IAC9E,gBAAgB,EAAE,CAChB,OAAO,EAAE,MAAM,EACf,YAAY,EAAE,MAAM,EACpB,GAAG,EAAE,aAAa,KACf,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CAAC;IAC5B,eAAe,EAAE,CAAC,CAAC,SAAS,MAAM,EAChC,OAAO,EAAE,MAAM,EACf,OAAO,EAAE,YAAY,CAAC,CAAC,CAAC,EAAE,EAC1B,GAAG,EAAE,aAAa,KACf,OAAO,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;IACvB,WAAW,EAAE,CACX,OAAO,EAAE,cAAc,EACvB,OAAO,EAAE,uBAAuB,EAChC,UAAU,EAAE,MAAM,KACf,OAAO,CAAC,uBAAuB,GAAG,IAAI,CAAC,CAAC;IAC7C,qBAAqB,EAAE,CACrB,QAAQ,EAAE,MAAM,EAChB,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,KACT,OAAO,CAAC,mBAAmB,CAAC,CAAC;IAClC,sBAAsB,EAAE,OAAO,sBAAsB,CAAC;IACtD,aAAa,EAAE,CAAC,QAAQ,EAAE,MAAM,KAAK,OAAO,CAAC,SAAS,CAAC,CAAC;IACxD,aAAa,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,aAAa,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;CAC1E;AA2MD;;;;;;;;;;GAUG;AACH,wBAAgB,oBAAoB,CAAC,OAAO,EAAE,uBAAuB,GAAG,MAAM,CAoC7E;AA0QD,wBAAgB,qBAAqB,CACnC,SAAS,GAAE,OAAO,CAAC,oBAAoB,CAAM,GAC5C,OAAO,CAiET"}

package/dist/commands/docs/init/index.js

@@ -1,10 +1,13 @@
+import { readFile } from 'node:fs/promises';
 import { join } from 'node:path';
 import { buildCommandContext, } from '../../../app/command-context.js';
+import { syncDocsNavigation } from '../../docs/nav/sync.js';
 import { formatAgentsMdGuidanceResult, formatAgentsMdMutationFailure, previewAgentsMdSection, upsertAgentsMdSection, } from '../../shared/agents-md.js';
 import { confirmAction, inputWithDefault, selectWithAbort, } from '../../shared/shared.prompts.js';
 import { readGlobalOptions } from '../../shared/shared.utils.js';
 import { readOatConfig, writeOatConfig, } from '../../../config/oat-config.js';
 import { resolveAssetsRoot } from '../../../fs/assets.js';
+import { atomicWriteJson, fileExists } from '../../../fs/io.js';
 import { Command, Option } from 'commander';
 import { buildDocsCommands } from './docs-commands.js';
 import { applyMarkdownDocsPlan, MarkdownDocsWriteError, planMarkdownDocs, validateMarkdownConfig, validateMarkdownTarget, } from './markdown.js';
@@ -146,7 +149,24 @@ const DEFAULT_DEPENDENCIES = {
             ...config.documentation,
             ...result.documentationConfig,
         };
-        await writeOatConfig(context.cwd, config);
+        // Fresh app creation replaces only the seeded documentation keys. Keep
+        // unknown repository and documentation siblings for other consumers.
+        const configPath = join(context.cwd, '.oat/config.json');
+        const raw = (await fileExists(configPath))
+            ? JSON.parse(await readFile(configPath, 'utf8'))
+            : config;
+        await atomicWriteJson(configPath, {
+            ...raw,
+            documentation: {
+                ...raw.documentation,
+                ...result.documentationConfig,
+            },
+        });
+        await syncDocsNavigation({
+            appRoot: result.appRoot,
+            configuredTooling: options.framework,
+            nonReaderPaths: config.documentation.nonReaderPaths,
+        });
         if (!context.json) {
             context.logger.info(`Scaffolded docs app at ${options.targetDir}`);
             context.logger.info(`  Framework: ${options.framework}`);

package/dist/commands/docs/init/scaffold.d.ts.map

@@ -1 +1 @@
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