@promptci/core 0.0.1

package/dist/dead-references.js

@@ -0,0 +1,607 @@
+/**
+ * Dead-reference detector for PromptCI.
+ *
+ * Scans instruction files for references to other local files and flags
+ * ones that don't exist on disk. Catches:
+ *   - Markdown links:  [text](./path/to/file.md)
+ *   - Reference-style links: [text][ref] with a `[ref]: path` definition
+ *   - @-file refs:     @AGENTS.md  |  @docs/guide.md
+ *
+ * External URLs (http/https), anchor-only links (#section), and mailto:
+ * are always skipped. Only paths with a recognisable file extension are
+ * checked to avoid false-positiving on badge shields, npm package names, etc.
+ *
+ * Findings are heuristic — wording is intentionally cautious.
+ */
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+import * as crypto from 'node:crypto';
+// ── Patterns ──────────────────────────────────────────────────────────────────
+/** Matches markdown inline links: [label](target) — captures target (may include a title). */
+const MD_LINK_RE = /\[(?:[^\]]*)\]\(([^)]+)\)/g;
+const NESTED_MD_LINK_RE = /\[(?:[^\]]|\]\([^)]*\))*\]\(([^)]+)\)/g;
+/**
+ * Matches markdown reference-style link definitions: `[ref]: path/to/file.md "Title"`
+ * These are easy to miss because the usage site `[text][ref]` never carries the path —
+ * only the definition line does.
+ */
+const LINK_REF_DEF_RE = /^[ \t]{0,3}\[[^\]]+\]:\s*(\S+)/gm;
+/**
+ * Matches @-file references: @AGENTS.md, @./path/file.ts, @docs/guide.md
+ * Only captures paths that have a recognisable file extension.
+ */
+const AT_FILE_RE = /(?<!\w)@((?:\.{1,2}\/)?[\w./\\-]+\.(?:md|ts|js|mjs|cjs|tsx|jsx|json|yml|yaml|toml|txt|sh|py|cs|go|rs))/g;
+/**
+ * Matches backtick-enclosed file paths: `scripts/setup-dev.sh`, `Assets/Scripts/Foo.cs`
+ * Only fires when the content looks like a file path:
+ *   - No spaces (commands like `npm run build` are excluded)
+ *   - Has a recognisable extension
+ * This catches prose references like "see `docs/guide.md`" that aren't markdown links.
+ * An optional trailing `:line` or `:line:col` suffix (e.g. `src/gone.ts:42`) is allowed
+ * after the extension but excluded from the captured path.
+ */
+const BACKTICK_PATH_RE = /`([^\s`\n]+\.(?:md|sh|py|ts|js|tsx|jsx|mjs|cjs|json|yml|yaml|toml|cs|go|rs|txt|lock|env|png|jpg|jpeg|gif|svg|webp|pdf))(?::\d+(?::\d+)?)?`/g;
+/**
+ * BUG-004: Bullet-list bare file paths in Repository Layout / Project Structure sections.
+ * Catches lines like:
+ *   - docs/runbook.md
+ *   * src/middleware/auth.rs
+ * Requires at least one slash (directory component) to avoid false-positiving on
+ * single-word filenames.
+ */
+const BULLET_PATH_RE = /^[ \t]*[-*+]\s+((?:[\w.-]+\/)+[\w.-]+\.(?:md|ts|js|tsx|jsx|mjs|cjs|json|yml|yaml|toml|sh|py|cs|go|rs|txt|png|jpg|jpeg|gif|svg|webp|pdf))\b/gm;
+/**
+ * BUG-004: ASCII/Unicode directory-tree listing paths.
+ * Catches Unicode tree drawings:
+ *   ├── docs/runbook.md
+ *   └── rate-limiting.md
+ * and their common ASCII-art equivalents:
+ *   |-- docs/runbook.md
+ *   `-- rate-limiting.md
+ * The Unicode connector chars are unambiguous, so a bare space run after them is enough.
+ * The ASCII fallback chars (`|`, `+`, backtick) are also ordinary punctuation elsewhere
+ * (table pipes, code spans), so we require at least one dash in the connector to avoid
+ * misreading a markdown table cell as a tree entry.
+ */
+/**
+ * BUG-004: Headings that indicate a repository/file layout section.
+ * When a file contains a heading matching this pattern, we also scan for
+ * bare paths in bullet lists and directory tree listings.
+ *
+ * Matches both real markdown headings (`## Project Structure`) and bolded
+ * pseudo-headings on their own line (`**Project Structure**`), since authors
+ * commonly use bold text in lieu of a heading for this kind of section.
+ */
+const LAYOUT_KEYWORDS_SRC = 'repository\\s+layout|project\\s+structure|file\\s+structure|folder\\s+structure|' +
+    'directory\\s+(?:structure|layout|tree|overview)|project\\s+tree|repo\\s+(?:structure|layout|map)|' +
+    'file\\s+tree|files?\\s+overview|codebase\\s+(?:map|overview|structure|layout)|layout';
+const LAYOUT_SECTION_HEADING_RE = new RegExp(`^(?:#{1,4}\\s+.*\\b(?:${LAYOUT_KEYWORDS_SRC})\\b|\\*\\*[^*\\n]*\\b(?:${LAYOUT_KEYWORDS_SRC})\\b[^*\\n]*\\*\\*\\s*)`, 'im');
+/**
+ * BUG-D1: Creation-intent phrasing. A reference introduced by an instruction to
+ * CREATE a file ("Create a file named `.github/workflows/promptci.yml` in your
+ * repository") is a template for the reader's own repo, not a claim that the
+ * file exists here — so its absence must not be flagged as a broken reference.
+ * Requires a creation verb + a file-ish noun + a connector, keeping it specific
+ * enough to avoid suppressing ordinary "see `docs/guide.md`" references.
+ *
+ * The trailing group captures the introduced target path so ONLY that ref is
+ * suppressed — an unrelated broken ref that merely shares the line (e.g.
+ * "Create a file named `ci.yml`, like the one in `docs/other.md`") is still
+ * flagged.
+ */
+const CREATION_INTENT_RE = /\b(?:create|add|generate|scaffold|place|put|save|make)\s+(?:a\s+|an\s+|the\s+|your\s+|this\s+|new\s+)*(?:file|workflow|config(?:uration)?|script|action|manifest|template|module|component)\b[^.\n]*?\b(?:named|called|at|as|in|to|like)\s+[`'"(]*([^\s`'"()]+)/i;
+/** Normalizes a ref for creation-target comparison (slashes, ./ prefix, case). */
+function normalizeRefPath(ref) {
+    return stripFragment(ref).replace(/\\/g, '/').replace(/^\.\//, '').toLowerCase();
+}
+/** File extensions we consider worth checking. */
+const CHECKABLE_EXTENSIONS = new Set([
+    '.md', '.ts', '.js', '.mjs', '.cjs', '.tsx', '.jsx',
+    '.json', '.yml', '.yaml', '.toml', '.txt', '.sh', '.py', '.cs', '.go', '.rs',
+    // BUG-006: image and document links (e.g. [./docs/architecture.png]) were previously
+    // ignored because their extensions weren't in this set.
+    '.png', '.jpg', '.jpeg', '.gif', '.svg', '.webp', '.pdf',
+]);
+// ── Helpers ───────────────────────────────────────────────────────────────────
+function isExternalRef(ref) {
+    return /^https?:\/\/|^mailto:|^#|^data:/.test(ref.trimStart());
+}
+/**
+ * Strips a markdown link title from a raw link target.
+ * `docs/missing.md "The Guide"` → `docs/missing.md`
+ * `docs/missing.md 'The Guide'` → `docs/missing.md`
+ * Titles are only recognised when quoted, per the CommonMark link title grammar.
+ */
+function stripLinkTitle(raw) {
+    const trimmed = raw.trim();
+    const angleMatch = /^<([^>]+)>(?:\s+(?:"[^"]*"|'[^']*'))?\s*$/.exec(trimmed);
+    if (angleMatch)
+        return angleMatch[1];
+    const titleMatch = /^(\S+)\s+(?:"[^"]*"|'[^']*')\s*$/.exec(trimmed);
+    return titleMatch ? titleMatch[1] : trimmed;
+}
+/**
+ * BUG-009 / BUG-012: Placeholder / example filenames and template paths.
+ *
+ * Skipped cases:
+ *   - Common placeholder stems: foo.ts, bar.go, example.py, sample.md
+ *   - ComponentName-style templates: ComponentName.tsx, MyComponent.tsx
+ *   - Angle-bracket templates: src/features/<domain>/slice.ts
+ *   - Numeric-suffix patterns: file1.ts, file2.go
+ */
+const PLACEHOLDER_STEM_RE = /^(foo|bar|baz|qux|quux|example|sample|placeholder|stub|demo|test|your[-_]?file|my[-_]?file|filename|file[-_]?name)(\.\w+)?$/i;
+/**
+ * BUG-C2: Generic bare filenames that commonly appear as naming-convention examples
+ * in instruction files (e.g. "name your files like `tokens.json`") rather than as
+ * references to specific existing files. Only suppressed when the reference has NO
+ * directory prefix — `src/tokens.json` is specific enough to check.
+ */
+const GENERIC_BARE_FILENAMES = new Set([
+    'tokens.json', 'config.json', 'settings.json', 'schema.json', 'manifest.json',
+    'types.ts', 'types.d.ts', 'index.ts', 'index.js', 'main.ts', 'main.go',
+    'app.ts', 'app.js', 'constants.ts', 'utils.ts', 'helpers.ts', 'globals.ts',
+    'routes.ts', 'store.ts', 'models.ts', 'services.ts',
+    // Universal project root files — always present in their respective ecosystems;
+    // flagging them as dead references is always a false positive in real projects.
+    'package.json', 'package-lock.json', 'pnpm-lock.yaml', 'yarn.lock',
+    'tsconfig.json', 'tsconfig.base.json',
+    'pyproject.toml', 'cargo.toml',
+    // Framework config roots
+    'next.config.js', 'next.config.ts', 'next.config.mjs',
+    'vite.config.ts', 'vite.config.js', 'vite.config.mjs',
+    'eslint.config.js', 'eslint.config.mjs', 'eslint.config.cjs',
+    '.eslintrc.json', '.eslintrc.js', '.eslintrc.yml',
+    'jest.config.ts', 'jest.config.js', 'jest.config.mjs',
+    'vitest.config.ts', 'vitest.config.mts',
+]);
+/**
+ * BUG-012: Component/entity name templates used in naming-convention examples.
+ * Matches PascalCase names that are clearly "fill in the blank" placeholders.
+ */
+// Allow multiple extension segments so ComponentName.test.tsx is also caught
+const COMPONENT_TEMPLATE_RE = /^(ComponentName|MyComponent|YourComponent|WidgetName|FeatureName|ModuleName|ServiceName|ModelName|EntityName|ResourceName|DomainName|ControllerName|ScreenName|PageName)(?:\.\w+)*$/i;
+function isPlaceholderRef(ref) {
+    // BUG-012: Angle-bracket template placeholders: src/features/<domain>/slice.ts
+    if (/<[A-Za-z][A-Za-z0-9_-]*>/.test(ref))
+        return true;
+    // BUG-009: Curly-brace template variables: public/locales/{locale}/{namespace}.json
+    // These are pattern descriptions, not real file paths.
+    if (/\{[A-Za-z][A-Za-z0-9_-]*\}/.test(ref))
+        return true;
+    // BUG-006 (eval): Ellipsis segments ("...") are glob placeholders, not real path components.
+    // e.g. "src/test/java/.../unit/" is a structural description, not a literal path.
+    if (ref.split('/').includes('...'))
+        return true;
+    const base = path.basename(stripFragment(ref));
+    // "Real" directory means a path segment beyond a bare `./` or `.\` prefix.
+    // `./sample.md` → dir = '.' → no real directory (still a bare ref)
+    // `scripts/test.sh` → dir = 'scripts' → real directory
+    const dir = path.dirname(stripFragment(ref));
+    const hasRealDirectory = dir !== '.' && dir !== '' && dir !== '.\\' && dir !== './';
+    // Common generic placeholder stems — only suppress when there is no real directory prefix.
+    // A path like `scripts/test.sh` is a real reference even though "test" is a generic stem;
+    // a bare `test.sh` or `./test.sh` is almost certainly a naming-convention example.
+    if (!hasRealDirectory && PLACEHOLDER_STEM_RE.test(base))
+        return true;
+    // BUG-012: PascalCase component/entity name templates
+    if (COMPONENT_TEMPLATE_RE.test(base))
+        return true;
+    const hasDirectoryComponent = hasRealDirectory;
+    if (!hasDirectoryComponent && GENERIC_BARE_FILENAMES.has(base.toLowerCase()))
+        return true;
+    // BUG-005 (eval): Filenames whose stem literally contains a naming-convention term
+    // (camelCase, PascalCase, kebab-case, snake_case) are almost certainly illustrative
+    // examples in a naming-convention section, not references to real project files.
+    // e.g. "useCamelCase.ts", "camelCase.types.ts", "my-kebab-case-component.tsx"
+    if (/camelCase|CamelCase|PascalCase|pascalCase|kebab[-_]?[Cc]ase|snake_?[Cc]ase/.test(base))
+        return true;
+    return false;
+}
+/**
+ * BUG-008: Commonly gitignored credential and environment config files, plus
+ * known tool output directories whose contents are never committed.
+ *
+ * These files/paths are intentionally absent from the repo. Flagging them as
+ * dead references is a false positive; instruction files legitimately reference
+ * them as "where to put your credentials / local config / tool output".
+ *
+ * Matched against the full ref path (not just basename) so that
+ * `config/secrets.py` and `secrets.py` are both caught.
+ */
+const GITIGNORED_CREDENTIAL_PATTERNS = [
+    // PromptCI output directory — config and reports are user-created, never committed
+    /(?:^|[/\\])\.promptci[/\\]/,
+    // Python secrets / credentials
+    /(?:^|[\\/])secrets?\.\w+$/i,
+    /(?:^|[\\/])credentials?\.\w+$/i,
+    // .NET environment-specific appsettings (Development / Production are always gitignored)
+    /appsettings\.(?:Development|Production|Staging|Local)\.\w+$/i,
+    // .env files of any form
+    /(?:^|[\\/])\.env(?:\.\w+)?$/i,
+    // Generic local-override configs
+    /(?:^|[\\/])local\.(?:json|yaml|yml|toml|ini|conf|config)$/i,
+    /\.local\.\w+$/i,
+    // Named private-key files without a cert/key extension (e.g. ~/.ssh/id_rsa)
+    /(?:^|[\\/])(?:private(?:key)?|id_rsa|id_ed25519)(?:\.\w+)?$/i,
+    // Certificate/key file EXTENSIONS, regardless of stem — `certs/server.pem`,
+    // `config/client.key`, and a bare `.pem` must all be treated the same way.
+    /\.(?:pem|key|pfx|p12)$/i,
+];
+function isGitignored(ref) {
+    const normalised = ref.replace(/\\/g, '/');
+    return GITIGNORED_CREDENTIAL_PATTERNS.some((re) => re.test(normalised));
+}
+function hasCheckableExtension(ref) {
+    const ext = path.extname(ref.split('#')[0] ?? '').toLowerCase();
+    return CHECKABLE_EXTENSIONS.has(ext);
+}
+/** Strip query strings and anchor fragments from a path reference. */
+function stripFragment(ref) {
+    return ref.split('#')[0].split('?')[0].trim();
+}
+function fileExists(p) {
+    try {
+        return fs.existsSync(p);
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * BUG-C1: Source-code file extensions. When a path has one of these extensions
+ * and its parent directory exists (but the file itself doesn't), the reference
+ * is likely architecture documentation — reduce confidence accordingly.
+ */
+const SOURCE_CODE_EXTENSIONS = new Set([
+    '.go', '.cs', '.ts', '.tsx', '.js', '.jsx', '.mjs', '.cjs',
+    '.py', '.rs', '.sh', '.java', '.kt', '.swift',
+]);
+/**
+ * BUG-002: Compiled/native source extensions that, when encountered as backtick
+ * inline spans (NOT markdown links or @-refs) in any instruction file type,
+ * should be skipped. These are almost always architecture documentation, not real
+ * file references — e.g. `internal/client/errors.go`, `src/components/Button.tsx`,
+ * `pkg/registry/`, `PlayerController.cs`.
+ *
+ * NOTE: .sh, .py, .js are intentionally excluded — shell/Python/JS scripts are often
+ * legitimately referenced by name in instruction files (e.g. `scripts/setup-dev.sh`).
+ */
+const BACKTICK_SKIP_SOURCE_EXTENSIONS = new Set([
+    '.go', '.rs', '.cs', '.java', '.kt', '.swift',
+    '.ts', '.tsx', // TypeScript source — not config/test scripts
+]);
+/**
+ * Backtick source paths are usually architecture descriptions, but explicit
+ * legacy/old/deprecated/archive examples are often stale file references that
+ * should be checked.
+ */
+const STALE_SOURCE_REF_RE = /(?:^|[/\\])(?:legacy|old|deprecated|archive|archived)(?:[/\\]|[-_.])/i;
+/**
+ * File types for which backtick-enclosed compiled/native source paths should be
+ * skipped. All instruction file types are included because architecture
+ * descriptions appear in all of them.
+ *
+ * BUG-002: Expanded from readme-only to all instruction file types.
+ *
+ * NOTE: this covers every FileType value, which also means backtick-quoted bare
+ * *directory* paths (no extension, e.g. `pkg/registry/`) are always treated as
+ * architecture descriptions rather than checked — that is intentional per
+ * BUG-002, not an oversight.
+ */
+const SKIP_SOURCE_BACKTICK_FILE_TYPES = new Set([
+    'readme', 'claude', 'agents', 'cursor', 'copilot', 'docs', 'prompt', 'unknown',
+]);
+/** Minimum confidence to emit a dead-reference issue. Below this the signal is too noisy. */
+const MIN_CONFIDENCE = 0.45;
+function parentDirExists(p) {
+    try {
+        return fs.existsSync(path.dirname(p));
+    }
+    catch {
+        return false;
+    }
+}
+function issueId(normRef) {
+    const key = `dead-ref:${normRef}`;
+    const hash = crypto.createHash('sha1').update(key).digest('hex').slice(0, 12);
+    return `dead-ref-${hash}`;
+}
+// ── Line-number tracking ────────────────────────────────────────────────────
+/** Offsets (into `content`) at which each line starts. `lineOffsets[i]` is line `i + 1`. */
+function buildLineOffsets(content) {
+    const offsets = [0];
+    for (let i = 0; i < content.length; i++) {
+        if (content[i] === '\n')
+            offsets.push(i + 1);
+    }
+    return offsets;
+}
+/** 1-indexed line number containing the given character offset. */
+function lineForOffset(lineOffsets, offset) {
+    let lo = 0;
+    let hi = lineOffsets.length - 1;
+    while (lo < hi) {
+        const mid = (lo + hi + 1) >> 1;
+        if (lineOffsets[mid] <= offset)
+            lo = mid;
+        else
+            hi = mid - 1;
+    }
+    return lo + 1;
+}
+/**
+ * BUG-002 (eval): Extract implied documentation paths from fenced code blocks inside
+ * Repository Layout sections. Handles listings where a parent directory line
+ * ("docs/") is followed by indented child file entries ("  runbook.md").
+ *
+ * Only extracts .md files — source code file references in layout blocks are
+ * intentionally skipped to avoid false positives in test/instruction-only repos
+ * where no source files are present on disk.
+ *
+ * Called only when the file is known to have a layout section heading.
+ */
+const CODE_BLOCK_LAYOUT_EXT_RE = /\.(?:md|png|jpg|jpeg|gif|svg|webp|pdf)$/i;
+function parseLayoutEntry(rawLine) {
+    const withoutComment = rawLine.replace(/\s*#.*$/, '');
+    const verticalPrefix = withoutComment.match(/^[ \t│|]*/)?.[0] ?? '';
+    const indent = verticalPrefix.replace(/[│|]/g, '    ').length;
+    const trimmed = withoutComment.trim();
+    if (!trimmed)
+        return null;
+    const connectorMatch = /^(?:[│|]\s*)*(?:[├└][-─\s]+|[|+`][-─]+\s*)(.+)$/.exec(trimmed);
+    const entry = (connectorMatch ? connectorMatch[1] : trimmed)?.trim() ?? '';
+    if (!entry)
+        return null;
+    if (!connectorMatch && /\s/.test(entry))
+        return null;
+    return {
+        entry,
+        indent,
+        hasConnector: Boolean(connectorMatch),
+    };
+}
+function collectLayoutEntryPaths(lines, lineOffsets, startOffset) {
+    const results = [];
+    const stack = [];
+    let lineOffset = startOffset;
+    for (const rawLine of lines) {
+        const thisLineOffset = lineOffset;
+        lineOffset += rawLine.length + 1;
+        const parsed = parseLayoutEntry(rawLine);
+        if (!parsed)
+            continue;
+        const entry = parsed.entry;
+        const isDir = /\/$/.test(entry);
+        if (isDir) {
+            const parent = [...stack].reverse().find((item) => item.indent < parsed.indent || (item.indent === parsed.indent && item.plain));
+            const dirPath = `${parent?.path ?? ''}${entry}`;
+            while (stack.length > 0 && stack[stack.length - 1].indent >= parsed.indent) {
+                stack.pop();
+            }
+            stack.push({ indent: parsed.indent, path: dirPath, plain: !parsed.hasConnector });
+            continue;
+        }
+        if (!CODE_BLOCK_LAYOUT_EXT_RE.test(entry))
+            continue;
+        const parent = [...stack].reverse().find((item) => item.indent < parsed.indent || (item.indent === parsed.indent && item.plain));
+        const ref = /[/\\]/.test(entry) ? entry : `${parent?.path ?? ''}${entry}`;
+        results.push({
+            ref,
+            evidence: rawLine.trim(),
+            line: lineForOffset(lineOffsets, thisLineOffset),
+        });
+    }
+    return results;
+}
+function extractCodeBlockLayoutPaths(content, lineOffsets) {
+    const results = [];
+    const fenceRe = /^```[^\n]*\n([\s\S]*?)^```/gm;
+    let blockMatch;
+    while ((blockMatch = fenceRe.exec(content)) !== null) {
+        const blockText = blockMatch[1] ?? '';
+        const firstLineEnd = content.indexOf('\n', blockMatch.index);
+        let lineOffset = firstLineEnd === -1 ? blockMatch.index : firstLineEnd + 1;
+        const lines = blockText.split('\n');
+        results.push(...collectLayoutEntryPaths(lines, lineOffsets, lineOffset));
+    }
+    return results;
+}
+function extractLayoutTreePaths(content, lineOffsets) {
+    return collectLayoutEntryPaths(content.split('\n'), lineOffsets, 0);
+}
+function collectRefs(content, opts = {}) {
+    const found = [];
+    const lineOffsets = buildLineOffsets(content);
+    // Markdown links: [label](target) or [label](target "Title")
+    let m;
+    const linkRe = new RegExp(MD_LINK_RE.source, MD_LINK_RE.flags);
+    while ((m = linkRe.exec(content)) !== null) {
+        if (m.index >= 2 && content[m.index - 2] === '[' && content[m.index - 1] === '!')
+            continue;
+        const raw = m[1] ?? '';
+        const ref = stripFragment(stripLinkTitle(raw));
+        if (ref && !isExternalRef(ref) && hasCheckableExtension(ref)) {
+            found.push({ ref, evidence: `[...](${raw})`, line: lineForOffset(lineOffsets, m.index) });
+        }
+    }
+    const nestedLinkRe = new RegExp(NESTED_MD_LINK_RE.source, NESTED_MD_LINK_RE.flags);
+    while ((m = nestedLinkRe.exec(content)) !== null) {
+        const labelPart = m[0].slice(0, m[0].lastIndexOf(']('));
+        if (!labelPart.includes(']('))
+            continue;
+        const raw = m[1] ?? '';
+        const ref = stripFragment(stripLinkTitle(raw));
+        if (ref && !isExternalRef(ref) && hasCheckableExtension(ref)) {
+            found.push({ ref, evidence: `[...](${raw})`, line: lineForOffset(lineOffsets, m.index) });
+        }
+    }
+    // Reference-style link definitions: [ref]: docs/missing.md "Title"
+    const linkDefRe = new RegExp(LINK_REF_DEF_RE.source, LINK_REF_DEF_RE.flags);
+    while ((m = linkDefRe.exec(content)) !== null) {
+        const raw = m[1] ?? '';
+        const ref = stripFragment(raw);
+        if (ref && !isExternalRef(ref) && hasCheckableExtension(ref)) {
+            found.push({ ref, evidence: m[0].trim(), line: lineForOffset(lineOffsets, m.index) });
+        }
+    }
+    // @-file refs
+    const atRe = new RegExp(AT_FILE_RE.source, AT_FILE_RE.flags);
+    while ((m = atRe.exec(content)) !== null) {
+        const ref = m[1] ?? '';
+        if (ref && !isExternalRef(ref)) {
+            found.push({ ref, evidence: `@${ref}`, line: lineForOffset(lineOffsets, m.index) });
+        }
+    }
+    // Backtick file paths: `scripts/setup-dev.sh`, `Assets/Scripts/Foo.cs`
+    // No spaces = file path not a command; must have a recognisable extension.
+    // Skip glob patterns (contain * or ?) — those are pattern documentation, not file refs.
+    // BUG-002: In all instruction file types (CLAUDE.md, AGENTS.md, .cursorrules, copilot, etc.)
+    // skip backtick-quoted compiled/native source files — they are almost always architecture
+    // descriptions (e.g. `internal/client/errors.go`), not references to committed files.
+    // Shell (.sh), Python (.py), and JS files are kept because they CAN be real script refs.
+    const btRe = new RegExp(BACKTICK_PATH_RE.source, BACKTICK_PATH_RE.flags);
+    while ((m = btRe.exec(content)) !== null) {
+        const ref = m[1] ?? '';
+        if (ref && !isExternalRef(ref) && !ref.includes('*') && !ref.includes('?')) {
+            if (opts.skipSourceBackticks) {
+                const ext = path.extname(ref).toLowerCase();
+                if (BACKTICK_SKIP_SOURCE_EXTENSIONS.has(ext) && !STALE_SOURCE_REF_RE.test(ref))
+                    continue;
+            }
+            found.push({ ref, evidence: `\`${ref}\``, line: lineForOffset(lineOffsets, m.index) });
+        }
+    }
+    // BUG-004: Bare paths in Repository Layout / Project Structure sections.
+    // These appear as bullet list items or ASCII tree lines without backticks.
+    if (LAYOUT_SECTION_HEADING_RE.test(content)) {
+        const bulletRe = new RegExp(BULLET_PATH_RE.source, BULLET_PATH_RE.flags);
+        while ((m = bulletRe.exec(content)) !== null) {
+            const ref = m[1] ?? '';
+            if (ref && !isExternalRef(ref)) {
+                found.push({ ref, evidence: m[0].trim(), line: lineForOffset(lineOffsets, m.index) });
+            }
+        }
+        found.push(...extractLayoutTreePaths(content, lineOffsets));
+        // BUG-002 (eval): Fenced code blocks in layout sections may list documentation
+        // files as indented children under a parent directory line ("docs/\n  runbook.md").
+        for (const item of extractCodeBlockLayoutPaths(content, lineOffsets)) {
+            found.push(item);
+        }
+    }
+    // BUG-D1: Drop only the reference the line instructs the reader to CREATE
+    // (a template for their repo), not every ref that happens to share the line.
+    const contentLines = content.split('\n');
+    return found.filter(({ ref, line }) => {
+        const lineText = contentLines[line - 1] ?? '';
+        const m = CREATION_INTENT_RE.exec(lineText);
+        if (!m)
+            return true;
+        const target = normalizeRefPath(m[1] ?? '');
+        if (!target)
+            return true;
+        const refNorm = normalizeRefPath(ref);
+        // Suppress the ref that IS the creation target (allow basename-level match so
+        // a `path/to/x.yml` ref matches a captured `x.yml` and vice-versa).
+        const isTarget = refNorm === target ||
+            refNorm.endsWith(`/${target}`) ||
+            target.endsWith(`/${refNorm}`);
+        return !isTarget;
+    });
+}
+// ── Detector ─────────────────────────────────────────────────────────────────
+/**
+ * Detect broken file references across all instruction files.
+ *
+ * @param files     Instruction files to scan.
+ * @param repoRoot  Absolute path to repo root — used as a second resolution base.
+ */
+/**
+ * BUG-004 / BUG-005: Group all unresolved references by their normalised path so
+ * that the same dead reference appearing in multiple instruction files produces ONE
+ * consolidated issue (listing all referencing files) instead of N separate issues.
+ *
+ * Previously each (filePath, ref) pair produced its own issue — a single dead path
+ * referenced in both CLAUDE.md and AGENTS.md would fire twice, inflating issue counts
+ * and health-score penalties.
+ */
+export function detectDeadReferences(files, repoRoot) {
+    // normRef → { displayRef, filePaths, fileLines, evidenceLines, minConfidence }
+    const byRef = new Map();
+    for (const file of files) {
+        const fileDir = path.dirname(file.path);
+        const refs = collectRefs(file.content, {
+            skipSourceBackticks: SKIP_SOURCE_BACKTICK_FILE_TYPES.has(file.fileType),
+        });
+        for (const { ref, evidence, line } of refs) {
+            // BUG-009: Skip obvious placeholder/example filenames (foo.ts, bar.go, etc.)
+            if (isPlaceholderRef(ref))
+                continue;
+            // BUG-008: Skip intentionally gitignored credential/config files.
+            if (isGitignored(ref))
+                continue;
+            // Resolve relative to the instruction file first, then repo root.
+            const candidates = [
+                path.resolve(fileDir, ref),
+                path.resolve(repoRoot, ref),
+            ];
+            if (candidates.some(fileExists))
+                continue;
+            // BUG-C1: Source-code paths whose parent directory exists → lower confidence
+            // (likely documentation references, not broken links).
+            const ext = path.extname(ref.split('#')[0] ?? '').toLowerCase();
+            const isSourceCodeRef = SOURCE_CODE_EXTENSIONS.has(ext);
+            const anyParentExists = candidates.some(parentDirExists);
+            const confidence = isSourceCodeRef && anyParentExists ? 0.5 : 0.85;
+            // Normalise for deduplication (case-insensitive, forward slashes)
+            const normRef = ref.toLowerCase().replace(/\\/g, '/');
+            const evidenceLine = `Reference: ${evidence}`;
+            if (!byRef.has(normRef)) {
+                byRef.set(normRef, {
+                    displayRef: ref,
+                    filePaths: new Set(),
+                    fileLines: new Map(),
+                    evidenceLines: [],
+                    minConfidence: confidence,
+                });
+            }
+            const entry = byRef.get(normRef);
+            entry.filePaths.add(file.path);
+            const existingLine = entry.fileLines.get(file.path);
+            if (existingLine === undefined || line < existingLine) {
+                entry.fileLines.set(file.path, line);
+            }
+            if (!entry.evidenceLines.includes(evidenceLine)) {
+                entry.evidenceLines.push(evidenceLine);
+            }
+            entry.minConfidence = Math.min(entry.minConfidence, confidence);
+        }
+    }
+    const issues = [];
+    const MIN_CONFIDENCE_THRESHOLD = MIN_CONFIDENCE;
+    for (const [normRef, { displayRef, filePaths, fileLines, evidenceLines, minConfidence }] of byRef) {
+        // BUG-002: Skip findings below the minimum confidence threshold.
+        // Low-confidence source-code path references are almost certainly architecture docs.
+        if (minConfidence < MIN_CONFIDENCE_THRESHOLD)
+            continue;
+        const allFilePaths = [...filePaths];
+        issues.push({
+            id: issueId(normRef),
+            severity: 'warning',
+            category: 'structure',
+            title: `Broken file reference: ${path.basename(stripFragment(displayRef))}`,
+            summary: `This instruction file references "${displayRef}" which does not appear to exist. ` +
+                `The file may have been renamed, moved, or deleted.`,
+            filePaths: allFilePaths,
+            locations: allFilePaths.map((fp) => {
+                const startLine = fileLines.get(fp);
+                return startLine !== undefined ? { filePath: fp, startLine } : { filePath: fp };
+            }),
+            evidence: evidenceLines,
+            recommendation: 'Verify the path is correct relative to the instruction file location, ' +
+                'or remove the reference if the file no longer exists.',
+            confidence: minConfidence,
+        });
+    }
+    return issues;
+}
+//# sourceMappingURL=dead-references.js.map

package/dist/dead-references.js.map

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package/dist/detectors.d.ts

@@ -0,0 +1,11 @@
+import type { PromptCiIssue } from './types.js';
+import type { RepoContext } from './repo-context.js';
+export type DetectorGroup = 'scan' | 'context';
+export type DetectorDefinition = {
+    id: string;
+    group: DetectorGroup;
+    run: (context: RepoContext) => PromptCiIssue[];
+};
+export declare const DETECTORS: DetectorDefinition[];
+export declare function runDetectors(context: RepoContext, group: DetectorGroup): PromptCiIssue[];
+//# sourceMappingURL=detectors.d.ts.map

package/dist/detectors.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"detectors.d.ts","sourceRoot":"","sources":["../src/detectors.ts"],"names":[],"mappings":"AAsBA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,YAAY,CAAC;AAChD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAErD,MAAM,MAAM,aAAa,GAAG,MAAM,GAAG,SAAS,CAAC;AAE/C,MAAM,MAAM,kBAAkB,GAAG;IAC/B,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,aAAa,CAAC;IACrB,GAAG,EAAE,CAAC,OAAO,EAAE,WAAW,KAAK,aAAa,EAAE,CAAC;CAChD,CAAC;AAEF,eAAO,MAAM,SAAS,EAAE,kBAAkB,EAmIzC,CAAC;AAEF,wBAAgB,YAAY,CAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,aAAa,GAAG,aAAa,EAAE,CAIxF"}