@open-agent-toolkit/cli 0.3.8 → 0.3.10

package/dist/commands/backlog/rewrite-references.js

@@ -0,0 +1,516 @@
+import { execFile } from 'node:child_process';
+import { randomBytes } from 'node:crypto';
+import { constants as fsConstants, lstatSync } from 'node:fs';
+import { lstat, open as openFile, readdir, realpath, rename, unlink, } from 'node:fs/promises';
+import { basename, dirname, join, relative, resolve, sep } from 'node:path';
+import { promisify } from 'node:util';
+const execFileAsync = promisify(execFile);
+/** Characters that end a path-like token when scanning Markdown text. */
+const TOKEN_DELIMITERS = new Set([
+    ' ',
+    '\t',
+    '\n',
+    '\r',
+    '(',
+    ')',
+    '[',
+    ']',
+    '<',
+    '>',
+    '"',
+    "'",
+    '`',
+    '|',
+    ',',
+    '=',
+]);
+const SKIPPED_DIRECTORIES = new Set(['.git', 'node_modules']);
+function toPosix(path) {
+    return path.split(sep).join('/');
+}
+/**
+ * Derive the scan layout from the backlog root. The canonical backlog lives at
+ * `<repo>/.oat/repo/pjm/backlog`; a non-canonical `--backlog-root` scans only
+ * the backlog root itself.
+ */
+function resolveLayout(backlogRoot) {
+    const backlog = resolve(backlogRoot);
+    const pjm = dirname(backlog);
+    if (basename(backlog) !== 'backlog' || basename(pjm) !== 'pjm') {
+        return { scanRoot: backlog, repoRoot: null };
+    }
+    const scanRoot = dirname(pjm);
+    const oatDir = dirname(scanRoot);
+    const repoRoot = basename(scanRoot) === 'repo' && basename(oatDir) === '.oat'
+        ? dirname(oatDir)
+        : null;
+    return { scanRoot, repoRoot };
+}
+async function isInsideGitWorkTree(cwd) {
+    try {
+        const { stdout } = await execFileAsync('git', ['rev-parse', '--is-inside-work-tree'], { cwd });
+        return stdout.trim() === 'true';
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * True only for a regular file (never a symlink) whose real path stays inside
+ * `realScanRoot`, so the scan can never read or write outside `.oat/repo`.
+ */
+async function isRegularFileInside(path, realScanRoot) {
+    try {
+        if (!(await lstat(path)).isFile()) {
+            return false;
+        }
+        const real = await realpath(path);
+        return real === realScanRoot || real.startsWith(`${realScanRoot}${sep}`);
+    }
+    catch {
+        return false;
+    }
+}
+/** True when anything (file, directory, or link) exists at `path`. */
+function pathExistsSync(path) {
+    try {
+        lstatSync(path);
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+/** `O_NOFOLLOW` where the platform has it: refuse to open through a symlink. */
+const NO_FOLLOW = fsConstants.O_NOFOLLOW ?? 0;
+async function readNoFollow(path) {
+    const handle = await openFile(path, fsConstants.O_RDONLY | NO_FOLLOW);
+    try {
+        const info = await handle.stat();
+        return {
+            content: await handle.readFile('utf8'),
+            identity: { dev: info.dev, ino: info.ino, mode: info.mode },
+        };
+    }
+    finally {
+        await handle.close();
+    }
+}
+/**
+ * Replace `path` with `content` without ever writing to its existing inode:
+ * write a temporary file in the same (already verified, in-tree) directory,
+ * then rename it over the original. Truncating in place would write through
+ * every other hard link to the same inode, including one outside `.oat/repo`.
+ * Immediately before the rename, the target must still be the regular,
+ * non-symlink file that was read (same device and inode); otherwise the
+ * replacement is abandoned. The original permission bits are preserved.
+ */
+async function replaceAtomically(path, content, identity) {
+    const temporary = join(dirname(path), `.${basename(path)}.oat-rewrite-${process.pid}-${randomBytes(6).toString('hex')}.tmp`);
+    const permissions = identity.mode & 0o7777;
+    const handle = await openFile(temporary, fsConstants.O_WRONLY | fsConstants.O_CREAT | fsConstants.O_EXCL | NO_FOLLOW, permissions);
+    try {
+        try {
+            await handle.writeFile(content, 'utf8');
+            // The creation mode is masked by the umask; set the exact bits.
+            await handle.chmod(permissions);
+        }
+        finally {
+            await handle.close();
+        }
+        const current = await lstat(path);
+        if (!current.isFile() ||
+            current.dev !== identity.dev ||
+            current.ino !== identity.ino) {
+            throw new Error(`${path} changed while its references were being rewritten; it was left untouched. Re-run \`oat backlog archive\` to retry.`);
+        }
+        await rename(temporary, path);
+    }
+    catch (error) {
+        await unlink(temporary).catch(() => undefined);
+        throw error;
+    }
+}
+async function walkMarkdown(directory) {
+    const entries = await readdir(directory, { withFileTypes: true });
+    const files = [];
+    for (const entry of entries) {
+        const path = join(directory, entry.name);
+        if (entry.isDirectory()) {
+            if (!SKIPPED_DIRECTORIES.has(entry.name)) {
+                files.push(...(await walkMarkdown(path)));
+            }
+        }
+        else if (entry.isFile() && entry.name.endsWith('.md')) {
+            files.push(path);
+        }
+    }
+    return files;
+}
+/**
+ * List Markdown files under the scan root: tracked plus untracked-but-not-
+ * ignored files inside a Git work tree, or a filesystem walk outside Git.
+ */
+async function listMarkdownFiles(scanRoot) {
+    const realScanRoot = await realpath(scanRoot);
+    if (await isInsideGitWorkTree(scanRoot)) {
+        const { stdout } = await execFileAsync('git', [
+            'ls-files',
+            '-z',
+            '--cached',
+            '--others',
+            '--exclude-standard',
+            '--',
+            '*.md',
+        ], { cwd: scanRoot, maxBuffer: 64 * 1024 * 1024 });
+        const unique = [...new Set(stdout.split('\0').filter(Boolean))];
+        const files = [];
+        for (const relativePath of unique) {
+            const path = join(scanRoot, relativePath);
+            if (await isRegularFileInside(path, realScanRoot)) {
+                files.push(path);
+            }
+        }
+        return files;
+    }
+    const walked = [];
+    for (const path of await walkMarkdown(scanRoot)) {
+        if (await isRegularFileInside(path, realScanRoot)) {
+            walked.push(path);
+        }
+    }
+    return walked;
+}
+function isRelativeTarget(target) {
+    return (target.length > 0 &&
+        !target.startsWith('/') &&
+        !target.startsWith('#') &&
+        !/^[A-Za-z][A-Za-z0-9+.-]*:/u.test(target));
+}
+/** Render `absolute` relative to `fromDirectory`, keeping a leading `./` style. */
+function relativeFrom(fromDirectory, absolute, original) {
+    const next = toPosix(relative(fromDirectory, absolute));
+    return original.startsWith('./') && !next.startsWith('..')
+        ? `./${next}`
+        : next;
+}
+/**
+ * Rewrite one path token that ends in `<id>.md`. Returns the replacement, or
+ * `null` when the token does not refer to the moved item.
+ */
+function rewriteItemToken(token, context) {
+    const { layout, itemsPath, archivedPath } = context;
+    const itemFile = basename(itemsPath);
+    if (isRelativeTarget(token)) {
+        const fromFile = resolve(context.baseDirectory, token);
+        if (fromFile === itemsPath) {
+            return relativeFrom(context.currentDirectory, archivedPath, token);
+        }
+        // A token that already resolves to a different, existing file is a
+        // working link: never repoint it through a fallback base.
+        if (pathExistsSync(fromFile)) {
+            return null;
+        }
+        for (const base of [layout.repoRoot, layout.scanRoot]) {
+            if (base !== null && resolve(base, token) === itemsPath) {
+                return toPosix(relative(base, archivedPath));
+            }
+        }
+    }
+    // Only a token that resolves to the former items/ path is rewritten. URLs
+    // (any scheme) are never touched or reported; an unresolved local form that
+    // still names `items/<id>.md` is reported for a manual fix. Only
+    // `/`-separated forms are recognized: the token scan requires `/` or a
+    // delimiter before the file name, so backslash paths never reach here.
+    const itemsSuffix = `items/${itemFile}`;
+    if (/^[A-Za-z][A-Za-z0-9+.-]*:/u.test(token)) {
+        return null;
+    }
+    if (token === itemsSuffix || token.endsWith(`/${itemsSuffix}`)) {
+        context.warnings.push(`${context.fileName} references \`${token}\`, which names archived backlog item ${basename(itemFile, '.md')} but does not resolve to its old items/ path; update it by hand.`);
+    }
+    return null;
+}
+/**
+ * Split Markdown into prose, inline code spans, and fenced code blocks.
+ * Fences (``` or ~~~) close on a same-character run at least as long, or run
+ * to the end of the file. Inline code spans pair a backtick run with the next
+ * run of the same length inside one paragraph (a blank line ends it), so a
+ * stray backtick never swallows later paragraphs.
+ */
+export function splitMarkdownCode(content) {
+    const segments = [];
+    const push = (kind, text) => {
+        if (text.length === 0) {
+            return;
+        }
+        const last = segments.at(-1);
+        if (last && last.kind === kind && kind === 'prose') {
+            last.text += text;
+        }
+        else {
+            segments.push({ kind, text });
+        }
+    };
+    const pushParagraph = (text) => {
+        let cursor = 0;
+        const opener = /`+/gu;
+        let match;
+        while ((match = opener.exec(text)) !== null) {
+            const run = match[0];
+            const closer = new RegExp(`(?<!\`)${run}(?!\`)`, 'u');
+            const rest = text.slice(match.index + run.length);
+            const close = closer.exec(rest);
+            if (!close) {
+                continue;
+            }
+            const end = match.index + run.length + close.index + run.length;
+            push('prose', text.slice(cursor, match.index));
+            push('span', text.slice(match.index, end));
+            cursor = end;
+            opener.lastIndex = end;
+        }
+        push('prose', text.slice(cursor));
+    };
+    const pushProse = (text) => {
+        // Blank lines end a paragraph; the separators stay prose.
+        for (const part of text.split(/(\r?\n[ \t]*\r?\n)/u)) {
+            pushParagraph(part);
+        }
+    };
+    const lines = content.split(/(?<=\n)/u);
+    let prose = '';
+    let fence = null;
+    let code = '';
+    for (const line of lines) {
+        if (fence) {
+            code += line;
+            const close = /^ {0,3}(`{3,}|~{3,})[ \t]*\r?\n?$/u.exec(line);
+            if (close &&
+                close[1][0] === fence.char &&
+                close[1].length >= fence.length) {
+                push('fence', code);
+                code = '';
+                fence = null;
+            }
+            continue;
+        }
+        const open = /^ {0,3}(`{3,}|~{3,})/u.exec(line);
+        if (open) {
+            pushProse(prose);
+            prose = '';
+            fence = { char: open[1][0], length: open[1].length };
+            code = line;
+            continue;
+        }
+        prose += line;
+    }
+    pushProse(prose);
+    push('fence', code);
+    return segments;
+}
+/** Report every `items/<id>.md` occurrence left inside code as written. */
+function warnCodeOccurrences(text, context) {
+    const itemFile = basename(context.itemsPath);
+    const needle = `items/${itemFile}`;
+    let index = text.indexOf(needle);
+    while (index !== -1) {
+        const after = text[index + needle.length] ?? '';
+        if (after === '' || !/[A-Za-z0-9_-]/u.test(after)) {
+            context.warnings.push(`${context.fileName} mentions \`${needle}\` inside code, which is left as written; update it by hand if it is a live reference to archived backlog item ${basename(itemFile, '.md')}.`);
+        }
+        index = text.indexOf(needle, index + needle.length);
+    }
+}
+/**
+ * Rewrite an inline code span whose whole content is one path (optionally
+ * with a `#anchor`) that resolves to the moved item — the external-plan
+ * "Source artifact or scope" citation form. Any other span naming the item is
+ * left as written with a warning, so recorded commands keep their meaning.
+ */
+function rewriteCodeSpan(span, context) {
+    const run = /^`+/u.exec(span)[0];
+    const inner = span.slice(run.length, span.length - run.length);
+    const single = /^(\s*)([^\s`]+)(\s*)$/u.exec(inner);
+    if (single) {
+        const [, leading, token, trailing] = single;
+        const hash = token.indexOf('#');
+        const path = hash === -1 ? token : token.slice(0, hash);
+        const anchor = hash === -1 ? '' : token.slice(hash);
+        const itemFile = basename(context.itemsPath);
+        if (path === itemFile || path.endsWith(`/${itemFile}`)) {
+            const replacement = rewriteItemToken(path, context);
+            return replacement === null || replacement === path
+                ? span
+                : `${run}${leading}${replacement}${anchor}${trailing}${run}`;
+        }
+    }
+    warnCodeOccurrences(inner, context);
+    return span;
+}
+/** Rewrite every token in `content` that ends in the item's file name. */
+function rewriteItemTokens(content, context) {
+    const itemFile = basename(context.itemsPath);
+    let output = '';
+    let cursor = 0;
+    let index = content.indexOf(itemFile);
+    while (index !== -1) {
+        const end = index + itemFile.length;
+        const before = index === 0 ? '' : content[index - 1];
+        const after = content[end] ?? '';
+        const boundedBefore = before === '' || before === '/' || TOKEN_DELIMITERS.has(before);
+        const boundedAfter = after === '' || !/[A-Za-z0-9_-]/u.test(after);
+        if (boundedBefore && boundedAfter) {
+            let start = index;
+            while (start > cursor && !TOKEN_DELIMITERS.has(content[start - 1])) {
+                start -= 1;
+            }
+            const token = content.slice(start, end);
+            const replacement = rewriteItemToken(token, context);
+            if (replacement !== null && replacement !== token) {
+                output += content.slice(cursor, start) + replacement;
+                cursor = end;
+            }
+        }
+        index = content.indexOf(itemFile, end);
+    }
+    return output + content.slice(cursor);
+}
+/**
+ * Rebase one relative link target of the moved item, or return it as-is.
+ * Only a target that existed relative to `items/` is rebased, so prose or an
+ * already-broken target is never rewritten into a new broken path.
+ */
+function rebaseTarget(target, context) {
+    if (!isRelativeTarget(target)) {
+        return target;
+    }
+    const absolute = resolve(context.baseDirectory, target);
+    if (absolute === context.itemsPath ||
+        resolve(context.currentDirectory, target) === absolute ||
+        !pathExistsSync(absolute)) {
+        return target;
+    }
+    return relativeFrom(context.currentDirectory, absolute, target);
+}
+/** Rebase `path?query#anchor`, keeping the query and anchor as written. */
+function rebaseWithAnchor(target, context) {
+    const split = target.search(/[?#]/u);
+    const path = split === -1 ? target : target.slice(0, split);
+    const suffix = split === -1 ? '' : target.slice(split);
+    return path.length === 0 ? target : `${rebaseTarget(path, context)}${suffix}`;
+}
+/** A CommonMark link title: `"…"`, `'…'`, or `(…)`. */
+const LINK_TITLE = String.raw `(?:"[^"\n]*"|'[^'\n]*'|\([^)\n]*\))`;
+const INLINE_LINK = new RegExp(String.raw `\]\((?:<([^<>\n]*)>|([^)\s<]+))((?:\s+${LINK_TITLE})?)\)`, 'gu');
+const REFERENCE_DEFINITION = new RegExp(String.raw `^( {0,3}\[(?!\^)[^\]\n]+\]:[ \t]*)(?:<([^<>\n]*)>|([^\s<>]+))((?:[ \t]+${LINK_TITLE})?[ \t]*\r?)$`, 'gmu');
+/**
+ * Rebase the moved item's inline `[text](target "title")` links (angle
+ * destinations and every title form) from `items/` to `archived/`.
+ */
+function rebaseMovedItemInlineLinks(content, context) {
+    return content.replace(INLINE_LINK, (_match, angled, bare, title) => angled !== undefined
+        ? `](<${rebaseWithAnchor(angled, context)}>${title})`
+        : `](${rebaseWithAnchor(bare, context)}${title})`);
+}
+/**
+ * Rebase the moved item's reference definitions (`[label]: <dest> "title"`)
+ * outside fenced code. Footnotes (`[^n]:`) and `[label]: prose` lines — a
+ * destination followed by anything but a title — are not definitions and are
+ * left untouched.
+ */
+function rebaseMovedItemDefinitions(content, context) {
+    const segments = splitMarkdownCode(content);
+    return segments
+        .map((segment, index) => {
+        // Code spans and fences stay exactly as written.
+        if (segment.kind !== 'prose') {
+            return segment.text;
+        }
+        // A prose segment that follows a code span mid-line does not start a
+        // line, so a match at its offset 0 is not a definition.
+        const previous = index === 0 ? null : segments[index - 1].text;
+        const startsLine = previous === null || previous.endsWith('\n');
+        return segment.text.replace(REFERENCE_DEFINITION, (match, prefix, angled, bare, rest, offset) => {
+            if (offset === 0 && !startsLine) {
+                return match;
+            }
+            return angled !== undefined
+                ? `${prefix}<${rebaseWithAnchor(angled, context)}>${rest}`
+                : `${prefix}${rebaseWithAnchor(bare, context)}${rest}`;
+        });
+    })
+        .join('');
+}
+/** Rewrite one file's content: prose tokens, citation spans, moved links. */
+function rewriteContent(content, context, moved) {
+    const itemFile = basename(context.itemsPath);
+    let next = content;
+    if (content.includes(itemFile)) {
+        next = splitMarkdownCode(content)
+            .map((segment) => {
+            if (segment.kind === 'prose') {
+                return rewriteItemTokens(segment.text, context);
+            }
+            if (segment.kind === 'span') {
+                return rewriteCodeSpan(segment.text, context);
+            }
+            warnCodeOccurrences(segment.text, context);
+            return segment.text;
+        })
+            .join('');
+    }
+    if (moved) {
+        next = splitMarkdownCode(next)
+            .map((segment) => segment.kind === 'prose'
+            ? rebaseMovedItemInlineLinks(segment.text, context)
+            : segment.text)
+            .join('');
+        next = rebaseMovedItemDefinitions(next, context);
+    }
+    return next;
+}
+/**
+ * After `items/<id>.md` moved to `archived/<id>.md`, rewrite every reference
+ * to the old path in Markdown under `.oat/repo/**` (links and repository-root
+ * path strings such as `oat_external_plan_sources` frontmatter). An inline code
+ * span is rewritten only when its whole content is a path to the item (the
+ * external-plan citation form); other spans and fenced code are left as
+ * written with a warning, so a recorded command keeps its meaning. References that name the item's `items/` path
+ * but cannot be resolved are reported as warnings and left untouched. The
+ * rewrite is idempotent, so a re-run on an already-archived item is safe.
+ */
+export async function rewriteInboundReferences(backlogRoot, itemsPath, archivedPath, options = {}) {
+    const rebaseMovedItem = options.rebaseMovedItem ?? true;
+    const layout = resolveLayout(backlogRoot);
+    const absoluteItemsPath = resolve(itemsPath);
+    const absoluteArchivedPath = resolve(archivedPath);
+    const displayRoot = layout.repoRoot ?? layout.scanRoot;
+    const rewritten = [];
+    const warnings = [];
+    // The moved item goes first, so a failure on a later file never leaves its
+    // own links half-rebased: a retry (which skips the rebase) stays correct.
+    const files = (await listMarkdownFiles(layout.scanRoot)).sort((left, right) => Number(resolve(right) === absoluteArchivedPath) -
+        Number(resolve(left) === absoluteArchivedPath) ||
+        left.localeCompare(right));
+    for (const file of files) {
+        const absoluteFile = resolve(file);
+        const moved = rebaseMovedItem && absoluteFile === absoluteArchivedPath;
+        const { content, identity } = await readNoFollow(absoluteFile);
+        const context = {
+            layout,
+            itemsPath: absoluteItemsPath,
+            archivedPath: absoluteArchivedPath,
+            fileName: toPosix(relative(displayRoot, absoluteFile)),
+            baseDirectory: moved ? dirname(absoluteItemsPath) : dirname(absoluteFile),
+            currentDirectory: dirname(absoluteFile),
+            warnings,
+        };
+        const next = rewriteContent(content, context, moved);
+        if (next !== content) {
+            await replaceAtomically(absoluteFile, next, identity);
+            rewritten.push(context.fileName);
+        }
+    }
+    return { rewritten, warnings };
+}

package/dist/commands/config/index.d.ts

@@ -12,6 +12,7 @@ interface ConfigCommandDependencies {
     readOatConfigForDefaultScopeRepair: (repoRoot: string) => Promise<OatConfig>;
     readOatConfigForDocumentationExcludesRepair: (repoRoot: string) => Promise<OatConfig>;
     readOatConfigForInstructionPointerExcludesRepair: (repoRoot: string) => Promise<OatConfig>;
+    readOatConfigForInstructionSyncStrategyRepair: (repoRoot: string) => Promise<OatConfig>;
     readOatConfigWithWarnings: (repoRoot: string) => Promise<OatConfigRead>;
     writeOatConfig: (repoRoot: string, config: OatConfig) => Promise<void>;
     readOatLocalConfig: (repoRoot: string) => Promise<OatLocalConfig>;

package/dist/commands/config/index.d.ts.map

@@ -1 +1 @@
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