@monoes/monomindcli 1.6.3 → 1.6.5

package/bundled-graph/dist/src/extract/languages/typescript.js

@@ -0,0 +1,295 @@
+import { basename } from 'path';
+import { tryLoadParser, walk, } from '../tree-sitter-runner.js';
+// ---- helpers ----
+function nodeName(node) {
+    // Most declaration nodes expose "name" as a named field
+    const nameNode = node.childForFieldName('name');
+    return nameNode?.text ?? '';
+}
+function loc(node) {
+    return `L${node.startPosition.row + 1}`;
+}
+// ---- tree-sitter extraction ----
+const CLASS_TYPES = new Set([
+    'class_declaration',
+    'abstract_class_declaration',
+]);
+const FUNCTION_TYPES = new Set([
+    'function_declaration',
+    'generator_function_declaration',
+]);
+function extractWithTreeSitter(filePath, content, language) {
+    const nodes = [];
+    const edges = [];
+    const errors = [];
+    const parser = tryLoadParser(language);
+    if (!parser) {
+        return { nodes, edges, filesProcessed: 1, fromCache: 0, errors };
+    }
+    let tree;
+    try {
+        tree = parser.parse(content);
+    }
+    catch (err) {
+        errors.push(`tree-sitter parse error in ${filePath}: ${String(err)}`);
+        return { nodes, edges, filesProcessed: 1, fromCache: 0, errors };
+    }
+    // Track current class/method context for call-edge attribution
+    const classStack = [];
+    const methodStack = [];
+    const addNode = (name, n) => {
+        if (!name)
+            return;
+        nodes.push({
+            id: name,
+            label: name,
+            fileType: 'code',
+            sourceFile: filePath,
+            sourceLocation: loc(n),
+        });
+    };
+    walk(tree.rootNode, (n) => {
+        // ---- classes ----
+        if (CLASS_TYPES.has(n.type)) {
+            const name = nodeName(n);
+            addNode(name, n);
+            if (name)
+                classStack.push(name);
+            // heritage: extends / implements
+            for (const child of n.children) {
+                if (child.type === 'class_heritage') {
+                    for (const clause of child.children) {
+                        if (clause.type !== 'extends_clause' && clause.type !== 'implements_clause')
+                            continue;
+                        const relation = clause.type === 'extends_clause' ? 'extends' : 'implements';
+                        // Each type_identifier inside the clause is a target
+                        for (const target of clause.children) {
+                            if (target.type === 'type_identifier' ||
+                                target.type === 'identifier') {
+                                edges.push({
+                                    source: name,
+                                    target: target.text,
+                                    relation,
+                                    confidence: 'EXTRACTED',
+                                    sourceFile: filePath,
+                                    sourceLocation: loc(clause),
+                                });
+                            }
+                        }
+                    }
+                }
+            }
+            return;
+        }
+        // ---- functions (top-level) ----
+        if (FUNCTION_TYPES.has(n.type)) {
+            const name = nodeName(n);
+            addNode(name, n);
+            if (name)
+                methodStack.push(name);
+            return;
+        }
+        // ---- method definitions (inside class body) ----
+        if (n.type === 'method_definition' || n.type === 'public_field_definition') {
+            const name = nodeName(n);
+            // Qualify name with class if available
+            const qualifiedName = classStack.length > 0 ? `${classStack[classStack.length - 1]}.${name}` : name;
+            addNode(qualifiedName, n);
+            if (qualifiedName)
+                methodStack.push(qualifiedName);
+            return;
+        }
+        // ---- interfaces ----
+        if (n.type === 'interface_declaration') {
+            const name = nodeName(n);
+            addNode(name, n);
+            // interface X extends Y
+            for (const child of n.children) {
+                if (child.type === 'extends_type_clause' || child.type === 'extends_clause') {
+                    for (const target of child.children) {
+                        if (target.type === 'type_identifier' || target.type === 'identifier') {
+                            edges.push({
+                                source: name,
+                                target: target.text,
+                                relation: 'extends',
+                                confidence: 'EXTRACTED',
+                                sourceFile: filePath,
+                                sourceLocation: loc(child),
+                            });
+                        }
+                    }
+                }
+            }
+            return;
+        }
+        // ---- type aliases ----
+        if (n.type === 'type_alias_declaration') {
+            const name = nodeName(n);
+            addNode(name, n);
+            return;
+        }
+        // ---- import statements ----
+        if (n.type === 'import_statement') {
+            // Extract the module specifier
+            const moduleSpecifier = n.childForFieldName('source');
+            const moduleText = moduleSpecifier
+                ? moduleSpecifier.text.replace(/^['"]|['"]$/g, '')
+                : '';
+            // Extract named specifiers: import { A, B } from '...'
+            for (const child of n.children) {
+                if (child.type === 'named_imports' || child.type === 'import_clause') {
+                    for (const spec of child.children) {
+                        if (spec.type === 'import_specifier') {
+                            const importedName = spec.childForFieldName('name')?.text ?? spec.text;
+                            if (importedName) {
+                                edges.push({
+                                    source: filePath,
+                                    target: importedName,
+                                    relation: 'imports',
+                                    confidence: 'EXTRACTED',
+                                    sourceFile: filePath,
+                                    sourceLocation: loc(n),
+                                });
+                            }
+                        }
+                    }
+                }
+                // Default import: import X from '...'
+                if (child.type === 'import_clause') {
+                    const defaultId = child.childForFieldName('name') ?? (child.children.find(c => c.type === 'identifier') ?? null);
+                    if (defaultId) {
+                        edges.push({
+                            source: filePath,
+                            target: defaultId.text,
+                            relation: 'imports',
+                            confidence: 'EXTRACTED',
+                            sourceFile: filePath,
+                            sourceLocation: loc(n),
+                        });
+                    }
+                }
+            }
+            // Always emit a file-level import edge to the module path
+            if (moduleText) {
+                edges.push({
+                    source: basename(filePath),
+                    target: moduleText,
+                    relation: 'imports',
+                    confidence: 'EXTRACTED',
+                    sourceFile: filePath,
+                    sourceLocation: loc(n),
+                });
+            }
+            return;
+        }
+        // ---- call expressions ----
+        if (n.type === 'call_expression') {
+            const fnNode = n.childForFieldName('function');
+            if (!fnNode)
+                return;
+            // Resolve callee name (may be `a.b()` or plain `foo()`)
+            let calleeName;
+            if (fnNode.type === 'member_expression') {
+                calleeName = fnNode.text;
+            }
+            else {
+                calleeName = fnNode.text;
+            }
+            // Attribute to deepest known method context
+            const caller = methodStack[methodStack.length - 1] ??
+                classStack[classStack.length - 1] ??
+                basename(filePath);
+            if (calleeName && caller && calleeName !== caller) {
+                edges.push({
+                    source: caller,
+                    target: calleeName,
+                    relation: 'calls',
+                    confidence: 'INFERRED',
+                    confidenceScore: 0.8,
+                    sourceFile: filePath,
+                    sourceLocation: loc(n),
+                });
+            }
+        }
+    });
+    return { nodes, edges, filesProcessed: 1, fromCache: 0, errors };
+}
+// ---- regex fallback ----
+function extractWithRegex(filePath, content) {
+    const nodes = [];
+    const edges = [];
+    const lines = content.split('\n');
+    lines.forEach((line, idx) => {
+        const location = `L${idx + 1}`;
+        // class
+        const classMatch = line.match(/^(export\s+)?(abstract\s+)?class\s+(\w+)/);
+        if (classMatch) {
+            const name = classMatch[3];
+            nodes.push({ id: name, label: name, fileType: 'code', sourceFile: filePath, sourceLocation: location });
+            // extends
+            const extendsMatch = line.match(/\bextends\s+(\w+)/);
+            if (extendsMatch) {
+                edges.push({ source: name, target: extendsMatch[1], relation: 'extends', confidence: 'EXTRACTED', sourceFile: filePath, sourceLocation: location });
+            }
+            // implements
+            const implementsMatch = line.match(/\bimplements\s+([\w,\s]+)/);
+            if (implementsMatch) {
+                for (const impl of implementsMatch[1].split(',')) {
+                    const implName = impl.trim().split(/\s/)[0];
+                    if (implName) {
+                        edges.push({ source: name, target: implName, relation: 'implements', confidence: 'EXTRACTED', sourceFile: filePath, sourceLocation: location });
+                    }
+                }
+            }
+        }
+        // interface
+        const ifaceMatch = line.match(/^(export\s+)?interface\s+(\w+)/);
+        if (ifaceMatch) {
+            const name = ifaceMatch[2];
+            nodes.push({ id: name, label: name, fileType: 'code', sourceFile: filePath, sourceLocation: location });
+        }
+        // type alias
+        const typeMatch = line.match(/^(export\s+)?type\s+(\w+)\s*=/);
+        if (typeMatch) {
+            const name = typeMatch[2];
+            nodes.push({ id: name, label: name, fileType: 'code', sourceFile: filePath, sourceLocation: location });
+        }
+        // function
+        const funcMatch = line.match(/^(export\s+)?(default\s+)?(async\s+)?function\s+(\w+)/);
+        if (funcMatch) {
+            const name = funcMatch[4];
+            nodes.push({ id: name, label: name, fileType: 'code', sourceFile: filePath, sourceLocation: location });
+        }
+        // import
+        const importMatch = line.match(/^import\s+.*from\s+['"]([^'"]+)['"]/);
+        if (importMatch) {
+            edges.push({ source: basename(filePath), target: importMatch[1], relation: 'imports', confidence: 'EXTRACTED', sourceFile: filePath, sourceLocation: location });
+            // Named specifiers
+            const namedMatch = line.match(/\{([^}]+)\}/);
+            if (namedMatch) {
+                for (const spec of namedMatch[1].split(',')) {
+                    const specName = spec.trim().split(/\s+as\s+/)[0].trim();
+                    if (specName) {
+                        edges.push({ source: filePath, target: specName, relation: 'imports', confidence: 'EXTRACTED', sourceFile: filePath, sourceLocation: location });
+                    }
+                }
+            }
+        }
+    });
+    return { nodes, edges, filesProcessed: 1, fromCache: 0, errors: [] };
+}
+// ---- extractor implementation ----
+export const typescriptExtractor = {
+    language: 'typescript',
+    extensions: ['.ts', '.tsx', '.js', '.jsx', '.mjs', '.cjs'],
+    extract(filePath, content) {
+        const lang = filePath.endsWith('.tsx') || filePath.endsWith('.jsx') ? 'tsx' : 'typescript';
+        const tsResult = extractWithTreeSitter(filePath, content, lang);
+        if (tsResult.nodes.length > 0 || tsResult.edges.length > 0 || tsResult.errors.length > 0) {
+            return tsResult;
+        }
+        // tree-sitter not available or produced nothing — fall back to regex
+        return extractWithRegex(filePath, content);
+    },
+};
+//# sourceMappingURL=typescript.js.map

package/bundled-graph/dist/src/extract/languages/typescript.js.map

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

@@ -0,0 +1,38 @@
+/**
+ * Semantic extraction via the Anthropic Claude API.
+ *
+ * Mirrors graphify's skill.md Step B1-B3 pipeline:
+ * - Groups files into chunks of ~20
+ * - Sends each chunk to Claude with the graphify extraction prompt
+ * - Merges results into a single ExtractionResult
+ *
+ * Gracefully returns empty results if ANTHROPIC_API_KEY is not set
+ * or the API call fails.
+ */
+import type { ExtractionResult } from '../types.js';
+export interface SemanticFile {
+    path: string;
+    relPath: string;
+    content: string;
+}
+export interface SemanticOptions {
+    apiKey?: string;
+    model?: string;
+    chunkSize?: number;
+    mode?: 'fast' | 'deep';
+    maxTokens?: number;
+    timeBudget?: number;
+    targetChunkTokens?: number;
+}
+/**
+ * Run semantic extraction on a set of files using the Anthropic Claude API.
+ *
+ * Returns an empty ExtractionResult (not an error) when:
+ * - No API key is available
+ * - The API call fails
+ *
+ * Only document/paper files benefit from semantic extraction.
+ * Code files may be included but the prompt instructs Claude not to re-extract imports.
+ */
+export declare function extractSemantic(files: SemanticFile[], options?: SemanticOptions): Promise<ExtractionResult>;
+//# sourceMappingURL=semantic.d.ts.map

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

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

@@ -0,0 +1,242 @@
+// ---------------------------------------------------------------------------
+// Prompt template (mirrors graphify skill.md lines 253-303)
+// ---------------------------------------------------------------------------
+function buildPrompt(files, mode, chunkNum, totalChunks) {
+    const deepInstructions = mode === 'deep'
+        ? '\nDEEP MODE: be aggressive with INFERRED edges - indirect deps, shared assumptions, latent couplings. Mark uncertain ones AMBIGUOUS instead of omitting.\n'
+        : '';
+    const fileList = files
+        .map((f) => `--- file: ${f.relPath} ---\n${f.content.slice(0, 6000)}\n---`)
+        .join('\n\n');
+    return `You are a graphify extraction subagent. Read the files listed and extract a knowledge graph fragment.
+Output ONLY valid JSON matching the schema below - no explanation, no markdown fences, no preamble.
+
+Files (chunk ${chunkNum} of ${totalChunks}):
+${fileList}
+
+Rules:
+- EXTRACTED: relationship explicit in source (import, call, citation, "see §3.2")
+- INFERRED: reasonable inference (shared data structure, implied dependency)
+- AMBIGUOUS: uncertain - flag for review, do not omit
+
+Code files: focus on semantic edges AST cannot find (call relationships, shared data, arch patterns).
+  Do not re-extract imports - AST already has those.
+Doc/paper files: extract named concepts, entities, citations. Also extract rationale — sections that explain WHY a decision was made, trade-offs chosen, or design intent. These become nodes with "rationale_for" edges pointing to the concept they explain.
+${deepInstructions}
+Semantic similarity: if two concepts in this chunk solve the same problem or represent the same idea without any structural link, add a "semantically_similar_to" edge marked INFERRED with a confidence_score reflecting how similar they are (0.6-0.95). Only add these when the similarity is genuinely non-obvious and cross-cutting.
+
+Hyperedges: if 3 or more nodes clearly participate together in a shared concept, flow, or pattern not captured by pairwise edges, add a hyperedge to the "hyperedges" array. Use sparingly — maximum 3 hyperedges per chunk.
+
+If a file has YAML frontmatter (--- ... ---), copy source_url, captured_at, author, contributor onto every node from that file.
+
+confidence_score is REQUIRED on every edge:
+- EXTRACTED edges: confidence_score = 1.0 always
+- INFERRED edges: Direct structural evidence: 0.8-0.9. Reasonable with uncertainty: 0.6-0.7. Weak/speculative: 0.4-0.5.
+- AMBIGUOUS edges: 0.1-0.3
+
+Output exactly this JSON (no other text):
+{"nodes":[{"id":"filestem_entityname","label":"Human Readable Name","file_type":"code|document|paper|image","source_file":"relative/path","source_location":null,"source_url":null,"captured_at":null,"author":null,"contributor":null}],"edges":[{"source":"node_id","target":"node_id","relation":"calls|implements|references|cites|conceptually_related_to|shares_data_with|semantically_similar_to|rationale_for","confidence":"EXTRACTED|INFERRED|AMBIGUOUS","confidence_score":1.0,"source_file":"relative/path","source_location":null,"weight":1.0}],"hyperedges":[{"id":"snake_case_id","label":"Human Readable Label","nodes":["node_id1","node_id2","node_id3"],"relation":"participate_in|implement|form","confidence":"EXTRACTED|INFERRED","confidence_score":0.75,"source_file":"relative/path"}],"input_tokens":0,"output_tokens":0}`;
+}
+async function callClaude(prompt, apiKey, model, maxTokens) {
+    const response = await fetch('https://api.anthropic.com/v1/messages', {
+        method: 'POST',
+        headers: {
+            'Content-Type': 'application/json',
+            'x-api-key': apiKey,
+            'anthropic-version': '2023-06-01',
+        },
+        body: JSON.stringify({
+            model,
+            max_tokens: maxTokens,
+            messages: [{ role: 'user', content: prompt }],
+        }),
+    });
+    if (!response.ok) {
+        const body = await response.text();
+        throw new Error(`Anthropic API error ${response.status}: ${body}`);
+    }
+    const msg = (await response.json());
+    const text = msg.content.find((c) => c.type === 'text')?.text ?? '';
+    return {
+        text,
+        inputTokens: msg.usage?.input_tokens ?? 0,
+        outputTokens: msg.usage?.output_tokens ?? 0,
+    };
+}
+function parseChunkResult(text, chunkFiles) {
+    // Strip markdown fences if model added them despite instructions
+    const cleaned = text.replace(/^```json\s*/i, '').replace(/\s*```\s*$/, '').trim();
+    let raw;
+    try {
+        raw = JSON.parse(cleaned);
+    }
+    catch {
+        return { nodes: [], edges: [], hyperedges: [], inputTokens: 0, outputTokens: 0 };
+    }
+    const fileSet = new Set(chunkFiles.map((f) => f.relPath));
+    const nodes = (raw.nodes ?? [])
+        .filter((n) => typeof n === 'object' && n !== null)
+        .map((n) => ({
+        id: String(n['id'] ?? ''),
+        label: String(n['label'] ?? n['id'] ?? ''),
+        fileType: n['file_type'] ?? 'document',
+        sourceFile: String(n['source_file'] ?? ''),
+        sourceLocation: n['source_location'] ?? undefined,
+        // Extra metadata from YAML frontmatter
+        ...(n['source_url'] ? { sourceUrl: n['source_url'] } : {}),
+        ...(n['captured_at'] ? { capturedAt: n['captured_at'] } : {}),
+        ...(n['author'] ? { author: n['author'] } : {}),
+    }))
+        .filter((n) => n.id && fileSet.has(n.sourceFile));
+    const edges = (raw.edges ?? [])
+        .filter((e) => typeof e === 'object' && e !== null)
+        .map((e) => ({
+        source: String(e['source'] ?? ''),
+        target: String(e['target'] ?? ''),
+        relation: String(e['relation'] ?? 'references'),
+        confidence: e['confidence'] ?? 'INFERRED',
+        confidenceScore: typeof e['confidence_score'] === 'number' ? e['confidence_score'] : 0.7,
+        sourceFile: e['source_file'] ?? undefined,
+        weight: typeof e['weight'] === 'number' ? e['weight'] : 1.0,
+    }))
+        .filter((e) => e.source && e.target);
+    const hyperedges = (raw.hyperedges ?? [])
+        .filter((h) => typeof h === 'object' && h !== null)
+        .map((h) => ({
+        label: String(h['label'] ?? h['id'] ?? ''),
+        nodes: Array.isArray(h['nodes']) ? h['nodes'] : [],
+        confidence: h['confidence'] ?? 'INFERRED',
+        confidenceScore: typeof h['confidence_score'] === 'number' ? h['confidence_score'] : 0.7,
+    }))
+        .filter((h) => h.label && h.nodes.length >= 2);
+    return {
+        nodes,
+        edges,
+        hyperedges,
+        inputTokens: raw.input_tokens ?? 0,
+        outputTokens: raw.output_tokens ?? 0,
+    };
+}
+// ---------------------------------------------------------------------------
+// Best-Fit Decreasing (BFD) chunk packing — from autoresearch experiment loop
+//
+// Instead of slicing files into equal-sized groups, BFD estimates the token
+// count of each file, sorts descending, and packs into bins that stay under
+// targetTokens.  This mirrors the document-packing dataloader in autoresearch
+// (best-fit + zero-waste) and produces denser, fairer prompts than fixed chunks.
+// ---------------------------------------------------------------------------
+/**
+ * Pack `files` into chunks using First-Fit Decreasing bin packing.
+ *
+ * Each file's token estimate = min(content.length / 4, 1500)
+ * (the prompt already truncates each file to 6000 chars = ~1500 tokens).
+ *
+ * @param files         - Files to pack
+ * @param targetTokens  - Soft upper bound on tokens per chunk (default 30 000)
+ * @returns             - Array of chunks; each chunk is an array of files
+ */
+function packChunksBFD(files, targetTokens) {
+    // Estimate tokens per file — capped at the 6 000-char prompt truncation limit
+    const sized = files.map((f) => ({
+        file: f,
+        tokens: Math.min(Math.ceil(f.content.length / 4), 1500),
+    }));
+    // Sort descending so large files get placed first (First Fit Decreasing)
+    sized.sort((a, b) => b.tokens - a.tokens);
+    const bins = [];
+    for (const item of sized) {
+        let placed = false;
+        for (const bin of bins) {
+            if (bin.tokens + item.tokens <= targetTokens) {
+                bin.files.push(item.file);
+                bin.tokens += item.tokens;
+                placed = true;
+                break;
+            }
+        }
+        if (!placed) {
+            // File is too large (or bins are all full) — open a new bin
+            bins.push({ files: [item.file], tokens: item.tokens });
+        }
+    }
+    return bins.map((b) => b.files);
+}
+// ---------------------------------------------------------------------------
+// Main export
+// ---------------------------------------------------------------------------
+/**
+ * Run semantic extraction on a set of files using the Anthropic Claude API.
+ *
+ * Returns an empty ExtractionResult (not an error) when:
+ * - No API key is available
+ * - The API call fails
+ *
+ * Only document/paper files benefit from semantic extraction.
+ * Code files may be included but the prompt instructs Claude not to re-extract imports.
+ */
+export async function extractSemantic(files, options = {}) {
+    const apiKey = options.apiKey ?? process.env['ANTHROPIC_API_KEY'] ?? '';
+    if (!apiKey) {
+        return { nodes: [], edges: [], hyperedges: [], filesProcessed: 0, fromCache: 0, errors: ['ANTHROPIC_API_KEY not set — semantic extraction skipped'] };
+    }
+    const model = options.model ?? 'claude-haiku-4-5-20251001';
+    const mode = options.mode ?? 'fast';
+    const maxTokens = options.maxTokens ?? 8192;
+    // BFD packing — targetChunkTokens defaults to 30 000 (~20 avg files × 1500 tok each).
+    // Fallback to legacy chunkSize if targetChunkTokens is not set and chunkSize was specified,
+    // so callers that relied on chunkSize still get predictable behaviour.
+    const targetChunkTokens = options.targetChunkTokens
+        ?? (options.chunkSize ? options.chunkSize * 1500 : 30_000);
+    // Time budget — undefined = no limit (run all chunks)
+    const deadline = options.timeBudget ? Date.now() + options.timeBudget : Infinity;
+    const allNodes = [];
+    const allEdges = [];
+    const allHyperedges = [];
+    const errors = [];
+    let totalInput = 0;
+    let totalOutput = 0;
+    // Pack files into token-aware chunks using BFD (replaces fixed equal-size slicing)
+    const chunks = packChunksBFD(files, targetChunkTokens);
+    for (let i = 0; i < chunks.length; i++) {
+        // Time budget enforcement — mirrors autoresearch's 5-min wall-clock limit
+        if (Date.now() > deadline) {
+            errors.push(`Time budget (${options.timeBudget}ms) exceeded after chunk ${i}/${chunks.length} — partial results returned`);
+            break;
+        }
+        const chunk = chunks[i];
+        const prompt = buildPrompt(chunk, mode, i + 1, chunks.length);
+        try {
+            const { text, inputTokens, outputTokens } = await callClaude(prompt, apiKey, model, maxTokens);
+            totalInput += inputTokens;
+            totalOutput += outputTokens;
+            const parsed = parseChunkResult(text, chunk);
+            allNodes.push(...parsed.nodes);
+            allEdges.push(...parsed.edges);
+            allHyperedges.push(...parsed.hyperedges);
+        }
+        catch (err) {
+            errors.push(`Chunk ${i + 1}/${chunks.length} failed: ${err instanceof Error ? err.message : String(err)}`);
+        }
+    }
+    // Deduplicate nodes by id
+    const seenNodeIds = new Set();
+    const dedupedNodes = allNodes.filter((n) => {
+        if (seenNodeIds.has(n.id))
+            return false;
+        seenNodeIds.add(n.id);
+        return true;
+    });
+    // Attach token totals as extra fields for report generation
+    const result = {
+        nodes: dedupedNodes,
+        edges: allEdges,
+        hyperedges: allHyperedges,
+        filesProcessed: files.length,
+        fromCache: 0,
+        errors,
+        inputTokens: totalInput,
+        outputTokens: totalOutput,
+    };
+    return result;
+}
+//# sourceMappingURL=semantic.js.map

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

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