@monoes/monomindcli 1.6.4 → 1.6.6

package/bundled-graph/dist/src/cluster.js

@@ -0,0 +1,120 @@
+import Graph from 'graphology';
+export async function detectCommunities(graph) {
+    let louvainFn = null;
+    try {
+        const mod = await import('graphology-communities-louvain');
+        louvainFn = mod.default;
+    }
+    catch { /* louvain not available */ }
+    if (louvainFn) {
+        try {
+            const assignment = louvainFn(graph);
+            for (const [nodeId, communityId] of Object.entries(assignment)) {
+                graph.setNodeAttribute(nodeId, 'community', communityId);
+            }
+            const communities = {};
+            for (const [nodeId, communityId] of Object.entries(assignment)) {
+                if (!communities[communityId])
+                    communities[communityId] = [];
+                communities[communityId].push(nodeId);
+            }
+            return splitOversizedCommunities(graph, communities, 0.25, louvainFn);
+        }
+        catch { /* fall through */ }
+    }
+    return splitOversizedCommunities(graph, fallbackCluster(graph), 0.25, louvainFn);
+}
+function fallbackCluster(graph) {
+    const dirMap = new Map();
+    let nextId = 0;
+    const communities = {};
+    graph.forEachNode((id, attrs) => {
+        const file = attrs.sourceFile || '';
+        const parts = file.split('/');
+        const dir = parts.length > 1 ? parts.slice(0, -1).join('/') : 'root';
+        if (!dirMap.has(dir))
+            dirMap.set(dir, nextId++);
+        const cid = dirMap.get(dir);
+        graph.setNodeAttribute(id, 'community', cid);
+        if (!communities[cid])
+            communities[cid] = [];
+        communities[cid].push(id);
+    });
+    return communities;
+}
+export function cohesionScore(graph, communityNodes) {
+    const memberSet = new Set(communityNodes);
+    let totalEdges = 0;
+    let internalEdges = 0;
+    graph.forEachEdge((_edge, _attrs, source, target) => {
+        const srcIn = memberSet.has(source);
+        const tgtIn = memberSet.has(target);
+        if (srcIn || tgtIn) {
+            totalEdges++;
+            if (srcIn && tgtIn)
+                internalEdges++;
+        }
+    });
+    return totalEdges === 0 ? 1.0 : internalEdges / totalEdges;
+}
+export function splitOversizedCommunities(graph, communities, threshold = 0.25, louvainFn = null) {
+    const maxSize = threshold * graph.order;
+    const allIds = Object.keys(communities).map(Number);
+    let nextId = allIds.length > 0 ? Math.max(...allIds) + 1 : 0;
+    for (const [cidStr, members] of Object.entries(communities)) {
+        if (members.length <= maxSize)
+            continue;
+        const cid = Number(cidStr);
+        // Attempt topology-based second pass via Louvain on the community subgraph
+        if (louvainFn && members.length >= 10) {
+            try {
+                const memberSet = new Set(members);
+                const subG = new Graph({ type: 'undirected', multi: false });
+                for (const nodeId of members)
+                    subG.addNode(nodeId);
+                graph.forEachEdge((_e, _a, source, target) => {
+                    if (memberSet.has(source) && memberSet.has(target) && source !== target && !subG.hasEdge(source, target))
+                        subG.addEdge(source, target);
+                });
+                const subAssignment = louvainFn(subG);
+                const subCommunityCount = new Set(Object.values(subAssignment)).size;
+                if (subCommunityCount > 1 && subCommunityCount <= Math.ceil(members.length / 2)) {
+                    const subIdMap = new Map();
+                    const newSubIds = {};
+                    for (const [nodeId, localId] of Object.entries(subAssignment)) {
+                        if (!subIdMap.has(localId))
+                            subIdMap.set(localId, nextId++);
+                        const globalId = subIdMap.get(localId);
+                        graph.setNodeAttribute(nodeId, 'community', globalId);
+                        if (!newSubIds[globalId])
+                            newSubIds[globalId] = [];
+                        newSubIds[globalId].push(nodeId);
+                    }
+                    delete communities[cid];
+                    Object.assign(communities, newSubIds);
+                    continue;
+                }
+            }
+            catch { /* fall through to directory heuristic */ }
+        }
+        // Directory heuristic fallback
+        const subMap = new Map();
+        const newSubIds = {};
+        for (const nodeId of members) {
+            const file = graph.getNodeAttribute(nodeId, 'sourceFile') || '';
+            const parts = file.split('/');
+            const parentDir = parts.length > 1 ? parts[parts.length - 2] : 'root';
+            if (!subMap.has(parentDir))
+                subMap.set(parentDir, nextId++);
+            const subId = subMap.get(parentDir);
+            graph.setNodeAttribute(nodeId, 'community', subId);
+            if (!newSubIds[subId])
+                newSubIds[subId] = [];
+            newSubIds[subId].push(nodeId);
+        }
+        delete communities[cid];
+        Object.assign(communities, newSubIds);
+    }
+    return communities;
+}
+//# sourceMappingURL=cluster.js.map

package/bundled-graph/dist/src/cluster.js.map

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package/bundled-graph/dist/src/detect.d.ts

@@ -0,0 +1,21 @@
+import type { BuildOptions, ClassifiedFile } from './types.js';
+/**
+ * Walks up the directory tree from rootPath to the filesystem root,
+ * collecting patterns from any `.graphifyignore` files found along the way.
+ * Lines beginning with `#` are comments; blank lines are skipped.
+ * Returns the combined list of pattern strings (closest dir first).
+ */
+export declare function loadIgnorePatterns(rootPath: string): string[];
+/**
+ * Recursively collects and classifies all files under rootPath, applying
+ * exclusion rules for directories, file size limits, security-sensitive filenames,
+ * .graphifyignore patterns, and optional language filtering from BuildOptions.
+ */
+export declare function collectFiles(rootPath: string, options?: BuildOptions): ClassifiedFile[];
+/**
+ * Analyses a collected file corpus and returns a list of human-readable warning
+ * strings describing potential issues. Returns an empty array when the corpus
+ * looks healthy.
+ */
+export declare function corpusHealth(files: ClassifiedFile[]): string[];
+//# sourceMappingURL=detect.d.ts.map

package/bundled-graph/dist/src/detect.d.ts.map

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package/bundled-graph/dist/src/detect.js

@@ -0,0 +1,195 @@
+import { readdirSync, readFileSync, statSync } from 'fs';
+import { join, extname, relative, dirname } from 'path';
+const DEFAULT_MAX_FILE_SIZE = 500 * 1024; // 500KB
+const EXCLUDED_DIRS = new Set([
+    'node_modules', '.git', 'dist', 'build', '.monomind',
+    '__pycache__', '.pytest_cache', 'target', '.cache',
+]);
+// Maps file extension to [fileType, language]
+const EXTENSION_MAP = {
+    '.ts': ['code', 'typescript'], '.tsx': ['code', 'typescript'],
+    '.mts': ['code', 'typescript'], '.cts': ['code', 'typescript'],
+    '.js': ['code', 'javascript'], '.jsx': ['code', 'javascript'],
+    '.mjs': ['code', 'javascript'], '.cjs': ['code', 'javascript'],
+    '.py': ['code', 'python'], '.go': ['code', 'go'],
+    '.rs': ['code', 'rust'], '.java': ['code', 'java'],
+    '.c': ['code', 'c'], '.cpp': ['code', 'cpp'],
+    '.h': ['code', 'c'], '.cs': ['code', 'csharp'],
+    '.rb': ['code', 'ruby'], '.php': ['code', 'php'],
+    '.swift': ['code', 'swift'], '.kt': ['code', 'kotlin'],
+    '.scala': ['code', 'scala'], '.md': ['document', 'markdown'],
+    '.txt': ['document', 'text'], '.rst': ['document', 'rst'],
+};
+// Patterns matching filenames/paths that may contain credentials or secrets.
+// Matched against both the basename and the relative path.
+const SECURITY_SENSITIVE_PATTERNS = [
+    // .env files
+    /^\.env(\.|$)/i,
+    /[/\\]\.env(\.|$)/i,
+    // PEM / key files
+    /\.(pem|key|p12|pfx)$/i,
+    // SSH private keys
+    /\b(id_rsa|id_dsa|id_ecdsa|id_ed25519)(\.[^/\\]*)?$/i,
+    // Credential / secret JSON / YAML
+    /\bcredentials\.json$/i,
+    /\bsecrets?\.(json|ya?ml)$/i,
+    // AWS
+    /\baws-credentials$/i,
+    /[/\\]\.aws[/\\]credentials$/i,
+    // GCP / Firebase
+    /\bservice-?account\.json$/i,
+    /\bclient_secret\.json$/i,
+    /\bgoogle-credentials\.json$/i,
+    /\bfirebase[^/\\]*\.json$/i,
+    // Auth-related
+    /\bprivate\.key$/i,
+    /\bprivate_key\.json$/i,
+    /\.htpasswd$/i,
+    /\bshadow$/i,
+    /\bvault-token$/i,
+    /\.token$/i,
+    /\bauth\.json$/i,
+    // Package auth files
+    /\.npmrc$/i,
+    /\.pypirc$/i,
+    /\bnetrc$/i,
+    /\.pgpass$/i,
+];
+/** Returns true if the given basename or relative path matches any security-sensitive pattern. */
+function isSecuritySensitive(basename, relPath) {
+    return SECURITY_SENSITIVE_PATTERNS.some((re) => re.test(basename) || re.test(relPath));
+}
+/**
+ * Converts a .graphifyignore pattern line into a RegExp.
+ * Escapes regex special chars then converts `*` to `.*`.
+ */
+function patternToRegex(pattern) {
+    const escaped = pattern.replace(/[.+^${}()|[\]\\]/g, '\\$&').replace(/\*/g, '.*');
+    return new RegExp(escaped);
+}
+/**
+ * Walks up the directory tree from rootPath to the filesystem root,
+ * collecting patterns from any `.graphifyignore` files found along the way.
+ * Lines beginning with `#` are comments; blank lines are skipped.
+ * Returns the combined list of pattern strings (closest dir first).
+ */
+export function loadIgnorePatterns(rootPath) {
+    const patterns = [];
+    let current = rootPath;
+    while (true) {
+        const candidate = join(current, '.graphifyignore');
+        try {
+            const contents = readFileSync(candidate, 'utf8');
+            for (const line of contents.split(/\r?\n/)) {
+                const trimmed = line.trim();
+                if (trimmed && !trimmed.startsWith('#')) {
+                    patterns.push(trimmed);
+                }
+            }
+        }
+        catch {
+            // File does not exist or is unreadable at this level — continue walking up
+        }
+        const parent = dirname(current);
+        if (parent === current)
+            break; // reached filesystem root
+        current = parent;
+    }
+    return patterns;
+}
+/**
+ * Recursively collects and classifies all files under rootPath, applying
+ * exclusion rules for directories, file size limits, security-sensitive filenames,
+ * .graphifyignore patterns, and optional language filtering from BuildOptions.
+ */
+export function collectFiles(rootPath, options = {}) {
+    const maxFileSizeBytes = options.maxFileSizeBytes ?? DEFAULT_MAX_FILE_SIZE;
+    const codeOnly = options.codeOnly ?? false;
+    const languageFilter = options.languages ? new Set(options.languages) : null;
+    const excludePatterns = options.excludePatterns ?? [];
+    // Load .graphifyignore patterns and compile to regexes
+    const ignorePatternStrings = loadIgnorePatterns(rootPath);
+    const ignoreRegexes = ignorePatternStrings.map(patternToRegex);
+    const results = [];
+    function walkDir(dirPath) {
+        let entries;
+        try {
+            entries = readdirSync(dirPath);
+        }
+        catch {
+            return;
+        }
+        for (const entry of entries) {
+            const fullPath = join(dirPath, entry);
+            const relPath = relative(rootPath, fullPath);
+            // Check against caller-supplied exclude patterns
+            if (excludePatterns.some((pat) => relPath.includes(pat)))
+                continue;
+            // Check against .graphifyignore patterns
+            if (ignoreRegexes.some((re) => re.test(relPath)))
+                continue;
+            let stat;
+            try {
+                stat = statSync(fullPath);
+            }
+            catch {
+                continue;
+            }
+            if (stat.isDirectory()) {
+                if (EXCLUDED_DIRS.has(entry))
+                    continue;
+                walkDir(fullPath);
+                continue;
+            }
+            if (!stat.isFile())
+                continue;
+            if (stat.size > maxFileSizeBytes)
+                continue;
+            // Skip security-sensitive files
+            if (isSecuritySensitive(entry, relPath))
+                continue;
+            const ext = extname(entry).toLowerCase();
+            const mapping = EXTENSION_MAP[ext];
+            if (!mapping)
+                continue;
+            const [fileType, language] = mapping;
+            if (codeOnly && fileType !== 'code')
+                continue;
+            if (languageFilter && !languageFilter.has(language))
+                continue;
+            results.push({ path: fullPath, fileType, language, sizeBytes: stat.size });
+        }
+    }
+    walkDir(rootPath);
+    return results;
+}
+/**
+ * Analyses a collected file corpus and returns a list of human-readable warning
+ * strings describing potential issues. Returns an empty array when the corpus
+ * looks healthy.
+ */
+export function corpusHealth(files) {
+    const warnings = [];
+    const codeFiles = files.filter((f) => f.fileType === 'code');
+    const docFiles = files.filter((f) => f.fileType === 'document');
+    const totalSize = files.reduce((sum, f) => sum + f.sizeBytes, 0);
+    if (codeFiles.length < 5) {
+        warnings.push(`Corpus is very small (${codeFiles.length} code files). Graph may be sparse.`);
+    }
+    if (totalSize < 50_000) {
+        const kb = Math.round(totalSize / 1024);
+        warnings.push(`Corpus total size is very small (~${kb}KB). Consider including more source files.`);
+    }
+    if (totalSize > 50_000_000) {
+        const mb = Math.round(totalSize / (1024 * 1024));
+        warnings.push(`Corpus is very large (~${mb}MB). Build may be slow. Consider using codeOnly or excludePatterns.`);
+    }
+    if (docFiles.length === 0) {
+        warnings.push('No documentation files found. Graph will have no document nodes.');
+    }
+    if (files.length > 0 && docFiles.length / files.length > 0.8) {
+        warnings.push('Corpus is mostly documentation. Consider codeOnly: true for a code-focused graph.');
+    }
+    return warnings;
+}
+//# sourceMappingURL=detect.js.map

package/bundled-graph/dist/src/detect.js.map

@@ -0,0 +1 @@
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package/bundled-graph/dist/src/export.d.ts

@@ -0,0 +1,21 @@
+import Graph from 'graphology';
+/**
+ * Serialize a graphology graph to disk as a JSON file.
+ * Creates the output directory if it does not exist.
+ * Returns the absolute path to the written file.
+ */
+export declare function saveGraph(graph: Graph, outputDir: string, projectPath: string): string;
+/**
+ * Deserialize a graph from a previously saved JSON file.
+ * Silently skips edges whose endpoints are missing from the node list.
+ */
+export declare function loadGraph(graphPath: string): Graph;
+/**
+ * Return true when a graph.json already exists in the given output directory.
+ */
+export declare function graphExists(outputDir: string): boolean;
+/**
+ * Return the canonical path to graph.json inside an output directory.
+ */
+export declare function getGraphPath(outputDir: string): string;
+//# sourceMappingURL=export.d.ts.map

package/bundled-graph/dist/src/export.d.ts.map

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package/bundled-graph/dist/src/export.js

@@ -0,0 +1,68 @@
+import { existsSync, readFileSync, writeFileSync, mkdirSync } from 'fs';
+import { join } from 'path';
+import Graph from 'graphology';
+/**
+ * Serialize a graphology graph to disk as a JSON file.
+ * Creates the output directory if it does not exist.
+ * Returns the absolute path to the written file.
+ */
+export function saveGraph(graph, outputDir, projectPath) {
+    mkdirSync(outputDir, { recursive: true });
+    const graphPath = join(outputDir, 'graph.json');
+    const nodes = [];
+    graph.forEachNode((id, attrs) => nodes.push({ id, ...attrs }));
+    const links = [];
+    graph.forEachEdge((_, attrs, source, target) => links.push({ source, target, ...attrs }));
+    const serialized = {
+        version: '1.0.0',
+        builtAt: new Date().toISOString(),
+        projectPath,
+        nodes,
+        links,
+        directed: graph.type === 'directed',
+        multigraph: graph.multi,
+    };
+    writeFileSync(graphPath, JSON.stringify(serialized, null, 2), 'utf-8');
+    return graphPath;
+}
+/**
+ * Deserialize a graph from a previously saved JSON file.
+ * Silently skips edges whose endpoints are missing from the node list.
+ */
+export function loadGraph(graphPath) {
+    const raw = readFileSync(graphPath, 'utf-8');
+    const data = JSON.parse(raw);
+    const graph = new Graph({
+        type: data.directed ? 'directed' : 'undirected',
+        multi: false,
+    });
+    for (const node of data.nodes) {
+        const { id, ...attrs } = node;
+        graph.addNode(id, attrs);
+    }
+    for (const link of data.links) {
+        const { source, target, ...attrs } = link;
+        if (!graph.hasNode(source) || !graph.hasNode(target))
+            continue;
+        try {
+            graph.addEdge(source, target, attrs);
+        }
+        catch {
+            // Duplicate edge — ignore
+        }
+    }
+    return graph;
+}
+/**
+ * Return true when a graph.json already exists in the given output directory.
+ */
+export function graphExists(outputDir) {
+    return existsSync(join(outputDir, 'graph.json'));
+}
+/**
+ * Return the canonical path to graph.json inside an output directory.
+ */
+export function getGraphPath(outputDir) {
+    return join(outputDir, 'graph.json');
+}
+//# sourceMappingURL=export.js.map

package/bundled-graph/dist/src/export.js.map

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package/bundled-graph/dist/src/extract/index.d.ts

@@ -0,0 +1,20 @@
+import type { ClassifiedFile, ExtractionResult, BuildOptions } from '../types.js';
+/**
+ * Extract graph nodes and edges from all classified files.
+ *
+ * Reads each file, checks the on-disk cache keyed by SHA-256 content hash,
+ * dispatches to the appropriate language extractor, and merges all results
+ * into a single ExtractionResult (nodes deduplicated by id, edges by source+target+relation).
+ *
+ * @param files      - Classified files to process (from the classify layer)
+ * @param outputDir  - Directory used for cache storage (.monomind/graph by default)
+ * @param options    - Build options (languages filter, maxFileSizeBytes, etc.)
+ */
+export declare function extractAll(files: ClassifiedFile[], outputDir: string, options?: BuildOptions): Promise<ExtractionResult>;
+export type { LanguageExtractor } from './types.js';
+export { typescriptExtractor } from './languages/typescript.js';
+export { pythonExtractor } from './languages/python.js';
+export { goExtractor } from './languages/go.js';
+export { rustExtractor } from './languages/rust.js';
+export { isTreeSitterAvailable, tryLoadParser, walk, parseFile, parseFileFromDisk } from './tree-sitter-runner.js';
+//# sourceMappingURL=index.d.ts.map

package/bundled-graph/dist/src/extract/index.d.ts.map

@@ -0,0 +1 @@
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package/bundled-graph/dist/src/extract/index.js

@@ -0,0 +1,158 @@
+import { readFileSync, mkdirSync } from 'fs';
+import { extname } from 'path';
+import { FileCache } from '../cache.js';
+import { typescriptExtractor } from './languages/typescript.js';
+import { pythonExtractor } from './languages/python.js';
+import { goExtractor } from './languages/go.js';
+import { rustExtractor } from './languages/rust.js';
+// ---- registry ----
+const EXTRACTORS = [
+    typescriptExtractor,
+    pythonExtractor,
+    goExtractor,
+    rustExtractor,
+];
+/** Build a lookup from file extension → extractor */
+const EXT_MAP = new Map(EXTRACTORS.flatMap((e) => e.extensions.map((ext) => [ext, e])));
+/** Build a lookup from language name → extractor */
+const LANG_MAP = new Map(EXTRACTORS.map((e) => [e.language, e]));
+function resolveExtractor(file) {
+    if (file.language) {
+        const byLang = LANG_MAP.get(file.language.toLowerCase());
+        if (byLang)
+            return byLang;
+    }
+    const ext = extname(file.path).toLowerCase();
+    return EXT_MAP.get(ext) ?? null;
+}
+// ---- result merging ----
+function mergeResults(results) {
+    const nodeMap = new Map();
+    const edgeSet = new Set();
+    const edges = [];
+    const errors = [];
+    let filesProcessed = 0;
+    let fromCache = 0;
+    for (const r of results) {
+        filesProcessed += r.filesProcessed;
+        fromCache += r.fromCache;
+        errors.push(...r.errors);
+        for (const node of r.nodes) {
+            // Deduplicate by id — keep the first occurrence
+            if (!nodeMap.has(node.id)) {
+                nodeMap.set(node.id, node);
+            }
+        }
+        for (const edge of r.edges) {
+            // Deduplicate edges by source+target+relation key
+            const key = `${edge.source}||${edge.target}||${edge.relation}`;
+            if (!edgeSet.has(key)) {
+                edgeSet.add(key);
+                edges.push(edge);
+            }
+        }
+    }
+    return {
+        nodes: Array.from(nodeMap.values()),
+        edges,
+        filesProcessed,
+        fromCache,
+        errors,
+    };
+}
+// ---- public API ----
+/**
+ * Extract graph nodes and edges from all classified files.
+ *
+ * Reads each file, checks the on-disk cache keyed by SHA-256 content hash,
+ * dispatches to the appropriate language extractor, and merges all results
+ * into a single ExtractionResult (nodes deduplicated by id, edges by source+target+relation).
+ *
+ * @param files      - Classified files to process (from the classify layer)
+ * @param outputDir  - Directory used for cache storage (.monomind/graph by default)
+ * @param options    - Build options (languages filter, maxFileSizeBytes, etc.)
+ */
+export async function extractAll(files, outputDir, options) {
+    const maxSize = options?.maxFileSizeBytes ?? 500 * 1024; // 500 KB
+    const langFilter = options?.languages?.map((l) => l.toLowerCase());
+    mkdirSync(outputDir, { recursive: true });
+    const cache = new FileCache(outputDir);
+    const results = [];
+    for (const file of files) {
+        // Skip files that are too large
+        if (file.sizeBytes > maxSize) {
+            results.push({
+                nodes: [],
+                edges: [],
+                filesProcessed: 1,
+                fromCache: 0,
+                errors: [`Skipped ${file.path}: file size ${file.sizeBytes} exceeds limit ${maxSize}`],
+            });
+            continue;
+        }
+        // Apply language filter
+        if (langFilter && langFilter.length > 0) {
+            const extractor = resolveExtractor(file);
+            const fileLang = (file.language ?? '').toLowerCase();
+            const extractorLang = extractor?.language ?? '';
+            if (!langFilter.includes(fileLang) && !langFilter.includes(extractorLang)) {
+                continue;
+            }
+        }
+        const extractor = resolveExtractor(file);
+        if (!extractor) {
+            // No extractor for this file type — skip silently
+            continue;
+        }
+        // Read content
+        let content;
+        try {
+            content = readFileSync(file.path, 'utf8');
+        }
+        catch (err) {
+            results.push({
+                nodes: [],
+                edges: [],
+                filesProcessed: 1,
+                fromCache: 0,
+                errors: [`Failed to read ${file.path}: ${err instanceof Error ? err.message : String(err)}`],
+            });
+            continue;
+        }
+        // Check cache using FileCache (keyed on filePath + content hash)
+        const cacheKey = cache.key(file.path, content);
+        const cached = cache.get(cacheKey);
+        if (cached) {
+            results.push({
+                ...cached,
+                filesProcessed: 1,
+                fromCache: 1,
+            });
+            continue;
+        }
+        // Extract
+        let result;
+        try {
+            result = extractor.extract(file.path, content);
+        }
+        catch (err) {
+            result = {
+                nodes: [],
+                edges: [],
+                filesProcessed: 1,
+                fromCache: 0,
+                errors: [`Extractor error for ${file.path}: ${err instanceof Error ? err.message : String(err)}`],
+            };
+        }
+        // Store in cache
+        cache.set(cacheKey, result);
+        results.push(result);
+    }
+    return mergeResults(results);
+}
+export { typescriptExtractor } from './languages/typescript.js';
+export { pythonExtractor } from './languages/python.js';
+export { goExtractor } from './languages/go.js';
+export { rustExtractor } from './languages/rust.js';
+export { isTreeSitterAvailable, tryLoadParser, walk, parseFile, parseFileFromDisk } from './tree-sitter-runner.js';
+//# sourceMappingURL=index.js.map

package/bundled-graph/dist/src/extract/index.js.map

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