@cleocode/nexus 2026.9.8 → 2026.9.9

package/dist/src/pipeline/filesystem-walker.js

@@ -3,7 +3,7 @@
  *
  * Scans the repository using Node's native `fs.glob` (Node 22+), stats each
  * file to filter large files, and returns a lightweight `ScannedFile[]` list
- * with paths and sizes. No file content is loaded into memory during this phase.
+ * with paths and sizes. Source hashes are streamed through bounded file batches during this phase.
  *
  * Memory footprint: approximately 10 MB for 100 K files (paths + sizes only).
  *
@@ -12,15 +12,19 @@
  *
  * Key adaptations:
  * - Replaces `glob` npm package with Node 24 native `fs.promises.glob`
- * - Replaces `ignore-service` with a minimal built-in gitignore reader
+ * - Uses Git-compatible ignore rules, including nested files and escaped patterns
  * - Adds `.cleo/` to the default exclude list for CLEO projects
  * - Language field added to `ScannedFile` (detected from extension)
  *
  * @task T532
  * @module pipeline/filesystem-walker
  */
+import { spawnSync } from 'node:child_process';
+import { createHash } from 'node:crypto';
+import { existsSync } from 'node:fs';
 import fs from 'node:fs/promises';
 import path from 'node:path';
+import ignore from 'ignore';
 import { detectLanguageFromPath } from './language-detection.js';
 // ---------------------------------------------------------------------------
 // Constants
@@ -71,68 +75,54 @@ const DEFAULT_EXCLUDED_DIRS = new Set([
 /**
  * Read and parse a single ignore file (`.gitignore` or `.cleoignore`) into a list of patterns.
  *
- * Returns an empty array if the file does not exist or cannot be read.
+ * Returns an empty array only when the ignore file does not exist.
  *
  * @param ignorePath - Absolute path to the ignore file
  */
 async function readIgnorePatterns(ignorePath) {
     try {
         const content = await fs.readFile(ignorePath, 'utf-8');
-        return content
-            .split('\n')
-            .map((line) => line.trim())
-            .filter((line) => line.length > 0 && !line.startsWith('#'));
+        return content.split('\n');
     }
-    catch {
-        return [];
+    catch (error) {
+        if (error instanceof Error && 'code' in error && error.code === 'ENOENT')
+            return [];
+        throw error;
     }
 }
-/**
- * Convert a gitignore pattern to a function that tests whether a relative
- * path matches that pattern.
- *
- * Supports the most common gitignore pattern forms:
- * - Plain directory name (`node_modules`) — matches any path component
- * - Negation prefix (`!`) — not implemented here (rare in practice)
- * - Trailing slash — matches only directories (treated as prefix match)
- * - `**` glob — matches any path segment sequence
- *
- * @param pattern - Raw gitignore pattern string
- * @returns Predicate or null if the pattern cannot be compiled
- */
-function buildIgnoreMatcher(pattern) {
-    if (pattern.startsWith('!'))
-        return null; // negation not supported
-    const stripped = pattern.endsWith('/') ? pattern.slice(0, -1) : pattern;
-    if (!stripped)
-        return null;
-    // Simple name-only patterns match any component (e.g. "*.log")
-    const hasSlash = stripped.includes('/');
-    if (!hasSlash) {
-        // Match the pattern against each path component
-        const re = globToRegex(stripped);
-        return (relPath) => {
-            const parts = relPath.split('/');
-            return parts.some((part) => re.test(part));
-        };
+/** Ask Git itself to apply repository, info/exclude and configured global excludes. */
+function gitExcludedPaths(repoPath, paths) {
+    const probe = spawnSync('git', ['rev-parse', '--is-inside-work-tree'], {
+        cwd: repoPath,
+        encoding: 'utf8',
+        timeout: 1000,
+    });
+    if (probe.error)
+        throw probe.error;
+    if (probe.status === 128 && !existsSync(path.join(repoPath, '.git')))
+        return new Set();
+    if (probe.status !== 0)
+        throw new Error(`Git source ownership check failed: ${probe.stderr.trim()}`);
+    const excluded = new Set();
+    for (let offset = 0; offset < paths.length; offset += 256) {
+        const batch = paths.slice(offset, offset + 256);
+        const result = spawnSync('git', ['check-ignore', '--no-index', '-z', '--stdin'], {
+            cwd: repoPath,
+            encoding: 'utf8',
+            input: `${batch.join('\0')}\0`,
+            timeout: 2000,
+            maxBuffer: 4 * 1024 * 1024,
+        });
+        if (result.error)
+            throw result.error;
+        // Git documents exit 1 for no ignored paths; other failures invalidate the scan.
+        if (result.status !== 0 && result.status !== 1)
+            throw new Error(`Git ignore assessment failed: ${result.stderr.trim()}`);
+        for (const ignored of result.stdout.split('\0'))
+            if (ignored)
+                excluded.add(ignored);
     }
-    // Anchored patterns match from the repo root
-    const re = globToRegex(stripped.startsWith('/') ? stripped.slice(1) : stripped);
-    return (relPath) => re.test(relPath);
-}
-/**
- * Convert a simple glob pattern (supporting `*`, `**`, `?`) to a RegExp.
- *
- * @param glob - Glob pattern string
- */
-function globToRegex(glob) {
-    const escaped = glob
-        .replace(/[.+^${}()|[\]\\]/g, '\\$&')
-        .replace(/\*\*/g, '\u0000') // placeholder for **
-        .replace(/\*/g, '[^/]*') // * matches within segment
-        .replace(/\?/g, '[^/]') // ? matches single non-slash char
-        .replace(/\u0000/g, '.*'); // ** matches across segments
-    return new RegExp(`^${escaped}$`);
+    return excluded;
 }
 // ---------------------------------------------------------------------------
 // Core walker
@@ -148,49 +138,116 @@ function globToRegex(glob) {
  * @param onProgress - Optional progress callback invoked for each processed file
  * @returns Array of scanned file entries sorted by relative path
  */
-export async function walkRepositoryPaths(repoPath, onProgress) {
+export async function walkRepositoryPaths(repoPath, onProgress, onFileReport, includedRepositories = []) {
     // Load root .gitignore and .cleoignore patterns
     const gitignorePatterns = await readIgnorePatterns(path.join(repoPath, '.gitignore'));
     const cleoignorePatterns = await readIgnorePatterns(path.join(repoPath, '.cleoignore'));
-    const allIgnorePatterns = [...gitignorePatterns, ...cleoignorePatterns];
-    const ignoreMatchers = allIgnorePatterns
-        .map(buildIgnoreMatcher)
-        .filter((m) => m !== null);
-    /**
-     * Test whether a relative path should be excluded.
-     *
-     * A path is excluded if:
-     * 1. Any component matches a DEFAULT_EXCLUDED_DIRS name, or
-     * 2. Any compiled gitignore matcher returns true for the relative path.
-     */
-    function isExcluded(relPath) {
+    const rootIgnore = ignore().add([...gitignorePatterns, ...cleoignorePatterns]);
+    const nestedPatterns = new Map();
+    /** Apply ordered ignore rules, respecting nested files and negations. */
+    async function isExcluded(relPath, isDirectory) {
         const parts = relPath.split('/');
-        // Check every component against the hard-coded exclusion set
-        for (const part of parts) {
-            if (DEFAULT_EXCLUDED_DIRS.has(part))
+        if (parts.some((part) => DEFAULT_EXCLUDED_DIRS.has(part)))
+            return true;
+        const rules = [['', rootIgnore]];
+        for (let index = 1; index < parts.length; index++) {
+            const directory = parts.slice(0, index).join('/');
+            if (!nestedPatterns.has(directory)) {
+                nestedPatterns.set(directory, ignore().add([
+                    ...(await readIgnorePatterns(path.join(repoPath, directory, '.gitignore'))),
+                    ...(await readIgnorePatterns(path.join(repoPath, directory, '.cleoignore'))),
+                ]));
+            }
+            rules.push([directory, nestedPatterns.get(directory)]);
+        }
+        // An ignored parent cannot be re-included solely by a child negation.
+        for (let index = 1; index <= parts.length; index++) {
+            const candidate = parts.slice(0, index).join('/');
+            let ignored = false;
+            for (const [directory, patterns] of rules) {
+                if (directory && !candidate.startsWith(`${directory}/`))
+                    continue;
+                const localPath = (directory ? candidate.slice(directory.length + 1) : candidate) +
+                    (index < parts.length || isDirectory ? '/' : '');
+                const result = patterns.test(localPath);
+                if (result.ignored)
+                    ignored = true;
+                else if (result.unignored)
+                    ignored = false;
+            }
+            if (ignored)
                 return true;
         }
-        // Check gitignore matchers
-        return ignoreMatchers.some((m) => m(relPath));
+        return false;
     }
     // Collect all relative paths via native glob
     const relativePaths = [];
-    for await (const relPath of fs.glob('**/*', {
+    for await (const entry of fs.glob('**/*', {
         cwd: repoPath,
-        exclude: (name) => DEFAULT_EXCLUDED_DIRS.has(name),
+        withFileTypes: true,
+        exclude: (candidate) => {
+            const absolutePath = path.join(candidate.parentPath, candidate.name);
+            const normalized = path.relative(repoPath, absolutePath).replace(/\\/g, '/');
+            const nestedRepository = (candidate.isDirectory() || candidate.isSymbolicLink()) &&
+                existsSync(path.join(absolutePath, '.git'));
+            const excluded = DEFAULT_EXCLUDED_DIRS.has(candidate.name) ||
+                (nestedRepository && !includedRepositories.includes(normalized));
+            if (excluded)
+                onFileReport?.({
+                    path: normalized,
+                    status: 'excluded',
+                    reason: nestedRepository
+                        ? 'Nested repository requires explicit inclusion'
+                        : 'Default excluded directory',
+                });
+            return excluded;
+        },
     })) {
         // Normalise to forward slashes
+        const relPath = path.relative(repoPath, path.join(entry.parentPath, entry.name));
         const normalised = relPath.replace(/\\/g, '/');
-        if (!isExcluded(normalised)) {
+        // Native directory entries avoid a serial stat for every source; metadata
+        // and content hashes are still captured by the bounded batches below.
+        const isDirectory = entry.isSymbolicLink()
+            ? (await fs.stat(path.join(repoPath, relPath))).isDirectory()
+            : entry.isDirectory();
+        if (!(await isExcluded(normalised, isDirectory))) {
             relativePaths.push(normalised);
         }
+        else {
+            onFileReport?.({ path: normalised, status: 'excluded', reason: 'Ignore rule' });
+        }
+    }
+    // Preserve the parent project binding while evaluating each explicitly included
+    // repository with its own Git configuration (including linked-worktree gitdirs).
+    const scopes = ['', ...includedRepositories].sort((a, b) => b.length - a.length);
+    const scopedPaths = new Map();
+    for (const file of relativePaths) {
+        const scope = scopes.find((candidate) => !candidate || file.startsWith(`${candidate}/`)) ?? '';
+        const local = scope ? file.slice(scope.length + 1) : file;
+        const paths = scopedPaths.get(scope) ?? [];
+        paths.push(local);
+        scopedPaths.set(scope, paths);
+    }
+    const gitExcluded = new Set();
+    for (const [scope, paths] of scopedPaths) {
+        for (const file of gitExcludedPaths(path.join(repoPath, scope), paths)) {
+            const full = scope ? `${scope}/${file}` : file;
+            gitExcluded.add(full);
+            onFileReport?.({
+                path: full,
+                status: 'excluded',
+                reason: 'Git ignore rule (including repository/global excludes)',
+            });
+        }
     }
+    const eligiblePaths = relativePaths.filter((file) => !gitExcluded.has(file));
     // Stat files in batches to filter by size and collect metadata
     const entries = [];
     let processed = 0;
     let skippedLarge = 0;
-    for (let start = 0; start < relativePaths.length; start += STAT_CONCURRENCY) {
-        const batch = relativePaths.slice(start, start + STAT_CONCURRENCY);
+    for (let start = 0; start < eligiblePaths.length; start += STAT_CONCURRENCY) {
+        const batch = eligiblePaths.slice(start, start + STAT_CONCURRENCY);
         const results = await Promise.allSettled(batch.map(async (relPath) => {
             const fullPath = path.join(repoPath, relPath);
             const stat = await fs.stat(fullPath);
@@ -199,9 +256,24 @@ export async function walkRepositoryPaths(repoPath, onProgress) {
                 return null;
             if (stat.size > MAX_FILE_SIZE) {
                 skippedLarge++;
+                onFileReport?.({
+                    path: relPath,
+                    status: 'oversized',
+                    reason: 'Exceeds 512 KB scan limit',
+                    size: stat.size,
+                    mtimeMs: stat.mtimeMs,
+                });
                 return null;
             }
-            return { path: relPath, size: stat.size, language: detectLanguageFromPath(relPath) };
+            return {
+                path: relPath,
+                size: stat.size,
+                mtimeMs: stat.mtimeMs,
+                contentHash: createHash('sha256')
+                    .update(await fs.readFile(fullPath))
+                    .digest('hex'),
+                language: detectLanguageFromPath(relPath),
+            };
         }));
         for (const result of results) {
             processed++;
@@ -212,6 +284,9 @@ export async function walkRepositoryPaths(repoPath, onProgress) {
             else {
                 const batchIndex = processed - 1 - start;
                 const approxPath = batch[batchIndex] ?? batch[batch.length - 1] ?? '';
+                if (result.status === 'rejected') {
+                    onFileReport?.({ path: approxPath, status: 'failed', reason: 'Cannot stat file' });
+                }
                 onProgress?.(processed, relativePaths.length, approxPath);
             }
         }
@@ -219,6 +294,6 @@ export async function walkRepositoryPaths(repoPath, onProgress) {
     if (skippedLarge > 0) {
         console.warn(`  [nexus/walker] Skipped ${skippedLarge} large files (>${MAX_FILE_SIZE / 1024}KB)`);
     }
-    return entries;
+    return entries.sort((left, right) => left.path.localeCompare(right.path));
 }
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package/dist/src/pipeline/heritage-processor.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"heritage-processor.d.ts","sourceRoot":"","sources":["../../../src/pipeline/heritage-processor.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2BG;AAIH,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,sCAAsC,CAAC;AAC9E,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAC3D,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,yBAAyB,CAAC;AAUjE;;;;;;;;;;GAUG;AACH,MAAM,WAAW,WAAW;IAC1B;;;OAGG;IACH,UAAU,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IAE1C;;;OAGG;IACH,YAAY,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IAE5C;;;;;;;;OAQG;IACH,mBAAmB,CAAC,aAAa,EAAE,MAAM,GAAG,WAAW,CAAC,MAAM,CAAC,CAAC;CACjE;AA8ED;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,gBAAgB,CAC9B,QAAQ,EAAE,SAAS,iBAAiB,EAAE,EACtC,GAAG,EAAE,iBAAiB,GACrB,WAAW,CAoFb;AAMD;;GAEG;AACH,MAAM,WAAW,wBAAwB;IACvC,uCAAuC;IACvC,YAAY,EAAE,MAAM,CAAC;IACrB,0CAA0C;IAC1C,eAAe,EAAE,MAAM,CAAC;IACxB,gDAAgD;IAChD,oBAAoB,EAAE,MAAM,CAAC;IAC7B,iDAAiD;IACjD,qBAAqB,EAAE,MAAM,CAAC;IAC9B,wEAAwE;IACxE,YAAY,EAAE,MAAM,CAAC;CACtB;AAED;;;;;;;;;;;;;;;GAeG;AACH,wBAAgB,eAAe,CAC7B,QAAQ,EAAE,iBAAiB,EAAE,EAC7B,KAAK,EAAE,cAAc,EACrB,GAAG,EAAE,iBAAiB,GACrB,wBAAwB,CAkF1B"}

package/dist/src/pipeline/heritage-processor.js

@@ -42,7 +42,7 @@ const EMPTY_SET = new Set();
  * Derive a synthetic stub node ID for unresolvable parent types.
  *
  * This keeps EXTENDS/IMPLEMENTS edges pointing at something unique-and-stable
- * without fabricating a real graph node. The prefix `__heritage__` makes stubs
+ * as an explicitly unresolved reference node. The prefix `__heritage__` makes references
  * easy to filter in downstream consumers that only want resolved edges.
  */
 function stubId(name) {
@@ -63,7 +63,12 @@ function resolveParentId(parentName, fromFile, ctx) {
     if (resolved && resolved.candidates.length > 0) {
         // Tier 3 with multiple candidates is ambiguous — use stub rather than guess
         if (resolved.tier === 'global' && resolved.candidates.length > 1) {
-            return { id: stubId(parentName), confidence: TIER_CONFIDENCE.global };
+            return {
+                id: `${stubId(parentName)}:${fromFile}`,
+                confidence: TIER_CONFIDENCE.global,
+                resolution: 'ambiguous',
+                candidates: resolved.candidates.map((candidate) => candidate.nodeId),
+            };
         }
         return {
             id: resolved.candidates[0].nodeId,
@@ -71,7 +76,7 @@ function resolveParentId(parentName, fromFile, ctx) {
         };
     }
     // Unresolved — external type; use stub at global-tier confidence
-    return { id: stubId(parentName), confidence: TIER_CONFIDENCE.global };
+    return { id: stubId(parentName), confidence: TIER_CONFIDENCE.global, resolution: 'unresolved' };
 }
 /**
  * Resolve a child type name (the declaring class/interface) to a node ID.
@@ -206,7 +211,27 @@ export function processHeritage(heritage, graph, ctx) {
             continue;
         }
         // Resolve parent via tiered lookup
-        const { id: parentId, confidence: parentConf } = resolveParentId(h.parentName, h.filePath, ctx);
+        const parent = resolveParentId(h.parentName, h.filePath, ctx);
+        const { id: parentId, confidence: parentConf } = parent;
+        if (parent.resolution && !graph.nodes.has(parentId)) {
+            graph.addNode({
+                id: parentId,
+                kind: h.kind === 'implements' ? 'interface' : 'class',
+                name: h.parentName,
+                filePath: '',
+                startLine: 0,
+                endLine: 0,
+                language: '',
+                exported: false,
+                isExternal: parent.resolution === 'unresolved',
+                meta: {
+                    resolution: parent.resolution,
+                    referenceKind: 'heritage',
+                    candidates: parent.candidates ?? [],
+                    sourceAnalyzed: false,
+                },
+            });
+        }
         // Child confidence is 0.95 (same-file lookup — we know it's there)
         const childConf = TIER_CONFIDENCE['same-file'];
         // Skip self-references

package/dist/src/pipeline/heritage-processor.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/import-processor.d.ts

@@ -325,12 +325,34 @@ export declare function buildBarrelExportMap(reExports: ExtractedReExportRecord[
  * @returns Canonical `{ canonicalFile, canonicalName }`, or null if not found
  */
 export declare function resolveBarrelBinding(barrelFile: string, exportedName: string, barrelMap: BarrelExportMap): BarrelExportEntry | null;
+/** Candidate source bindings plus explicit traversal limits/cycles. */
+export interface BarrelResolutionCandidates {
+    /** All distinct candidate bindings; callers must verify actual exported declarations. */
+    candidates: BarrelExportEntry[];
+    /** Reasons traversal cannot establish a complete candidate set. */
+    incomplete: string[];
+}
 /**
- * Hard limit for tree-sitter 0.21.x: native code uses a 15-bit byte-offset
- * counter that overflows at 32768 characters. Files larger than this threshold
- * cannot be parsed by tree-sitter and should use the regex fallback.
- *
- * Exported for use in parse-loop.ts and parse-worker.ts.
+ * Enumerate re-export candidates without selecting the first wildcard source.
+ * @param barrelFile - Imported source module.
+ * @param exportedName - Imported name, after explicit alias normalization.
+ * @param barrelMap - Existing re-export inventory.
+ * @param hasDeclaration - Optional AST oracle for a directly exported declaration.
+ * @returns Distinct candidate locations and any cycle/depth/breadth limitations.
+ * @remarks Every branch carries its visited identities; cycles never reset the
+ * depth budget. Direct declarations and named re-exports take precedence over stars.
+ * @example
+ * ```ts
+ * const result = resolveBarrelCandidates('index.ts', 'create', barrelMap);
+ * if (result.incomplete.length) reportUnresolved(result.incomplete);
+ * ```
+ */
+export declare function resolveBarrelCandidates(barrelFile: string, exportedName: string, barrelMap: BarrelExportMap, hasDeclaration?: (entry: BarrelExportEntry) => boolean): BarrelResolutionCandidates;
+/**
+ * Historical threshold for direct-string parser input, retained for compatibility.
+ * @deprecated This is not a parser capacity limit. The native callback input path
+ * parses larger original Unicode sources under explicit byte/time/process limits.
+ * The current parse loop and parser worker do not use this threshold.
  */
 export declare const TREE_SITTER_MAX_CHARS = 32767;
 /**
@@ -345,7 +367,7 @@ export declare const TREE_SITTER_MAX_CHARS = 32767;
  * statements. False negatives are acceptable (they result in missing CALLS edges,
  * not incorrect ones). Dynamic or computed re-exports are not handled.
  *
- * Used as a fallback when tree-sitter cannot parse a file due to its 32K limit.
+ * Legacy opt-in helper; the current bounded parser does not fall back here based on source length.
  *
  * @param content - Raw file content (non-ASCII chars are ignored by regex patterns)
  * @param filePath - File path relative to repo root

package/dist/src/pipeline/import-processor.d.ts.map

@@ -1 +1 @@
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