npm - @dreamtree-org/graphify - Versions diffs - 1.3.0 → 1.4.0 - Mend

@dreamtree-org/graphify 1.3.0 → 1.4.0

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package/dist/{chunk-K322XB4U.js → chunk-7LTO76UD.js} +2 -1
package/dist/chunk-7LTO76UD.js.map +1 -0
package/dist/{chunk-UBXYMMXJ.js → chunk-QEB7A5KB.js} +2 -2
package/dist/cli/index.cjs.map +1 -1
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package/dist/index.cjs +137 -0
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package/dist/index.d.cts +68 -1
package/dist/index.d.ts +68 -1
package/dist/index.js +139 -2
package/dist/index.js.map +1 -1
package/dist/mcp/server.cjs.map +1 -1
package/dist/mcp/server.js +1 -1
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package/dist/mcp/server.cjs.map CHANGED Viewed

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1	- {"version":3,"sources":["../../src/mcp/server.ts","../../src/query.ts","../../src/context.ts","../../src/graphStore.ts","../../src/store/localFile.ts","../../src/security.ts","../../src/store/serialize.ts","../../src/impact.ts","../../src/testmap.ts"],"sourcesContent":["/*\n MCP stdio server exposing query/path/explain as tools against an existing\n * graphify-out/graph.json. Stdio only — never opens a network listener.\n * All graph file paths go through security.validateGraphPath().\n \n This module is a pure library: importing it has no side effects (it does\n * not read argv or start a server on import). `startServer()` is called\n * explicitly by `bin/graphify-mcp.js` (the standalone `graphify-mcp` CLI\n * entry point) and by `graphify --mcp` (see src/cli/index.ts).\n /\nimport as fs from 'node:fs/promises';\nimport * as path from 'node:path';\nimport { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';\nimport { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';\nimport type { Transport } from '@modelcontextprotocol/sdk/shared/transport.js';\nimport { z } from 'zod';\nimport { buildContextPack, renderContextPack } from '../context.js';\nimport { loadGraph } from '../graphStore.js';\nimport { affectedBy } from '../impact.js';\nimport { explainNode, queryGraph, shortestPath } from '../query.js';\nimport { testsForNode } from '../testmap.js';\nimport { validateGraphPath } from '../security.js';\n\nfunction textResult(text: string): { content: Array<{ type: 'text'; text: string }> } {\n return { content: [{ type: 'text', text }] };\n}\n\n/*\n Build the McpServer instance (tools registered, nothing connected yet).\n * Split out from startServer() so tests can connect it to an in-memory\n * transport instead of real stdio (see tests/mcp/server.test.ts).\n /\nexport function createGraphifyMcpServer(outDir: string): McpServer {\n const server = new McpServer({ name: 'graphify', version: '0.1.0' });\n\n server.registerTool(\n 'query',\n {\n description:\n 'BFS (default) or DFS traversal of the graphify knowledge graph, seeded from nodes ' +\n 'whose label matches the question. Returns the matched seeds, the visited node ' +\n 'context, and the edges among them — broad context for answering a structural question.',\n inputSchema: {\n question: z.string().describe('Natural-language question or keywords to search the graph for.'),\n dfs: z.boolean().optional().describe('Use depth-first traversal instead of the default breadth-first.'),\n budget: z.number().int().positive().optional().describe('Hard cap on how many nodes to include.'),\n tokenBudget: z\n .number()\n .int()\n .positive()\n .optional()\n .describe('Approximate cap, in tokens, on the serialized size of the result (default 2000).'),\n },\n },\n async ({ question, dfs, budget, tokenBudget }) => {\n const graph = await loadGraph(outDir);\n const result = queryGraph(graph, question, { dfs, budget, tokenBudget });\n return textResult(JSON.stringify(result, null, 2));\n },\n );\n\n server.registerTool(\n 'path',\n {\n description: 'Shortest path between two named nodes in the graphify knowledge graph.',\n inputSchema: {\n from: z.string().describe('Name/label of the starting node.'),\n to: z.string().describe('Name/label of the destination node.'),\n },\n },\n async ({ from, to }) => {\n const graph = await loadGraph(outDir);\n const result = shortestPath(graph, from, to);\n if (!result) {\n return textResult(`Could not resolve \"${from}\" and/or \"${to}\" to a node in the graph.`);\n }\n return textResult(JSON.stringify(result, null, 2));\n },\n );\n\n server.registerTool(\n 'explain',\n {\n description:\n 'Plain-language-ready explanation of a single node: its source location, community, ' +\n 'and incoming/outgoing edges.',\n inputSchema: {\n node: z.string().describe('Name/label (or id) of the node to explain.'),\n },\n },\n async ({ node }) => {\n const graph = await loadGraph(outDir);\n const result = explainNode(graph, node);\n if (!result) {\n return textResult(`No node matched \"${node}\".`);\n }\n return textResult(JSON.stringify(result, null, 2));\n },\n );\n\n server.registerTool(\n 'affected',\n {\n description:\n 'Reverse impact analysis — \"what breaks if I change X\". Walks incoming dependency ' +\n 'edges (calls/imports/inherits/...) transitively and returns everything that depends ' +\n 'on the node, grouped by depth, with per-confidence blast-radius counts.',\n inputSchema: {\n node: z.string().describe('Name/label (or id) of the node being changed.'),\n depth: z.number().int().positive().optional().describe('How many reverse hops to follow (default 3).'),\n limit: z.number().int().positive().optional().describe('Cap on affected nodes reported (default 200).'),\n },\n },\n async ({ node, depth, limit }) => {\n const graph = await loadGraph(outDir);\n const result = affectedBy(graph, node, { maxDepth: depth, limit });\n if (!result) {\n return textResult(`No node matched \"${node}\".`);\n }\n return textResult(JSON.stringify(result, null, 2));\n },\n );\n\n server.registerTool(\n 'context',\n {\n description:\n 'Token-budgeted working-set pack: the actual code snippets relevant to a task, ' +\n 'graph-ranked and packed to a budget. Call this FIRST when starting a task — it ' +\n 'replaces query-then-read-whole-files.',\n inputSchema: {\n task: z.string().describe('What you are about to do, in natural language.'),\n budget: z.number().int().positive().optional().describe('Approximate token cap (default 4000).'),\n },\n },\n async ({ task, budget }) => {\n const graph = await loadGraph(outDir);\n const pack = await buildContextPack(graph, task, (p) => fs.readFile(p, 'utf-8'), {\n tokenBudget: budget,\n });\n return textResult(renderContextPack(pack));\n },\n );\n\n server.registerTool(\n 'tests',\n {\n description:\n 'Structural test selection: the minimal test files worth running to verify a change ' +\n 'to the given node, via reverse dependency reachability — no coverage instrumentation.',\n inputSchema: {\n node: z.string().describe('Name/label (or id) of the changed node.'),\n },\n },\n async ({ node }) => {\n const graph = await loadGraph(outDir);\n const result = testsForNode(graph, node);\n if (!result) {\n return textResult(`No node matched \"${node}\".`);\n }\n return textResult(JSON.stringify(result, null, 2));\n },\n );\n\n return server;\n}\n\n/\n Start the MCP server, serving `query`/`path`/`explain` tools against the\n * graph.json found in `graphPath`'s directory. `graphPath` is validated\n * (via security.validateGraphPath()) up front so a bad path fails\n * immediately with a clear error instead of the first time a client calls\n * a tool. `transport` defaults to real stdio; tests substitute an\n * in-memory transport.\n /\nexport async function startServer(graphPath: string, transport: Transport = new StdioServerTransport()): Promise<void> {\n const outDir = path.dirname(path.resolve(graphPath));\n const fileName = path.basename(graphPath);\n // Fail fast (and clearly) if the graph path escapes/doesn't exist, rather\n // than only surfacing that the first time a tool is called.\n validateGraphPath(fileName, outDir);\n\n const server = createGraphifyMcpServer(outDir);\n await server.connect(transport);\n}\n\n/* Entry point used by bin/graphify-mcp.js. /\nexport async function main(argv: string[] = process.argv): Promise<void> {\n const graphPath = argv[2] ?? path.join(process.cwd(), 'graphify-out', 'graph.json');\n await startServer(graphPath);\n}\n","import type Graph from 'graphology';\n\n/\n Library-level graph queries shared by the CLI (`graphify query/path/\n * explain`) and the MCP server tools of the same name. None of this is an\n * LLM call — it's lexical node matching + graph traversal, so it works\n * fully offline and deterministically.\n /\n\nconst STOPWORDS = new Set([\n 'a', 'an', 'the', 'is', 'are', 'was', 'were', 'do', 'does', 'did', 'how',\n 'what', 'where', 'when', 'why', 'who', 'which', 'to', 'of', 'in', 'on',\n 'for', 'and', 'or', 'this', 'that', 'it', 'does', 'that\\'s',\n]);\n\n/* Insert spaces at camelCase boundaries so identifier words become separate tokens. /\nfunction splitCamelCase(text: string): string {\n return text\n .replace(/([a-z0-9])([A-Z])/g, '$1 $2')\n .replace(/([A-Z]+)([A-Z][a-z])/g, '$1 $2');\n}\n\nfunction tokenize(text: string): string[] {\n return splitCamelCase(text)\n .toLowerCase()\n .split(/[^a-z0-9]+/)\n .filter((token) => token.length > 1 && !STOPWORDS.has(token));\n}\n\n/\n Split an identifier-ish string (node label/id) into its word subtokens:\n * camelCase, snake_case, kebab-case, dots, and path separators all become\n * boundaries, so `src/a/fileStorage.js::saveAttachment` yields\n * `src, file, storage, js, save, attachment`.\n /\nfunction subtokenize(text: string): string[] {\n return splitCamelCase(text)\n .toLowerCase()\n .split(/[^a-z0-9]+/)\n .filter((token) => token.length > 1);\n}\n\n/* Don't run the fuzzy tier on tokens this short — too many false positives. /\nconst FUZZY_MIN_TOKEN_LEN = 3;\n/* Minimum similarity for a fuzzy match to count at all. /\nconst FUZZY_THRESHOLD = 0.7;\nconst SUBTOKEN_MATCH_SCORE = 1;\nconst SUBSTRING_MATCH_SCORE = 0.6;\nconst FUZZY_MATCH_WEIGHT = 0.5;\n\n/\n Optimal-string-alignment Damerau-Levenshtein distance. Chosen over\n * bigram-set similarity because the common code-search typo is a\n * transposition (\"sorceNodes\"), which OSA counts as one edit but bigram\n * overlap punishes brutally.\n /\nfunction osaDistance(a: string, b: string): number {\n let prev2: number[] = [];\n let prev: number[] = Array.from({ length: b.length + 1 }, (_, j) => j);\n let curr: number[] = new Array<number>(b.length + 1).fill(0);\n\n for (let i = 1; i <= a.length; i++) {\n curr[0] = i;\n for (let j = 1; j <= b.length; j++) {\n const substitution = a[i - 1] === b[j - 1] ? 0 : 1;\n let best = Math.min(\n (prev[j] as number) + 1,\n (curr[j - 1] as number) + 1,\n (prev[j - 1] as number) + substitution,\n );\n if (i > 1 && j > 1 && a[i - 1] === b[j - 2] && a[i - 2] === b[j - 1]) {\n best = Math.min(best, (prev2[j - 2] as number) + 1);\n }\n curr[j] = best;\n }\n [prev2, prev, curr] = [prev, curr, new Array<number>(b.length + 1).fill(0)];\n }\n return prev[b.length] as number;\n}\n\n/* Normalized similarity in [0, 1]; short-circuits pairs whose length gap alone puts them under FUZZY_THRESHOLD. /\nfunction fuzzySimilarity(a: string, b: string): number {\n if (a === b) return 1;\n const maxLen = Math.max(a.length, b.length);\n if (maxLen === 0) return 1;\n if (Math.abs(a.length - b.length) / maxLen > 1 - FUZZY_THRESHOLD) return 0;\n return 1 - osaDistance(a, b) / maxLen;\n}\n\nexport interface NodeMatch {\n id: string;\n label: string;\n score: number;\n}\n\n/\n Score every node against the query's tokens. Identifier-aware and\n * typo-tolerant, in three tiers per token (best tier wins):\n \n 1. exact subtoken match (camelCase/snake_case-split word of the label\n * or id) — \"storage\" matches `fileStorage.js`;\n * 2. plain substring of the label/id (the original v1 behavior);\n * 3. fuzzy (Damerau-Levenshtein) match against a subtoken — \"sorce\"\n * still finds `scoreNodes`.\n \n Still fully lexical and deterministic — no LLM, no randomness.\n /\nexport function scoreNodes(graph: Graph, query: string): NodeMatch[] {\n const tokens = tokenize(query);\n const matches: NodeMatch[] = [];\n\n graph.forEachNode((id, attributes) => {\n const label = (attributes.label as string \| undefined) ?? id;\n const haystack = `${label} ${id}`.toLowerCase();\n const subtokens = new Set(subtokenize(`${label} ${id}`));\n let score = 0;\n for (const token of tokens) {\n if (subtokens.has(token)) {\n score += SUBTOKEN_MATCH_SCORE;\n continue;\n }\n if (haystack.includes(token)) {\n score += SUBSTRING_MATCH_SCORE;\n continue;\n }\n if (token.length >= FUZZY_MIN_TOKEN_LEN) {\n let best = 0;\n for (const subtoken of subtokens) {\n const similarity = fuzzySimilarity(token, subtoken);\n if (similarity > best) best = similarity;\n }\n if (best >= FUZZY_THRESHOLD) score += best FUZZY_MATCH_WEIGHT;\n }\n }\n if (score > 0) matches.push({ id, label, score });\n });\n\n // On equal score, real source nodes beat module:/external: placeholders —\n // \"devtools\" should resolve to the devtools middleware, not the\n // @redux-devtools package node that happens to share a subtoken.\n const placeholderRank = (id: string): number =>\n id.startsWith('module:') \|\| id.startsWith('external:') ? 1 : 0;\n matches.sort(\n (a, b) =>\n b.score - a.score \|\| placeholderRank(a.id) - placeholderRank(b.id) \|\| a.id.localeCompare(b.id),\n );\n return matches;\n}\n\n/*\n Best-effort single-node resolution: the highest-scoring lexical match,\n * or null if nothing in the graph matches at all. Deliberately does not\n * fall back to \"the most connected node\" — path/explain name a specific\n * node by intent, and silently substituting an unrelated one would be\n * more misleading than clearly saying \"no match\".\n /\nexport function resolveNode(graph: Graph, query: string): NodeMatch \| null {\n const matches = scoreNodes(graph, query);\n return matches[0] ?? null;\n}\n\nexport interface VisitedNode {\n id: string;\n label: string;\n sourceFile: string;\n sourceLocation: string;\n depth: number;\n}\n\nexport interface TraversalEdge {\n source: string;\n target: string;\n relation: string;\n confidence: string;\n}\n\nexport interface QueryResult {\n seeds: NodeMatch[];\n visited: VisitedNode[];\n edges: TraversalEdge[];\n}\n\nexport interface QueryOptions {\n dfs?: boolean;\n /* Hard cap on how many nodes to include. Defaults to a generous ceiling derived from `tokenBudget`. /\n budget?: number;\n /* Approximate cap, in tokens (~4 chars each), on the serialized size of the result. Default 2000. /\n tokenBudget?: number;\n maxDepth?: number;\n maxSeeds?: number;\n}\n\nconst DEFAULT_MAX_DEPTH = 2;\nconst DEFAULT_MAX_SEEDS = 5;\nconst DEFAULT_BUDGET = 40;\nconst DEFAULT_TOKEN_BUDGET = 2000;\n/* When only tokenBudget is given, allow up to this many nodes per budgeted token-decile as a safety ceiling. /\nconst NODES_PER_TOKEN = 1 / 10;\n\n/\n Estimated token contribution of one node to the rendered result: its own\n * line (label, file, location) plus a rough allowance for the edge lines\n * that mention its id. Chars/4 is the usual serviceable approximation.\n /\nfunction nodeTokenCost(graph: Graph, id: string): number {\n const attrs = graph.getNodeAttributes(id);\n const label = (attrs.label as string \| undefined) ?? id;\n const sourceFile = (attrs.sourceFile as string \| undefined) ?? '';\n return Math.ceil((id.length 2 + label.length + sourceFile.length + 24) / 4);\n}\n\n/*\n BFS (default, broad context) or DFS (--dfs, trace a specific path)\n * traversal from the nodes whose label best matches `question`'s\n * keywords. This is lexical retrieval, not natural-language\n * understanding — it surfaces the neighborhood of the graph an agent (or\n * a human) should look at to answer the question, it does not itself\n * compose an answer.\n /\nexport function queryGraph(graph: Graph, question: string, options: QueryOptions = {}): QueryResult {\n const maxDepth = options.maxDepth ?? DEFAULT_MAX_DEPTH;\n const maxSeeds = options.maxSeeds ?? DEFAULT_MAX_SEEDS;\n const tokenBudget = options.tokenBudget ?? DEFAULT_TOKEN_BUDGET;\n const budget = options.budget ?? Math.max(DEFAULT_BUDGET, Math.ceil(tokenBudget NODES_PER_TOKEN));\n\n const allMatches = scoreNodes(graph, question);\n const seeds = allMatches.length > 0 ? allMatches.slice(0, maxSeeds) : [];\n\n const visited = new Map<string, number>(); // id -> depth\n const frontier: Array<{ id: string; depth: number }> = seeds.map((s) => ({ id: s.id, depth: 0 }));\n let spentTokens = 0;\n for (const seed of seeds) {\n visited.set(seed.id, 0);\n spentTokens += nodeTokenCost(graph, seed.id);\n }\n\n while (frontier.length > 0 && visited.size < budget && spentTokens < tokenBudget) {\n const current = options.dfs ? (frontier.pop() as { id: string; depth: number }) : (frontier.shift() as { id: string; depth: number });\n if (current.depth >= maxDepth) continue;\n\n const neighbors = [...graph.neighbors(current.id)].sort((a, b) => a.localeCompare(b));\n for (const neighbor of neighbors) {\n if (visited.has(neighbor) \|\| visited.size >= budget \|\| spentTokens >= tokenBudget) continue;\n visited.set(neighbor, current.depth + 1);\n spentTokens += nodeTokenCost(graph, neighbor);\n frontier.push({ id: neighbor, depth: current.depth + 1 });\n }\n }\n\n const visitedNodes: VisitedNode[] = [...visited.entries()]\n .map(([id, depth]) => {\n const attrs = graph.getNodeAttributes(id);\n return {\n id,\n label: (attrs.label as string \| undefined) ?? id,\n sourceFile: (attrs.sourceFile as string \| undefined) ?? '',\n sourceLocation: (attrs.sourceLocation as string \| undefined) ?? '',\n depth,\n };\n })\n .sort((a, b) => a.depth - b.depth \|\| a.id.localeCompare(b.id));\n\n const edges: TraversalEdge[] = [];\n graph.forEachEdge((_edge, attrs, source, target) => {\n if (visited.has(source) && visited.has(target)) {\n edges.push({\n source,\n target,\n relation: String(attrs.relation),\n confidence: String(attrs.confidence),\n });\n }\n });\n edges.sort(\n (a, b) => a.source.localeCompare(b.source) \|\| a.target.localeCompare(b.target) \|\| a.relation.localeCompare(b.relation),\n );\n\n return enforceTokenBudget({ seeds, visited: visitedNodes, edges }, tokenBudget);\n}\n\n/*\n The traversal-time cost estimate can't see how densely connected the\n * visited neighborhood is — a hub-heavy subgraph induces far more edge\n * lines than nodes. Enforce the budget on the actual result: drop the\n * deepest/last nodes (and the edges that touched them) until the\n * serialized size fits. Seeds are never dropped.\n /\nfunction enforceTokenBudget(result: QueryResult, tokenBudget: number): QueryResult {\n const cost = (value: unknown): number => Math.ceil(JSON.stringify(value).length / 4);\n\n const visited = [...result.visited];\n let edges = [...result.edges];\n let total = cost(result.seeds) + visited.reduce((s, n) => s + cost(n), 0) + edges.reduce((s, e) => s + cost(e), 0);\n\n const seedIds = new Set(result.seeds.map((s) => s.id));\n // visited is sorted by (depth, id) — pop from the end so the deepest,\n // least-central context goes first and the result stays deterministic.\n while (total > tokenBudget && visited.length > 0) {\n const last = visited[visited.length - 1] as VisitedNode;\n if (seedIds.has(last.id)) break;\n visited.pop();\n total -= cost(last);\n const remaining: TraversalEdge[] = [];\n for (const edge of edges) {\n if (edge.source === last.id \|\| edge.target === last.id) {\n total -= cost(edge);\n } else {\n remaining.push(edge);\n }\n }\n edges = remaining;\n }\n\n return { seeds: result.seeds, visited, edges };\n}\n\nexport interface PathResult {\n from: NodeMatch;\n to: NodeMatch;\n found: boolean;\n path: string[];\n edges: TraversalEdge[];\n}\n\n/* Shortest path between the nodes that best match `fromQuery` and `toQuery` (undirected BFS — connectivity, not call direction). /\nexport function shortestPath(graph: Graph, fromQuery: string, toQuery: string): PathResult \| null {\n const from = resolveNode(graph, fromQuery);\n const to = resolveNode(graph, toQuery);\n if (!from \|\| !to) return null;\n\n if (from.id === to.id) {\n return { from, to, found: true, path: [from.id], edges: [] };\n }\n\n const predecessor = new Map<string, string>();\n const visited = new Set<string>([from.id]);\n const queue: string[] = [from.id];\n\n while (queue.length > 0) {\n const current = queue.shift() as string;\n if (current === to.id) break;\n const neighbors = [...graph.neighbors(current)].sort((a, b) => a.localeCompare(b));\n for (const neighbor of neighbors) {\n if (visited.has(neighbor)) continue;\n visited.add(neighbor);\n predecessor.set(neighbor, current);\n queue.push(neighbor);\n }\n }\n\n if (!visited.has(to.id)) {\n return { from, to, found: false, path: [], edges: [] };\n }\n\n const path: string[] = [to.id];\n let cursor = to.id;\n while (cursor !== from.id) {\n const prev = predecessor.get(cursor);\n if (!prev) break;\n path.unshift(prev);\n cursor = prev;\n }\n\n const edges: TraversalEdge[] = [];\n for (let i = 0; i < path.length - 1; i++) {\n const a = path[i] as string;\n const b = path[i + 1] as string;\n const key = graph.edges(a, b)[0] ?? graph.edges(b, a)[0];\n if (key) {\n const attrs = graph.getEdgeAttributes(key);\n edges.push({ source: a, target: b, relation: String(attrs.relation), confidence: String(attrs.confidence) });\n }\n }\n\n return { from, to, found: true, path, edges };\n}\n\nexport interface ExplainResult {\n id: string;\n label: string;\n sourceFile: string;\n sourceLocation: string;\n communityLabel?: string;\n outgoing: TraversalEdge[];\n incoming: TraversalEdge[];\n}\n\n/* Plain-language-ready explanation of the node that best matches `query`. /\nexport function explainNode(graph: Graph, query: string): ExplainResult \| null {\n const match = resolveNode(graph, query);\n if (!match) return null;\n\n const attrs = graph.getNodeAttributes(match.id);\n const outgoing: TraversalEdge[] = [];\n const incoming: TraversalEdge[] = [];\n\n graph.forEachOutEdge(match.id, (_edge, edgeAttrs, source, target) => {\n outgoing.push({ source, target, relation: String(edgeAttrs.relation), confidence: String(edgeAttrs.confidence) });\n });\n graph.forEachInEdge(match.id, (_edge, edgeAttrs, source, target) => {\n incoming.push({ source, target, relation: String(edgeAttrs.relation), confidence: String(edgeAttrs.confidence) });\n });\n\n outgoing.sort((a, b) => a.target.localeCompare(b.target) \|\| a.relation.localeCompare(b.relation));\n incoming.sort((a, b) => a.source.localeCompare(b.source) \|\| a.relation.localeCompare(b.relation));\n\n return {\n id: match.id,\n label: match.label,\n sourceFile: (attrs.sourceFile as string \| undefined) ?? '',\n sourceLocation: (attrs.sourceLocation as string \| undefined) ?? '',\n communityLabel: attrs.communityLabel as string \| undefined,\n outgoing,\n incoming,\n };\n}\n","import type Graph from 'graphology';\nimport { scoreNodes } from './query.js';\n\n/\n `graphify context` — the working-set pack. Instead of returning node\n * names for the agent to chase (query -> then read whole files anyway),\n * this fuses the two steps: the graph knows every entity's file and line,\n * so rank the nodes relevant to the task, read just the relevant line\n * ranges, and pack the actual code into a token budget. One call returns\n * the code an agent needs to start a task.\n /\n\nexport interface ContextSnippet {\n nodeId: string;\n label: string;\n file: string;\n startLine: number;\n endLine: number;\n code: string;\n /* Why this snippet is in the pack (lexical match / neighbor-of relation). /\n reason: string;\n score: number;\n}\n\nexport interface ContextPack {\n task: string;\n snippets: ContextSnippet[];\n /* Approximate tokens used out of the budget. /\n tokens: number;\n tokenBudget: number;\n /* Ranked nodes that didn't fit the budget — the agent can pull them explicitly. /\n overflow: Array<{ nodeId: string; file: string }>;\n}\n\nexport interface ContextOptions {\n /* Approximate token cap for the pack (default 4000). /\n tokenBudget?: number;\n maxSeeds?: number;\n /* Cap on snippet length in lines (default 60). /\n maxSnippetLines?: number;\n}\n\nexport type FileReader = (path: string) => Promise<string>;\n\nconst DEFAULT_CONTEXT_BUDGET = 4000;\nconst DEFAULT_MAX_SEEDS = 8;\nconst DEFAULT_MAX_SNIPPET_LINES = 60;\n/* A neighbor inherits this fraction of the score of the node that pulled it in. /\nconst NEIGHBOR_DECAY = 0.4;\n\nconst tokensOf = (text: string): number => Math.ceil(text.length / 4);\n\nfunction lineNumberOf(sourceLocation: string): number \| null {\n const match = /^L(\\d+)$/.exec(sourceLocation);\n return match ? Number(match[1]) : null;\n}\n\nfunction isReadableFile(sourceFile: string): boolean {\n return sourceFile !== '' && !sourceFile.startsWith('<') && !sourceFile.includes('://');\n}\n\ninterface RankedNode {\n id: string;\n score: number;\n reason: string;\n}\n\n/\n Rank nodes for the task: lexical seeds first (their match score), then\n * their graph neighbors at a decayed score, labeled with the relation that\n * connects them. Deterministic (score desc, id asc).\n /\nexport function rankForTask(graph: Graph, task: string, maxSeeds = DEFAULT_MAX_SEEDS): RankedNode[] {\n const seeds = scoreNodes(graph, task).slice(0, maxSeeds);\n const ranked = new Map<string, RankedNode>();\n for (const seed of seeds) {\n ranked.set(seed.id, { id: seed.id, score: seed.score, reason: 'matches the task' });\n }\n\n for (const seed of seeds) {\n graph.forEachEdge(seed.id, (_edge, attrs, source, target) => {\n const neighbor = source === seed.id ? target : source;\n if (ranked.has(neighbor)) return;\n const relation = String(attrs.relation);\n const direction = source === seed.id ? `${relation} ->` : `<- ${relation}`;\n ranked.set(neighbor, {\n id: neighbor,\n score: seed.score NEIGHBOR_DECAY,\n reason: `${direction} ${seed.label}`,\n });\n });\n }\n\n return [...ranked.values()].sort((a, b) => b.score - a.score \|\| a.id.localeCompare(b.id));\n}\n\n/*\n Extract the snippet for a node: from its declaration line to just before\n * the next known entity in the same file (capped), so snippets align with\n * real code block boundaries without needing a parser here.\n /\nfunction snippetRange(\n startLine: number,\n fileLineCount: number,\n entityStartsInFile: number[],\n maxLines: number,\n): { start: number; end: number } {\n const nextStart = entityStartsInFile.find((l) => l > startLine);\n const hardEnd = nextStart !== undefined ? nextStart - 1 : fileLineCount;\n return { start: startLine, end: Math.min(hardEnd, startLine + maxLines - 1) };\n}\n\nexport async function buildContextPack(\n graph: Graph,\n task: string,\n readFile: FileReader,\n options: ContextOptions = {},\n): Promise<ContextPack> {\n const tokenBudget = options.tokenBudget ?? DEFAULT_CONTEXT_BUDGET;\n const maxSnippetLines = options.maxSnippetLines ?? DEFAULT_MAX_SNIPPET_LINES;\n const ranked = rankForTask(graph, task, options.maxSeeds);\n\n // Every known entity start line per file — used to end snippets at the\n // next declaration instead of an arbitrary window.\n const entityStarts = new Map<string, number[]>();\n graph.forEachNode((_id, attrs) => {\n const file = attrs.sourceFile as string \| undefined;\n const line = lineNumberOf((attrs.sourceLocation as string \| undefined) ?? '');\n if (file && line !== null) {\n const starts = entityStarts.get(file) ?? [];\n starts.push(line);\n entityStarts.set(file, starts);\n }\n });\n for (const starts of entityStarts.values()) starts.sort((a, b) => a - b);\n\n const fileCache = new Map<string, string[] \| null>();\n const readLines = async (file: string): Promise<string[] \| null> => {\n const cached = fileCache.get(file);\n if (cached !== undefined) return cached;\n let lines: string[] \| null;\n try {\n lines = (await readFile(file)).split('\\n');\n } catch {\n lines = null;\n }\n fileCache.set(file, lines);\n return lines;\n };\n\n const snippets: ContextSnippet[] = [];\n const overflow: Array<{ nodeId: string; file: string }> = [];\n const coveredRanges = new Map<string, Array<{ start: number; end: number }>>();\n let tokens = 0;\n\n for (const node of ranked) {\n const attrs = graph.getNodeAttributes(node.id);\n const file = (attrs.sourceFile as string \| undefined) ?? '';\n const startLine = lineNumberOf((attrs.sourceLocation as string \| undefined) ?? '');\n if (!isReadableFile(file) \|\| startLine === null) continue;\n\n const lines = await readLines(file);\n if (lines === null) continue;\n\n const { start, end } = snippetRange(startLine, lines.length, entityStarts.get(file) ?? [], maxSnippetLines);\n\n // Skip if an already-packed snippet from the same file covers this range.\n const covered = (coveredRanges.get(file) ?? []).some((r) => start >= r.start && end <= r.end);\n if (covered) continue;\n\n const code = lines.slice(start - 1, end).join('\\n');\n const cost = tokensOf(code) + 15; // header overhead\n if (tokens + cost > tokenBudget) {\n overflow.push({ nodeId: node.id, file: `${file}:L${startLine}` });\n continue;\n }\n\n tokens += cost;\n snippets.push({\n nodeId: node.id,\n label: (attrs.label as string \| undefined) ?? node.id,\n file,\n startLine: start,\n endLine: end,\n code,\n reason: node.reason,\n score: node.score,\n });\n const ranges = coveredRanges.get(file) ?? [];\n ranges.push({ start, end });\n coveredRanges.set(file, ranges);\n }\n\n return { task, snippets, tokens, tokenBudget, overflow };\n}\n\n/* Render a pack as agent-ready markdown. /\nexport function renderContextPack(pack: ContextPack): string {\n const lines: string[] = [\n `# Context pack: ${pack.task}`,\n '',\n `_~${pack.tokens} of ${pack.tokenBudget} token budget, ${pack.snippets.length} snippet(s)._`,\n '',\n ];\n\n if (pack.snippets.length === 0) {\n lines.push('No matching code found — try different keywords.');\n return lines.join('\\n');\n }\n\n for (const snippet of pack.snippets) {\n lines.push(`## ${snippet.label} — \\`${snippet.file}:L${snippet.startLine}-L${snippet.endLine}\\``);\n lines.push(`_${snippet.reason}_`);\n lines.push('```');\n lines.push(snippet.code);\n lines.push('```');\n lines.push('');\n }\n\n if (pack.overflow.length > 0) {\n lines.push(`## Didn't fit the budget (${pack.overflow.length})`);\n for (const item of pack.overflow.slice(0, 15)) {\n lines.push(`- ${item.nodeId} (${item.file})`);\n }\n lines.push('');\n }\n\n return lines.join('\\n');\n}\n","import as path from 'node:path';\nimport type Graph from 'graphology';\nimport { LocalFileGraphStore } from './store/localFile.js';\n\n/*\n Load a previously-exported graph.json back into a graphology Graph.\n * Thin wrapper over LocalFileGraphStore (which enforces the path-traversal\n * guard — see SECURITY.md) that throws when no graph exists, because every\n * CLI/MCP caller treats \"no graph yet\" as a hard error. Library callers who\n * want the null-on-missing contract should use a GraphStore directly.\n /\nexport async function loadGraph(outDir: string = path.join(process.cwd(), 'graphify-out')): Promise<Graph> {\n const graph = await new LocalFileGraphStore().load(outDir);\n if (graph === null) {\n throw new Error(`No graph found in ${outDir} — run \\`graphify <path>\\` to build one first.`);\n }\n return graph;\n}\n","import as fs from 'node:fs/promises';\nimport type Graph from 'graphology';\nimport { validateGraphPath } from '../security.js';\nimport { deserializeGraph, serializeGraph } from './serialize.js';\nimport type { GraphStore, SerializedGraph } from './types.js';\n\n/*\n The reference GraphStore: one graph.json per directory, `ref` = the\n * outDir path. Reproduces the classic graphify-out/ behavior byte-for-byte\n * (same pretty-printed JSON exportGraph() writes) and routes every path\n * through security.validateGraphPath(), so a caller-supplied ref — or a\n * symlinked graph.json — can never read or write outside the directory it\n * resolves to.\n /\nexport class LocalFileGraphStore implements GraphStore {\n async load(ref: string): Promise<Graph \| null> {\n let jsonPath: string;\n try {\n jsonPath = validateGraphPath('graph.json', ref);\n } catch (error) {\n // A ref whose directory doesn't exist simply has no graph yet;\n // traversal/symlink-escape rejections must still propagate.\n if ((error as Error).message.startsWith('Base directory does not exist')) return null;\n throw error;\n }\n\n let raw: string;\n try {\n raw = await fs.readFile(jsonPath, 'utf-8');\n } catch (error) {\n if ((error as NodeJS.ErrnoException).code === 'ENOENT') return null;\n throw error;\n }\n return deserializeGraph(JSON.parse(raw) as SerializedGraph);\n }\n\n async save(ref: string, graph: Graph): Promise<void> {\n await fs.mkdir(ref, { recursive: true });\n const jsonPath = validateGraphPath('graph.json', ref);\n await fs.writeFile(jsonPath, JSON.stringify(serializeGraph(graph), null, 2), 'utf-8');\n }\n}\n","/\n Security helpers — URL validation, SSRF-guarded fetch, path guards, label\n * sanitization, prompt-injection defenses. Every control listed in\n * SECURITY.md must have a corresponding function here and a unit test in\n * tests/security.test.ts. See the master prompt §5 for the full checklist.\n /\n\nimport { createHash } from 'node:crypto';\nimport as dns from 'node:dns';\nimport * as http from 'node:http';\nimport * as https from 'node:https';\nimport * as fs from 'node:fs';\nimport * as net from 'node:net';\nimport * as nodePath from 'node:path';\n\nconst ALLOWED_SCHEMES = new Set(['http:', 'https:']);\nconst MAX_FETCH_BYTES = 50 * 1024 * 1024;\nconst MAX_TEXT_BYTES = 10 * 1024 * 1024;\nconst MAX_LABEL_LEN = 256;\nconst MAX_REDIRECTS = 5;\nconst REQUEST_TIMEOUT_MS = 15_000;\n\n/** Hostnames that must never be reachable, regardless of what they resolve to. /\nconst BLOCKED_HOSTNAMES = new Set([\n 'metadata.google.internal',\n 'metadata.internal',\n 'metadata',\n 'metadata.azure.com',\n 'instance-data',\n 'instance-data.ec2.internal',\n]);\n\n// ---------------------------------------------------------------------------\n// IP range checks (SSRF guard core). Implemented without extra dependencies.\n// ---------------------------------------------------------------------------\n\nfunction ipv4ToInt(ip: string): number \| null {\n const parts = ip.split('.');\n if (parts.length !== 4) return null;\n let result = 0;\n for (const part of parts) {\n if (!/^\\d{1,3}$/.test(part)) return null;\n const n = Number(part);\n if (n > 255) return null;\n result = (result << 8) \| n;\n }\n return result >>> 0;\n}\n\nfunction ipv4InCidr(ipInt: number, cidr: string): boolean {\n const [base, prefixStr] = cidr.split('/');\n const prefix = Number(prefixStr);\n const baseInt = ipv4ToInt(base ?? '');\n if (baseInt === null) return false;\n const mask = prefix === 0 ? 0 : (~0 << (32 - prefix)) >>> 0;\n return (ipInt & mask) >>> 0 === (baseInt & mask) >>> 0;\n}\n\n/* IPv4 ranges that must never be connected to from a server-side fetch. /\nconst BLOCKED_IPV4_CIDRS = [\n '0.0.0.0/8', // \"this\" network\n '10.0.0.0/8', // private\n '100.64.0.0/10', // carrier-grade NAT (CGN)\n '127.0.0.0/8', // loopback\n '169.254.0.0/16', // link-local (covers 169.254.169.254 cloud metadata)\n '172.16.0.0/12', // private\n '192.0.0.0/24', // IETF protocol assignments\n '192.0.2.0/24', // TEST-NET-1\n '192.168.0.0/16', // private\n '198.18.0.0/15', // benchmarking\n '198.51.100.0/24', // TEST-NET-2\n '203.0.113.0/24', // TEST-NET-3\n '224.0.0.0/4', // multicast\n '240.0.0.0/4', // reserved\n '255.255.255.255/32', // broadcast\n];\n\nexport function isForbiddenIpv4(ip: string): boolean {\n const ipInt = ipv4ToInt(ip);\n if (ipInt === null) return true; // malformed -> treat as forbidden, fail closed\n return BLOCKED_IPV4_CIDRS.some((cidr) => ipv4InCidr(ipInt, cidr));\n}\n\n/* Expand a (possibly `::`-compressed) IPv6 address into 8 16-bit groups. /\nfunction expandIpv6(ip: string): number[] \| null {\n const withoutZone = ip.split('%')[0] ?? '';\n const parts = withoutZone.split('::');\n if (parts.length > 2) return null;\n\n const head = parts[0] ? parts[0].split(':').filter((s) => s.length > 0) : [];\n const tail = parts.length === 2 && parts[1] ? parts[1].split(':').filter((s) => s.length > 0) : [];\n\n let missing = 0;\n if (parts.length === 2) {\n missing = 8 - head.length - tail.length;\n if (missing < 0) return null;\n } else if (head.length + tail.length !== 8) {\n return null;\n }\n\n const groupsHex = [...head, ...Array(missing).fill('0'), ...tail];\n if (groupsHex.length !== 8) return null;\n\n const groups: number[] = [];\n for (const g of groupsHex) {\n if (!/^[0-9a-fA-F]{1,4}$/.test(g)) return null;\n groups.push(parseInt(g, 16));\n }\n return groups;\n}\n\nexport function isForbiddenIpv6(ip: string): boolean {\n const lower = ip.toLowerCase();\n if (lower === '::1' \|\| lower === '::') return true;\n\n const mapped = /^::ffff:(\\d+\\.\\d+\\.\\d+\\.\\d+)$/.exec(lower);\n if (mapped) return isForbiddenIpv4(mapped[1] as string);\n\n const groups = expandIpv6(lower);\n if (groups === null) return true; // unparsable -> fail closed\n const first = groups[0] as number;\n if ((first & 0xffc0) === 0xfe80) return true; // fe80::/10 link-local\n if ((first & 0xfe00) === 0xfc00) return true; // fc00::/7 unique local\n if ((first & 0xff00) === 0xff00) return true; // ff00::/8 multicast\n if (groups.every((g) => g === 0)) return true; // unspecified/all-zero\n return false;\n}\n\nexport function isForbiddenIp(ip: string): boolean {\n return net.isIPv6(ip) ? isForbiddenIpv6(ip) : isForbiddenIpv4(ip);\n}\n\n// ---------------------------------------------------------------------------\n// URL validation\n// ---------------------------------------------------------------------------\n\n/\n Validate a URL is http/https and, when the hostname is itself a literal\n * IP or a known cloud-metadata hostname, reject it synchronously. DNS-bound\n * hostnames are re-validated at connect time by safeFetch() (see below) —\n * this function alone cannot rule out DNS rebinding for a hostname that\n * currently resolves to a public IP.\n /\nexport function validateUrl(url: string): string {\n let parsed: URL;\n try {\n parsed = new URL(url);\n } catch {\n throw new Error(`Invalid URL: ${url}`);\n }\n\n if (!ALLOWED_SCHEMES.has(parsed.protocol)) {\n throw new Error(\n `URL scheme not allowed: \"${parsed.protocol}\" (allowed: ${[...ALLOWED_SCHEMES].join(', ')})`,\n );\n }\n\n const hostname = parsed.hostname.toLowerCase();\n if (BLOCKED_HOSTNAMES.has(hostname)) {\n throw new Error(`URL targets a blocked host: ${hostname}`);\n }\n\n // WHATWG URL keeps the brackets on an IPv6 literal host (e.g. \"[::1]\") —\n // strip them before checking net.isIP()/isForbiddenIp().\n const bareHost =\n hostname.startsWith('[') && hostname.endsWith(']') ? hostname.slice(1, -1) : hostname;\n if (net.isIP(bareHost) && isForbiddenIp(bareHost)) {\n throw new Error(`URL targets a forbidden IP address: ${bareHost}`);\n }\n\n return parsed.toString();\n}\n\n// ---------------------------------------------------------------------------\n// safeFetch — SSRF-guarded, size-capped, redirect-revalidating fetch\n// ---------------------------------------------------------------------------\n\nexport type LookupFn = (hostname: string) => Promise<{ address: string; family: number }>;\n\n/\n Resolve a hostname (or pass through a literal IP) and validate the\n * result. `lookup` defaults to the real `dns.promises.lookup` — tests\n * substitute a fake to exercise the rebind guard deterministically without\n * making a real DNS query.\n /\nexport async function resolveAndValidate(\n hostname: string,\n lookup: LookupFn = dns.promises.lookup,\n): Promise<{ address: string; family: number }> {\n if (net.isIP(hostname)) {\n if (isForbiddenIp(hostname)) {\n throw new Error(`Refusing to connect to forbidden IP: ${hostname}`);\n }\n return { address: hostname, family: net.isIPv6(hostname) ? 6 : 4 };\n }\n const result = await lookup(hostname);\n if (isForbiddenIp(result.address)) {\n throw new Error(`Refusing to connect to forbidden IP: ${hostname} -> ${result.address}`);\n }\n return result;\n}\n\nexport interface RawResponse {\n statusCode: number;\n headers: http.IncomingHttpHeaders;\n body: Buffer;\n}\n\n/* Minimal shape of the `http`/`https` modules that requestOnce() needs — narrow on purpose so tests can substitute a fake transport instead of mocking network I/O. /\nexport type RequestTransport = Pick<typeof http, 'request'>;\n\n/\n Issue a single HTTP(S) request, connecting to `resolvedAddress` directly\n * (via a `lookup` override) rather than re-resolving DNS at connect time —\n * this is what prevents a DNS-rebind attacker from swapping the target\n * between validation and connection (TOCTOU). Streams the body and aborts\n * once it exceeds the byte cap for its declared content type.\n /\nexport function requestOnce(\n target: URL,\n resolvedAddress: string,\n resolvedFamily: number,\n transport: RequestTransport = target.protocol === 'https:' ? https : http,\n): Promise<RawResponse> {\n return new Promise((resolve, reject) => {\n const req = transport.request(\n {\n protocol: target.protocol,\n hostname: target.hostname,\n host: target.hostname,\n port: target.port \|\| (target.protocol === 'https:' ? 443 : 80),\n path: `${target.pathname}${target.search}`,\n method: 'GET',\n timeout: REQUEST_TIMEOUT_MS,\n headers: { 'user-agent': 'graphify/0.1', accept: '/' },\n // Force the connection to the address we already validated — do not\n // let Node re-resolve `target.hostname` at connect time.\n lookup: (\n _hostname: string,\n options: unknown,\n callback: (err: NodeJS.ErrnoException \| null, address: string, family: number) => void,\n ) => {\n callback(null, resolvedAddress, resolvedFamily);\n },\n } as http.RequestOptions,\n (res) => {\n const statusCode = res.statusCode ?? 0;\n const contentType = String(res.headers['content-type'] ?? '');\n const isTextual = /^text\\/\|json\|xml\|html\|charset=/i.test(contentType);\n const cap = isTextual ? MAX_TEXT_BYTES : MAX_FETCH_BYTES;\n\n const chunks: Buffer[] = [];\n let total = 0;\n let aborted = false;\n\n res.on('data', (chunk: Buffer) => {\n total += chunk.length;\n if (total > cap) {\n aborted = true;\n res.destroy();\n req.destroy();\n reject(new Error(`Response exceeded ${cap} byte cap (content-type: ${contentType})`));\n return;\n }\n chunks.push(chunk);\n });\n res.on('end', () => {\n if (aborted) return;\n resolve({ statusCode, headers: res.headers, body: Buffer.concat(chunks) });\n });\n res.on('error', (err) => {\n if (!aborted) reject(err);\n });\n },\n );\n\n req.on('timeout', () => {\n req.destroy(new Error(`Request timed out after ${REQUEST_TIMEOUT_MS}ms`));\n });\n req.on('error', reject);\n req.end();\n });\n}\n\nexport interface SafeFetchDeps {\n /* Override DNS resolution + IP validation (default: resolveAndValidate). /\n resolve?: (hostname: string) => Promise<{ address: string; family: number }>;\n /* Override the actual request (default: requestOnce against real http/https). /\n request?: (target: URL, address: string, family: number) => Promise<RawResponse>;\n}\n\n/\n Fetch a URL with the SSRF guards from validateUrl() plus streaming size\n * caps (MAX_FETCH_BYTES / MAX_TEXT_BYTES) and a hard error on non-2xx\n * status. Every redirect hop is independently validated and re-resolved —\n * a redirect to a private/loopback/metadata address is rejected exactly\n * like a direct request would be.\n \n `deps` exists so tests can substitute the DNS/network collaborators with\n * deterministic fakes (see tests/security.test.ts) instead of mocking\n * Node's core modules or hitting real sockets — production callers should\n * never need to pass it.\n /\nexport async function safeFetch(url: string, deps: SafeFetchDeps = {}): Promise<Buffer> {\n const resolve = deps.resolve ?? resolveAndValidate;\n const doRequest = deps.request ?? requestOnce;\n\n let current = validateUrl(url);\n for (let hop = 0; hop <= MAX_REDIRECTS; hop++) {\n const target = new URL(current);\n const { address, family } = await resolve(target.hostname);\n const response = await doRequest(target, address, family);\n\n if (response.statusCode >= 300 && response.statusCode < 400) {\n const location = response.headers.location;\n if (!location) {\n throw new Error(`Redirect response (${response.statusCode}) missing Location header`);\n }\n const next = new URL(location, target).toString();\n current = validateUrl(next);\n continue;\n }\n\n if (response.statusCode < 200 \|\| response.statusCode >= 300) {\n throw new Error(`Non-2xx response: ${response.statusCode}`);\n }\n\n return response.body;\n }\n throw new Error(`Too many redirects (> ${MAX_REDIRECTS}) while fetching ${url}`);\n}\n\n// ---------------------------------------------------------------------------\n// Database DSN validation (MySQL schema extraction)\n// ---------------------------------------------------------------------------\n\nexport interface ValidatedDsn {\n /\n Credential-free rendering (`mysql://host:port/db`). This is the ONLY\n * form that may ever appear in graph nodes, reports, logs, or errors —\n * the password exists solely inside `connection`.\n /\n safeDisplay: string;\n connection: {\n host: string;\n port: number;\n user: string;\n password: string;\n database: string;\n };\n}\n\nconst DEFAULT_MYSQL_PORT = 3306;\n\n/\n Parse and validate a `mysql://user:pass@host:port/database` DSN.\n \n Deliberately does NOT apply the SSRF IP blocklist that safeFetch()\n * enforces: connecting to a localhost/private-network database is the\n * primary legitimate use of an explicitly user-supplied DSN, unlike a URL\n * scraped out of corpus content. The security property that matters here\n * is credential containment — see ValidatedDsn.safeDisplay.\n /\nexport function validateDsn(dsn: string): ValidatedDsn {\n let parsed: URL;\n try {\n parsed = new URL(dsn);\n } catch {\n throw new Error('Invalid DSN — expected mysql://user:pass@host:port/database');\n }\n\n if (parsed.protocol !== 'mysql:') {\n throw new Error(`DSN scheme not supported: \"${parsed.protocol}\" (only mysql: is supported)`);\n }\n\n const database = decodeURIComponent(parsed.pathname.replace(/^\\//, ''));\n if (!database \|\| database.includes('/')) {\n throw new Error('DSN must name exactly one database, e.g. mysql://localhost:3306/mydb');\n }\n if (!parsed.hostname) {\n throw new Error('DSN must include a host, e.g. mysql://localhost:3306/mydb');\n }\n\n const port = parsed.port ? Number(parsed.port) : DEFAULT_MYSQL_PORT;\n return {\n safeDisplay: `mysql://${parsed.hostname}:${port}/${database}`,\n connection: {\n host: parsed.hostname,\n port,\n user: decodeURIComponent(parsed.username) \|\| 'root',\n password: decodeURIComponent(parsed.password),\n database,\n },\n };\n}\n\n// ---------------------------------------------------------------------------\n// Path traversal guard\n// ---------------------------------------------------------------------------\n\n/\n Resolve `path` and require it stays inside `base` (defaults to\n * `<cwd>/graphify-out`). `base` must already exist. Throws on traversal\n * attempts (`../`, absolute escapes, symlink-resolved escapes).\n /\nexport function validateGraphPath(path: string, base?: string): string {\n const baseDir = base ?? nodePath.join(process.cwd(), 'graphify-out');\n\n let resolvedBase: string;\n try {\n resolvedBase = fs.realpathSync(baseDir);\n } catch {\n throw new Error(`Base directory does not exist: ${baseDir}`);\n }\n\n const candidate = nodePath.isAbsolute(path) ? path : nodePath.join(resolvedBase, path);\n const resolvedCandidate = nodePath.resolve(candidate);\n\n // Resolve symlinks for whichever is the deepest existing ancestor, so a\n // symlink inside an otherwise-valid path can't escape the base dir either.\n let realCandidate = resolvedCandidate;\n try {\n realCandidate = fs.realpathSync(resolvedCandidate);\n } catch {\n // Path (or part of it) may not exist yet (e.g. a file we're about to\n // write) — fall back to the lexically-resolved path for the check.\n }\n\n const relative = nodePath.relative(resolvedBase, realCandidate);\n const escapes = relative === '..' \|\| relative.startsWith(`..${nodePath.sep}`) \|\| nodePath.isAbsolute(relative);\n if (escapes) {\n throw new Error(`Path escapes graphify-out/: ${path}`);\n }\n\n return realCandidate;\n}\n\n// ---------------------------------------------------------------------------\n// Label sanitization (unchanged reference implementation) + HTML escaping\n// ---------------------------------------------------------------------------\n\n/* Strip control characters, cap length. Apply to every node/edge label. /\nexport function sanitizeLabel(text: string \| null \| undefined): string {\n if (text == null) return '';\n // eslint-disable-next-line no-control-regex -- intentional: stripping raw control chars\n const stripped = String(text).replace(/[\\x00-\\x1f\\x7f]/g, '');\n return stripped.slice(0, MAX_LABEL_LEN);\n}\n\n/\n HTML-escape a string. Callers must run sanitizeLabel() first for\n * length/control-char stripping, then escapeHtml() immediately before\n * embedding into graph.html (XSS control, see SECURITY.md).\n /\nexport function escapeHtml(text: string): string {\n return text\n .replace(/&/g, '&')\n .replace(/</g, '<')\n .replace(/>/g, '>')\n .replace(/\"/g, '"')\n .replace(/'/g, ''');\n}\n\n// ---------------------------------------------------------------------------\n// Prompt-injection defenses for LLM-bound file content\n// ---------------------------------------------------------------------------\n\n/\n Known jailbreak / chat-template sentinels that must never reach a prompt\n * unescaped, whether they occur in source files or are forged to spoof our\n * own <untrusted_source> delimiter.\n /\nconst SENTINEL_PATTERNS: RegExp[] = [\n /<\\\|im_start\\\|>/gi,\n /<\\\|im_end\\\|>/gi,\n /<\\\|system\\\|>/gi,\n /\\[INST\\]/gi,\n /\\[\\/INST\\]/gi,\n /<<SYS>>/gi,\n /<<\\/SYS>>/gi,\n /<\\/untrusted_source>/gi,\n /<untrusted_source/gi,\n];\n\n/\n Render brackets as fullwidth lookalikes (＜＞［］) so the defanged\n * echo is human-visible but no longer byte-identical to the original\n * sentinel — a naive downstream scan for the literal delimiter/sentinel\n * text will not re-match our own \"we found one\" marker.\n /\nfunction toFullwidthBrackets(text: string): string {\n return text\n .replace(/</g, '＜')\n .replace(/>/g, '＞')\n .replace(/\\[/g, '［')\n .replace(/\\]/g, '］');\n}\n\n/\n Replace known jailbreak/chat-template sentinels with a visibly defanged\n * form — never silently stripped (silent stripping can itself be an\n * injection vector if it changes meaning unexpectedly).\n /\nfunction defangSentinels(content: string): string {\n let result = content;\n for (const pattern of SENTINEL_PATTERNS) {\n result = result.replace(pattern, (match) => `[DEFANGED:${toFullwidthBrackets(match)}]`);\n }\n return result;\n}\n\n/\n Wrap file content for LLM prompts in a hash-stamped untrusted-source\n * delimiter and neutralize known jailbreak/chat-template sentinels. This\n * raises the bar against prompt injection; it does not eliminate it —\n * document that plainly wherever this is referenced.\n /\nexport function wrapUntrustedSource(path: string, content: string): string {\n const sha256 = createHash('sha256').update(content, 'utf8').digest('hex');\n const safePath = escapeHtml(sanitizeLabel(path));\n const defanged = defangSentinels(content);\n return `<untrusted_source path=\"${safePath}\" sha256=\"${sha256}\">\\n${defanged}\\n</untrusted_source>`;\n}\n","import Graph from 'graphology';\nimport type { SerializedGraph } from './types.js';\n\n/\n The stable serialization contract for graphs at rest: graphology's\n * node-link JSON. exportGraph() has always written exactly this shape to\n * graph.json, so anything serialized here stays loadable by every existing\n * consumer (and vice versa).\n /\nexport function serializeGraph(graph: Graph): SerializedGraph {\n return graph.export();\n}\n\nexport function deserializeGraph(data: SerializedGraph): Graph {\n return Graph.from(data);\n}\n","import type Graph from 'graphology';\nimport { resolveNode, type NodeMatch } from './query.js';\nimport type { Confidence, Relation } from './types.js';\n\n/\n Reverse impact analysis — \"what breaks if I change X\". Walks incoming\n * dependency edges (who calls / imports / inherits from the target)\n * transitively, so depth 1 is the direct blast radius and deeper levels are\n * ripple effects. Like everything in query.ts this is lexical + structural,\n * fully offline and deterministic.\n /\n\n/\n Relations where `source --rel--> target` means \"source depends on target\",\n * i.e. changing the target can break the source. `contains`/`method` are\n * included because changing an entity plausibly affects its container file\n * or class signature consumers see.\n /\nconst DEPENDENCY_RELATIONS: ReadonlySet<Relation> = new Set([\n 'calls',\n 'imports',\n 'imports_from',\n 'inherits',\n 'implements',\n 'mixes_in',\n 'embeds',\n 'references',\n 're_exports',\n 'method',\n 'contains',\n] satisfies Relation[]);\n\nexport interface AffectedNode {\n id: string;\n label: string;\n sourceFile: string;\n sourceLocation: string;\n /* 1 = depends on the target directly, 2 = one step removed, ... /\n depth: number;\n /* The dependency edge that pulled this node in (this node -> something already affected). /\n via: {\n relation: Relation;\n confidence: Confidence;\n /* The already-affected node this one depends on. /\n dependsOn: string;\n };\n}\n\nexport interface ImpactResult {\n target: NodeMatch;\n affected: AffectedNode[];\n /* How many affected nodes there are per confidence tier of the edge that pulled each one in. /\n byConfidence: Record<Confidence, number>;\n maxDepth: number;\n truncated: boolean;\n}\n\nexport interface ImpactOptions {\n /* How many reverse hops to follow (default 3). /\n maxDepth?: number;\n /* Hard cap on affected nodes reported (default 200). /\n limit?: number;\n /* Restrict the traversal to these relations (default: every dependency-carrying relation). /\n relations?: Relation[];\n}\n\nconst DEFAULT_IMPACT_DEPTH = 3;\nconst DEFAULT_IMPACT_LIMIT = 200;\n\nconst CONFIDENCE_RANK: Record<Confidence, number> = { EXTRACTED: 3, INFERRED: 2, AMBIGUOUS: 1 };\n\n/\n Resolve `nodeQuery` to its best-matching node, then reverse-BFS over\n * incoming dependency edges. Returns null when nothing in the graph matches\n * the query at all (same contract as explainNode()).\n /\nexport function affectedBy(graph: Graph, nodeQuery: string, options: ImpactOptions = {}): ImpactResult \| null {\n const target = resolveNode(graph, nodeQuery);\n if (!target) return null;\n\n const maxDepth = options.maxDepth ?? DEFAULT_IMPACT_DEPTH;\n const limit = options.limit ?? DEFAULT_IMPACT_LIMIT;\n const followed: ReadonlySet<Relation> = options.relations ? new Set(options.relations) : DEPENDENCY_RELATIONS;\n\n const affected: AffectedNode[] = [];\n const visited = new Set<string>([target.id]);\n let frontier: string[] = [target.id];\n let truncated = false;\n\n for (let depth = 1; depth <= maxDepth && frontier.length > 0 && !truncated; depth++) {\n // Collect every dependent of the current frontier before descending, so\n // each node's reported depth is its shortest* reverse distance.\n const nextFrontier = new Map<string, AffectedNode>();\n\n for (const current of [...frontier].sort((a, b) => a.localeCompare(b))) {\n graph.forEachInEdge(current, (_edge, edgeAttrs, source) => {\n if (visited.has(source)) return;\n const relation = edgeAttrs.relation as Relation;\n if (!followed.has(relation)) return;\n\n const confidence = edgeAttrs.confidence as Confidence;\n const existing = nextFrontier.get(source);\n // Same node reachable via several edges this round: keep the\n // strongest-confidence one, mirroring buildGraph()'s merge rule.\n if (existing && CONFIDENCE_RANK[existing.via.confidence] >= CONFIDENCE_RANK[confidence]) return;\n\n const attrs = graph.getNodeAttributes(source);\n nextFrontier.set(source, {\n id: source,\n label: (attrs.label as string \| undefined) ?? source,\n sourceFile: (attrs.sourceFile as string \| undefined) ?? '',\n sourceLocation: (attrs.sourceLocation as string \| undefined) ?? '',\n depth,\n via: { relation, confidence, dependsOn: current },\n });\n });\n }\n\n const roundNodes = [...nextFrontier.values()].sort((a, b) => a.id.localeCompare(b.id));\n for (const node of roundNodes) {\n if (affected.length >= limit) {\n truncated = true;\n break;\n }\n visited.add(node.id);\n affected.push(node);\n }\n frontier = roundNodes.filter((n) => visited.has(n.id)).map((n) => n.id);\n }\n\n const byConfidence: Record<Confidence, number> = { EXTRACTED: 0, INFERRED: 0, AMBIGUOUS: 0 };\n for (const node of affected) byConfidence[node.via.confidence] += 1;\n\n return { target, affected, byConfidence, maxDepth, truncated };\n}\n","import type Graph from 'graphology';\nimport { affectedBy } from './impact.js';\nimport { resolveNode } from './query.js';\nimport type { Relation } from './types.js';\n\n/*\n `graphify tests` — structural test selection. Coverage tools need\n * instrumentation and a full test run to know what covers what; the graph\n * already knows, statically: a test file imports/calls the code it\n * exercises, so the test files inside a change's reverse blast radius are\n * exactly the ones worth running. Cross-language, no instrumentation.\n /\n\n/* Test-file naming conventions across the supported languages. /\nconst TEST_FILE_PATTERNS: RegExp[] = [\n /(^\|\\/)tests?\\//, // tests/ or test/ directory\n /(^\|\\/)__tests__\\//,\n /(^\|\\/)spec\\//,\n /\\.test\\.[cm]?[jt]sx?$/,\n /\\.spec\\.[cm]?[jt]sx?$/,\n /(^\|\\/)test_[^/]+\\.py$/,\n /_test\\.py$/,\n /_test\\.go$/,\n /Tests?\\.(java\|cs)$/,\n /_spec\\.rb$/,\n /_test\\.rb$/,\n];\n\nexport function isTestFile(path: string): boolean {\n return TEST_FILE_PATTERNS.some((p) => p.test(path));\n}\n\nexport interface TestSelection {\n /* What the selection was computed for (resolved node id, or the changed files). /\n target: string;\n /* Unique test files, most directly affected first. /\n testFiles: Array<{ file: string; depth: number; via: string }>;\n /* How many non-test nodes were in the blast radius (context for confidence). /\n affectedNodeCount: number;\n /\n `usage` — selected by following actual use (calls/inheritance), tight;\n * `import-reachability` — the broad fallback: anything that can reach the\n * target through imports/re-exports, which over-includes files that share\n * a barrel entry with the target.\n /\n precision: 'usage' \| 'import-reachability';\n}\n\nconst TEST_REACH_DEPTH = 4;\nconst TEST_REACH_LIMIT = 2000;\n\n/* Relations that mean \"actually uses it\", as opposed to \"can merely reach it through an import\". /\nconst USAGE_RELATIONS: Relation[] = ['calls', 'inherits', 'implements', 'mixes_in', 'embeds', 'references'];\n\nfunction selectionFromImpact(\n graph: Graph,\n targetIds: string[],\n targetLabel: string,\n relations?: Relation[],\n): TestSelection {\n const best = new Map<string, { depth: number; via: string }>();\n let affectedNodeCount = 0;\n\n for (const id of targetIds) {\n const impact = affectedBy(graph, id, { maxDepth: TEST_REACH_DEPTH, limit: TEST_REACH_LIMIT, relations });\n if (!impact) continue;\n affectedNodeCount += impact.affected.length;\n for (const node of impact.affected) {\n if (!isTestFile(node.sourceFile)) continue;\n const existing = best.get(node.sourceFile);\n if (!existing \|\| node.depth < existing.depth) {\n best.set(node.sourceFile, { depth: node.depth, via: node.via.dependsOn });\n }\n }\n }\n\n const testFiles = [...best.entries()]\n .map(([file, info]) => ({ file, depth: info.depth, via: info.via }))\n .sort((a, b) => a.depth - b.depth \|\| a.file.localeCompare(b.file));\n\n return {\n target: targetLabel,\n testFiles,\n affectedNodeCount,\n precision: relations ? 'usage' : 'import-reachability',\n };\n}\n\n/* A file node's entities (so a usage-relation traversal has call targets to start from). /\nfunction entityRootsOf(graph: Graph, id: string): string[] {\n if (id.includes('::')) return [id];\n const roots: string[] = [];\n graph.forEachOutEdge(id, (_edge, attrs, _source, target) => {\n if (String(attrs.relation) === 'contains') roots.push(target);\n });\n roots.sort((a, b) => a.localeCompare(b));\n return roots.length > 0 ? roots : [id];\n}\n\n/\n Test files reachable (reverse) from the node best matching `nodeQuery`.\n * Tries a tight usage-relation pass first (tests that actually CALL the\n * target — precise even when many files share a barrel entry point); falls\n * back to full import-reachability when usage finds nothing. Null if\n * nothing matches the query.\n /\nexport function testsForNode(graph: Graph, nodeQuery: string): TestSelection \| null {\n const match = resolveNode(graph, nodeQuery);\n if (!match) return null;\n\n const precise = selectionFromImpact(graph, entityRootsOf(graph, match.id), match.id, USAGE_RELATIONS);\n if (precise.testFiles.length > 0) return precise;\n\n return selectionFromImpact(graph, [match.id], match.id);\n}\n\n/\n Test files reachable from any of the given changed files (as reported by\n * `git diff --name-only`). Changed test files select themselves. Unknown\n * files (not in the graph) are skipped.\n */\nexport function testsForChangedFiles(graph: Graph, changedFiles: string[]): TestSelection {\n const fileIds: string[] = [];\n const selfSelected = new Map<string, { depth: number; via: string }>();\n\n for (const file of changedFiles) {\n if (isTestFile(file)) {\n selfSelected.set(file, { depth: 0, via: '(changed directly)' });\n continue;\n }\n if (graph.hasNode(file)) fileIds.push(file);\n }\n\n const label = changedFiles.join(', ');\n const preciseRoots = fileIds.flatMap((f) => entityRootsOf(graph, f));\n let selection = selectionFromImpact(graph, preciseRoots, label, USAGE_RELATIONS);\n if (selection.testFiles.length === 0) {\n selection = selectionFromImpact(graph, fileIds, label);\n }\n for (const [file, info] of selfSelected) {\n if (!selection.testFiles.some((t) => t.file === file)) {\n selection.testFiles.push({ file, depth: info.depth, via: info.via });\n }\n }\n selection.testFiles.sort((a, b) => a.depth - b.depth \|\| 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1	+ {"version":3,"sources":["../../src/mcp/server.ts","../../src/query.ts","../../src/context.ts","../../src/graphStore.ts","../../src/store/localFile.ts","../../src/security.ts","../../src/store/serialize.ts","../../src/impact.ts","../../src/testmap.ts"],"sourcesContent":["/*\n MCP stdio server exposing query/path/explain as tools against an existing\n * graphify-out/graph.json. Stdio only — never opens a network listener.\n * All graph file paths go through security.validateGraphPath().\n \n This module is a pure library: importing it has no side effects (it does\n * not read argv or start a server on import). `startServer()` is called\n * explicitly by `bin/graphify-mcp.js` (the standalone `graphify-mcp` CLI\n * entry point) and by `graphify --mcp` (see src/cli/index.ts).\n /\nimport as fs from 'node:fs/promises';\nimport * as path from 'node:path';\nimport { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';\nimport { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';\nimport type { Transport } from '@modelcontextprotocol/sdk/shared/transport.js';\nimport { z } from 'zod';\nimport { buildContextPack, renderContextPack } from '../context.js';\nimport { loadGraph } from '../graphStore.js';\nimport { affectedBy } from '../impact.js';\nimport { explainNode, queryGraph, shortestPath } from '../query.js';\nimport { testsForNode } from '../testmap.js';\nimport { validateGraphPath } from '../security.js';\n\nfunction textResult(text: string): { content: Array<{ type: 'text'; text: string }> } {\n return { content: [{ type: 'text', text }] };\n}\n\n/*\n Build the McpServer instance (tools registered, nothing connected yet).\n * Split out from startServer() so tests can connect it to an in-memory\n * transport instead of real stdio (see tests/mcp/server.test.ts).\n /\nexport function createGraphifyMcpServer(outDir: string): McpServer {\n const server = new McpServer({ name: 'graphify', version: '0.1.0' });\n\n server.registerTool(\n 'query',\n {\n description:\n 'BFS (default) or DFS traversal of the graphify knowledge graph, seeded from nodes ' +\n 'whose label matches the question. Returns the matched seeds, the visited node ' +\n 'context, and the edges among them — broad context for answering a structural question.',\n inputSchema: {\n question: z.string().describe('Natural-language question or keywords to search the graph for.'),\n dfs: z.boolean().optional().describe('Use depth-first traversal instead of the default breadth-first.'),\n budget: z.number().int().positive().optional().describe('Hard cap on how many nodes to include.'),\n tokenBudget: z\n .number()\n .int()\n .positive()\n .optional()\n .describe('Approximate cap, in tokens, on the serialized size of the result (default 2000).'),\n },\n },\n async ({ question, dfs, budget, tokenBudget }) => {\n const graph = await loadGraph(outDir);\n const result = queryGraph(graph, question, { dfs, budget, tokenBudget });\n return textResult(JSON.stringify(result, null, 2));\n },\n );\n\n server.registerTool(\n 'path',\n {\n description: 'Shortest path between two named nodes in the graphify knowledge graph.',\n inputSchema: {\n from: z.string().describe('Name/label of the starting node.'),\n to: z.string().describe('Name/label of the destination node.'),\n },\n },\n async ({ from, to }) => {\n const graph = await loadGraph(outDir);\n const result = shortestPath(graph, from, to);\n if (!result) {\n return textResult(`Could not resolve \"${from}\" and/or \"${to}\" to a node in the graph.`);\n }\n return textResult(JSON.stringify(result, null, 2));\n },\n );\n\n server.registerTool(\n 'explain',\n {\n description:\n 'Plain-language-ready explanation of a single node: its source location, community, ' +\n 'and incoming/outgoing edges.',\n inputSchema: {\n node: z.string().describe('Name/label (or id) of the node to explain.'),\n },\n },\n async ({ node }) => {\n const graph = await loadGraph(outDir);\n const result = explainNode(graph, node);\n if (!result) {\n return textResult(`No node matched \"${node}\".`);\n }\n return textResult(JSON.stringify(result, null, 2));\n },\n );\n\n server.registerTool(\n 'affected',\n {\n description:\n 'Reverse impact analysis — \"what breaks if I change X\". Walks incoming dependency ' +\n 'edges (calls/imports/inherits/...) transitively and returns everything that depends ' +\n 'on the node, grouped by depth, with per-confidence blast-radius counts.',\n inputSchema: {\n node: z.string().describe('Name/label (or id) of the node being changed.'),\n depth: z.number().int().positive().optional().describe('How many reverse hops to follow (default 3).'),\n limit: z.number().int().positive().optional().describe('Cap on affected nodes reported (default 200).'),\n },\n },\n async ({ node, depth, limit }) => {\n const graph = await loadGraph(outDir);\n const result = affectedBy(graph, node, { maxDepth: depth, limit });\n if (!result) {\n return textResult(`No node matched \"${node}\".`);\n }\n return textResult(JSON.stringify(result, null, 2));\n },\n );\n\n server.registerTool(\n 'context',\n {\n description:\n 'Token-budgeted working-set pack: the actual code snippets relevant to a task, ' +\n 'graph-ranked and packed to a budget. Call this FIRST when starting a task — it ' +\n 'replaces query-then-read-whole-files.',\n inputSchema: {\n task: z.string().describe('What you are about to do, in natural language.'),\n budget: z.number().int().positive().optional().describe('Approximate token cap (default 4000).'),\n },\n },\n async ({ task, budget }) => {\n const graph = await loadGraph(outDir);\n const pack = await buildContextPack(graph, task, (p) => fs.readFile(p, 'utf-8'), {\n tokenBudget: budget,\n });\n return textResult(renderContextPack(pack));\n },\n );\n\n server.registerTool(\n 'tests',\n {\n description:\n 'Structural test selection: the minimal test files worth running to verify a change ' +\n 'to the given node, via reverse dependency reachability — no coverage instrumentation.',\n inputSchema: {\n node: z.string().describe('Name/label (or id) of the changed node.'),\n },\n },\n async ({ node }) => {\n const graph = await loadGraph(outDir);\n const result = testsForNode(graph, node);\n if (!result) {\n return textResult(`No node matched \"${node}\".`);\n }\n return textResult(JSON.stringify(result, null, 2));\n },\n );\n\n return server;\n}\n\n/\n Start the MCP server, serving `query`/`path`/`explain` tools against the\n * graph.json found in `graphPath`'s directory. `graphPath` is validated\n * (via security.validateGraphPath()) up front so a bad path fails\n * immediately with a clear error instead of the first time a client calls\n * a tool. `transport` defaults to real stdio; tests substitute an\n * in-memory transport.\n /\nexport async function startServer(graphPath: string, transport: Transport = new StdioServerTransport()): Promise<void> {\n const outDir = path.dirname(path.resolve(graphPath));\n const fileName = path.basename(graphPath);\n // Fail fast (and clearly) if the graph path escapes/doesn't exist, rather\n // than only surfacing that the first time a tool is called.\n validateGraphPath(fileName, outDir);\n\n const server = createGraphifyMcpServer(outDir);\n await server.connect(transport);\n}\n\n/* Entry point used by bin/graphify-mcp.js. /\nexport async function main(argv: string[] = process.argv): Promise<void> {\n const graphPath = argv[2] ?? path.join(process.cwd(), 'graphify-out', 'graph.json');\n await startServer(graphPath);\n}\n","import type Graph from 'graphology';\n\n/\n Library-level graph queries shared by the CLI (`graphify query/path/\n * explain`) and the MCP server tools of the same name. None of this is an\n * LLM call — it's lexical node matching + graph traversal, so it works\n * fully offline and deterministically.\n /\n\nconst STOPWORDS = new Set([\n 'a', 'an', 'the', 'is', 'are', 'was', 'were', 'do', 'does', 'did', 'how',\n 'what', 'where', 'when', 'why', 'who', 'which', 'to', 'of', 'in', 'on',\n 'for', 'and', 'or', 'this', 'that', 'it', 'does', 'that\\'s',\n]);\n\n/* Insert spaces at camelCase boundaries so identifier words become separate tokens. /\nfunction splitCamelCase(text: string): string {\n return text\n .replace(/([a-z0-9])([A-Z])/g, '$1 $2')\n .replace(/([A-Z]+)([A-Z][a-z])/g, '$1 $2');\n}\n\nfunction tokenize(text: string): string[] {\n return splitCamelCase(text)\n .toLowerCase()\n .split(/[^a-z0-9]+/)\n .filter((token) => token.length > 1 && !STOPWORDS.has(token));\n}\n\n/\n Split an identifier-ish string (node label/id) into its word subtokens:\n * camelCase, snake_case, kebab-case, dots, and path separators all become\n * boundaries, so `src/a/fileStorage.js::saveAttachment` yields\n * `src, file, storage, js, save, attachment`.\n /\nfunction subtokenize(text: string): string[] {\n return splitCamelCase(text)\n .toLowerCase()\n .split(/[^a-z0-9]+/)\n .filter((token) => token.length > 1);\n}\n\n/* Don't run the fuzzy tier on tokens this short — too many false positives. /\nconst FUZZY_MIN_TOKEN_LEN = 3;\n/* Minimum similarity for a fuzzy match to count at all. /\nconst FUZZY_THRESHOLD = 0.7;\nconst SUBTOKEN_MATCH_SCORE = 1;\nconst SUBSTRING_MATCH_SCORE = 0.6;\nconst FUZZY_MATCH_WEIGHT = 0.5;\n\n/\n Optimal-string-alignment Damerau-Levenshtein distance. Chosen over\n * bigram-set similarity because the common code-search typo is a\n * transposition (\"sorceNodes\"), which OSA counts as one edit but bigram\n * overlap punishes brutally.\n /\nfunction osaDistance(a: string, b: string): number {\n let prev2: number[] = [];\n let prev: number[] = Array.from({ length: b.length + 1 }, (_, j) => j);\n let curr: number[] = new Array<number>(b.length + 1).fill(0);\n\n for (let i = 1; i <= a.length; i++) {\n curr[0] = i;\n for (let j = 1; j <= b.length; j++) {\n const substitution = a[i - 1] === b[j - 1] ? 0 : 1;\n let best = Math.min(\n (prev[j] as number) + 1,\n (curr[j - 1] as number) + 1,\n (prev[j - 1] as number) + substitution,\n );\n if (i > 1 && j > 1 && a[i - 1] === b[j - 2] && a[i - 2] === b[j - 1]) {\n best = Math.min(best, (prev2[j - 2] as number) + 1);\n }\n curr[j] = best;\n }\n [prev2, prev, curr] = [prev, curr, new Array<number>(b.length + 1).fill(0)];\n }\n return prev[b.length] as number;\n}\n\n/* Normalized similarity in [0, 1]; short-circuits pairs whose length gap alone puts them under FUZZY_THRESHOLD. /\nfunction fuzzySimilarity(a: string, b: string): number {\n if (a === b) return 1;\n const maxLen = Math.max(a.length, b.length);\n if (maxLen === 0) return 1;\n if (Math.abs(a.length - b.length) / maxLen > 1 - FUZZY_THRESHOLD) return 0;\n return 1 - osaDistance(a, b) / maxLen;\n}\n\nexport interface NodeMatch {\n id: string;\n label: string;\n score: number;\n}\n\n/\n Score every node against the query's tokens. Identifier-aware and\n * typo-tolerant, in three tiers per token (best tier wins):\n \n 1. exact subtoken match (camelCase/snake_case-split word of the label\n * or id) — \"storage\" matches `fileStorage.js`;\n * 2. plain substring of the label/id (the original v1 behavior);\n * 3. fuzzy (Damerau-Levenshtein) match against a subtoken — \"sorce\"\n * still finds `scoreNodes`.\n \n Still fully lexical and deterministic — no LLM, no randomness.\n /\nexport function scoreNodes(graph: Graph, query: string): NodeMatch[] {\n const tokens = tokenize(query);\n const matches: NodeMatch[] = [];\n\n graph.forEachNode((id, attributes) => {\n const label = (attributes.label as string \| undefined) ?? id;\n const haystack = `${label} ${id}`.toLowerCase();\n const subtokens = new Set(subtokenize(`${label} ${id}`));\n let score = 0;\n for (const token of tokens) {\n if (subtokens.has(token)) {\n score += SUBTOKEN_MATCH_SCORE;\n continue;\n }\n if (haystack.includes(token)) {\n score += SUBSTRING_MATCH_SCORE;\n continue;\n }\n if (token.length >= FUZZY_MIN_TOKEN_LEN) {\n let best = 0;\n for (const subtoken of subtokens) {\n const similarity = fuzzySimilarity(token, subtoken);\n if (similarity > best) best = similarity;\n }\n if (best >= FUZZY_THRESHOLD) score += best FUZZY_MATCH_WEIGHT;\n }\n }\n if (score > 0) matches.push({ id, label, score });\n });\n\n // On equal score, real source nodes beat module:/external: placeholders —\n // \"devtools\" should resolve to the devtools middleware, not the\n // @redux-devtools package node that happens to share a subtoken.\n const placeholderRank = (id: string): number =>\n id.startsWith('module:') \|\| id.startsWith('external:') ? 1 : 0;\n matches.sort(\n (a, b) =>\n b.score - a.score \|\| placeholderRank(a.id) - placeholderRank(b.id) \|\| a.id.localeCompare(b.id),\n );\n return matches;\n}\n\n/*\n Best-effort single-node resolution: the highest-scoring lexical match,\n * or null if nothing in the graph matches at all. Deliberately does not\n * fall back to \"the most connected node\" — path/explain name a specific\n * node by intent, and silently substituting an unrelated one would be\n * more misleading than clearly saying \"no match\".\n /\nexport function resolveNode(graph: Graph, query: string): NodeMatch \| null {\n const matches = scoreNodes(graph, query);\n return matches[0] ?? null;\n}\n\nexport interface VisitedNode {\n id: string;\n label: string;\n sourceFile: string;\n sourceLocation: string;\n depth: number;\n}\n\nexport interface TraversalEdge {\n source: string;\n target: string;\n relation: string;\n confidence: string;\n}\n\nexport interface QueryResult {\n seeds: NodeMatch[];\n visited: VisitedNode[];\n edges: TraversalEdge[];\n}\n\nexport interface QueryOptions {\n dfs?: boolean;\n /* Hard cap on how many nodes to include. Defaults to a generous ceiling derived from `tokenBudget`. /\n budget?: number;\n /* Approximate cap, in tokens (~4 chars each), on the serialized size of the result. Default 2000. /\n tokenBudget?: number;\n maxDepth?: number;\n maxSeeds?: number;\n}\n\nconst DEFAULT_MAX_DEPTH = 2;\nconst DEFAULT_MAX_SEEDS = 5;\nconst DEFAULT_BUDGET = 40;\nconst DEFAULT_TOKEN_BUDGET = 2000;\n/* When only tokenBudget is given, allow up to this many nodes per budgeted token-decile as a safety ceiling. /\nconst NODES_PER_TOKEN = 1 / 10;\n\n/\n Estimated token contribution of one node to the rendered result: its own\n * line (label, file, location) plus a rough allowance for the edge lines\n * that mention its id. Chars/4 is the usual serviceable approximation.\n /\nexport function nodeTokenCost(graph: Graph, id: string): number {\n const attrs = graph.getNodeAttributes(id);\n const label = (attrs.label as string \| undefined) ?? id;\n const sourceFile = (attrs.sourceFile as string \| undefined) ?? '';\n return Math.ceil((id.length 2 + label.length + sourceFile.length + 24) / 4);\n}\n\n/*\n BFS (default, broad context) or DFS (--dfs, trace a specific path)\n * traversal from the nodes whose label best matches `question`'s\n * keywords. This is lexical retrieval, not natural-language\n * understanding — it surfaces the neighborhood of the graph an agent (or\n * a human) should look at to answer the question, it does not itself\n * compose an answer.\n /\nexport function queryGraph(graph: Graph, question: string, options: QueryOptions = {}): QueryResult {\n const maxDepth = options.maxDepth ?? DEFAULT_MAX_DEPTH;\n const maxSeeds = options.maxSeeds ?? DEFAULT_MAX_SEEDS;\n const tokenBudget = options.tokenBudget ?? DEFAULT_TOKEN_BUDGET;\n const budget = options.budget ?? Math.max(DEFAULT_BUDGET, Math.ceil(tokenBudget NODES_PER_TOKEN));\n\n const allMatches = scoreNodes(graph, question);\n const seeds = allMatches.length > 0 ? allMatches.slice(0, maxSeeds) : [];\n\n const visited = new Map<string, number>(); // id -> depth\n const frontier: Array<{ id: string; depth: number }> = seeds.map((s) => ({ id: s.id, depth: 0 }));\n let spentTokens = 0;\n for (const seed of seeds) {\n visited.set(seed.id, 0);\n spentTokens += nodeTokenCost(graph, seed.id);\n }\n\n while (frontier.length > 0 && visited.size < budget && spentTokens < tokenBudget) {\n const current = options.dfs ? (frontier.pop() as { id: string; depth: number }) : (frontier.shift() as { id: string; depth: number });\n if (current.depth >= maxDepth) continue;\n\n const neighbors = [...graph.neighbors(current.id)].sort((a, b) => a.localeCompare(b));\n for (const neighbor of neighbors) {\n if (visited.has(neighbor) \|\| visited.size >= budget \|\| spentTokens >= tokenBudget) continue;\n visited.set(neighbor, current.depth + 1);\n spentTokens += nodeTokenCost(graph, neighbor);\n frontier.push({ id: neighbor, depth: current.depth + 1 });\n }\n }\n\n const visitedNodes: VisitedNode[] = [...visited.entries()]\n .map(([id, depth]) => {\n const attrs = graph.getNodeAttributes(id);\n return {\n id,\n label: (attrs.label as string \| undefined) ?? id,\n sourceFile: (attrs.sourceFile as string \| undefined) ?? '',\n sourceLocation: (attrs.sourceLocation as string \| undefined) ?? '',\n depth,\n };\n })\n .sort((a, b) => a.depth - b.depth \|\| a.id.localeCompare(b.id));\n\n const edges: TraversalEdge[] = [];\n graph.forEachEdge((_edge, attrs, source, target) => {\n if (visited.has(source) && visited.has(target)) {\n edges.push({\n source,\n target,\n relation: String(attrs.relation),\n confidence: String(attrs.confidence),\n });\n }\n });\n edges.sort(\n (a, b) => a.source.localeCompare(b.source) \|\| a.target.localeCompare(b.target) \|\| a.relation.localeCompare(b.relation),\n );\n\n return enforceTokenBudget({ seeds, visited: visitedNodes, edges }, tokenBudget);\n}\n\n/*\n The traversal-time cost estimate can't see how densely connected the\n * visited neighborhood is — a hub-heavy subgraph induces far more edge\n * lines than nodes. Enforce the budget on the actual result: drop the\n * deepest/last nodes (and the edges that touched them) until the\n * serialized size fits. Seeds are never dropped.\n /\nfunction enforceTokenBudget(result: QueryResult, tokenBudget: number): QueryResult {\n const cost = (value: unknown): number => Math.ceil(JSON.stringify(value).length / 4);\n\n const visited = [...result.visited];\n let edges = [...result.edges];\n let total = cost(result.seeds) + visited.reduce((s, n) => s + cost(n), 0) + edges.reduce((s, e) => s + cost(e), 0);\n\n const seedIds = new Set(result.seeds.map((s) => s.id));\n // visited is sorted by (depth, id) — pop from the end so the deepest,\n // least-central context goes first and the result stays deterministic.\n while (total > tokenBudget && visited.length > 0) {\n const last = visited[visited.length - 1] as VisitedNode;\n if (seedIds.has(last.id)) break;\n visited.pop();\n total -= cost(last);\n const remaining: TraversalEdge[] = [];\n for (const edge of edges) {\n if (edge.source === last.id \|\| edge.target === last.id) {\n total -= cost(edge);\n } else {\n remaining.push(edge);\n }\n }\n edges = remaining;\n }\n\n return { seeds: result.seeds, visited, edges };\n}\n\nexport interface PathResult {\n from: NodeMatch;\n to: NodeMatch;\n found: boolean;\n path: string[];\n edges: TraversalEdge[];\n}\n\n/* Shortest path between the nodes that best match `fromQuery` and `toQuery` (undirected BFS — connectivity, not call direction). /\nexport function shortestPath(graph: Graph, fromQuery: string, toQuery: string): PathResult \| null {\n const from = resolveNode(graph, fromQuery);\n const to = resolveNode(graph, toQuery);\n if (!from \|\| !to) return null;\n\n if (from.id === to.id) {\n return { from, to, found: true, path: [from.id], edges: [] };\n }\n\n const predecessor = new Map<string, string>();\n const visited = new Set<string>([from.id]);\n const queue: string[] = [from.id];\n\n while (queue.length > 0) {\n const current = queue.shift() as string;\n if (current === to.id) break;\n const neighbors = [...graph.neighbors(current)].sort((a, b) => a.localeCompare(b));\n for (const neighbor of neighbors) {\n if (visited.has(neighbor)) continue;\n visited.add(neighbor);\n predecessor.set(neighbor, current);\n queue.push(neighbor);\n }\n }\n\n if (!visited.has(to.id)) {\n return { from, to, found: false, path: [], edges: [] };\n }\n\n const path: string[] = [to.id];\n let cursor = to.id;\n while (cursor !== from.id) {\n const prev = predecessor.get(cursor);\n if (!prev) break;\n path.unshift(prev);\n cursor = prev;\n }\n\n const edges: TraversalEdge[] = [];\n for (let i = 0; i < path.length - 1; i++) {\n const a = path[i] as string;\n const b = path[i + 1] as string;\n const key = graph.edges(a, b)[0] ?? graph.edges(b, a)[0];\n if (key) {\n const attrs = graph.getEdgeAttributes(key);\n edges.push({ source: a, target: b, relation: String(attrs.relation), confidence: String(attrs.confidence) });\n }\n }\n\n return { from, to, found: true, path, edges };\n}\n\nexport interface ExplainResult {\n id: string;\n label: string;\n sourceFile: string;\n sourceLocation: string;\n communityLabel?: string;\n outgoing: TraversalEdge[];\n incoming: TraversalEdge[];\n}\n\n/* Plain-language-ready explanation of the node that best matches `query`. /\nexport function explainNode(graph: Graph, query: string): ExplainResult \| null {\n const match = resolveNode(graph, query);\n if (!match) return null;\n\n const attrs = graph.getNodeAttributes(match.id);\n const outgoing: TraversalEdge[] = [];\n const incoming: TraversalEdge[] = [];\n\n graph.forEachOutEdge(match.id, (_edge, edgeAttrs, source, target) => {\n outgoing.push({ source, target, relation: String(edgeAttrs.relation), confidence: String(edgeAttrs.confidence) });\n });\n graph.forEachInEdge(match.id, (_edge, edgeAttrs, source, target) => {\n incoming.push({ source, target, relation: String(edgeAttrs.relation), confidence: String(edgeAttrs.confidence) });\n });\n\n outgoing.sort((a, b) => a.target.localeCompare(b.target) \|\| a.relation.localeCompare(b.relation));\n incoming.sort((a, b) => a.source.localeCompare(b.source) \|\| a.relation.localeCompare(b.relation));\n\n return {\n id: match.id,\n label: match.label,\n sourceFile: (attrs.sourceFile as string \| undefined) ?? '',\n sourceLocation: (attrs.sourceLocation as string \| undefined) ?? '',\n communityLabel: attrs.communityLabel as string \| undefined,\n outgoing,\n incoming,\n };\n}\n","import type Graph from 'graphology';\nimport { scoreNodes } from './query.js';\n\n/\n `graphify context` — the working-set pack. Instead of returning node\n * names for the agent to chase (query -> then read whole files anyway),\n * this fuses the two steps: the graph knows every entity's file and line,\n * so rank the nodes relevant to the task, read just the relevant line\n * ranges, and pack the actual code into a token budget. One call returns\n * the code an agent needs to start a task.\n /\n\nexport interface ContextSnippet {\n nodeId: string;\n label: string;\n file: string;\n startLine: number;\n endLine: number;\n code: string;\n /* Why this snippet is in the pack (lexical match / neighbor-of relation). /\n reason: string;\n score: number;\n}\n\nexport interface ContextPack {\n task: string;\n snippets: ContextSnippet[];\n /* Approximate tokens used out of the budget. /\n tokens: number;\n tokenBudget: number;\n /* Ranked nodes that didn't fit the budget — the agent can pull them explicitly. /\n overflow: Array<{ nodeId: string; file: string }>;\n}\n\nexport interface ContextOptions {\n /* Approximate token cap for the pack (default 4000). /\n tokenBudget?: number;\n maxSeeds?: number;\n /* Cap on snippet length in lines (default 60). /\n maxSnippetLines?: number;\n}\n\nexport type FileReader = (path: string) => Promise<string>;\n\nconst DEFAULT_CONTEXT_BUDGET = 4000;\nconst DEFAULT_MAX_SEEDS = 8;\nconst DEFAULT_MAX_SNIPPET_LINES = 60;\n/* A neighbor inherits this fraction of the score of the node that pulled it in. /\nconst NEIGHBOR_DECAY = 0.4;\n\nconst tokensOf = (text: string): number => Math.ceil(text.length / 4);\n\nfunction lineNumberOf(sourceLocation: string): number \| null {\n const match = /^L(\\d+)$/.exec(sourceLocation);\n return match ? Number(match[1]) : null;\n}\n\nfunction isReadableFile(sourceFile: string): boolean {\n return sourceFile !== '' && !sourceFile.startsWith('<') && !sourceFile.includes('://');\n}\n\ninterface RankedNode {\n id: string;\n score: number;\n reason: string;\n}\n\n/\n Rank nodes for the task: lexical seeds first (their match score), then\n * their graph neighbors at a decayed score, labeled with the relation that\n * connects them. Deterministic (score desc, id asc).\n /\nexport function rankForTask(graph: Graph, task: string, maxSeeds = DEFAULT_MAX_SEEDS): RankedNode[] {\n const seeds = scoreNodes(graph, task).slice(0, maxSeeds);\n const ranked = new Map<string, RankedNode>();\n for (const seed of seeds) {\n ranked.set(seed.id, { id: seed.id, score: seed.score, reason: 'matches the task' });\n }\n\n for (const seed of seeds) {\n graph.forEachEdge(seed.id, (_edge, attrs, source, target) => {\n const neighbor = source === seed.id ? target : source;\n if (ranked.has(neighbor)) return;\n const relation = String(attrs.relation);\n const direction = source === seed.id ? `${relation} ->` : `<- ${relation}`;\n ranked.set(neighbor, {\n id: neighbor,\n score: seed.score NEIGHBOR_DECAY,\n reason: `${direction} ${seed.label}`,\n });\n });\n }\n\n return [...ranked.values()].sort((a, b) => b.score - a.score \|\| a.id.localeCompare(b.id));\n}\n\n/*\n Extract the snippet for a node: from its declaration line to just before\n * the next known entity in the same file (capped), so snippets align with\n * real code block boundaries without needing a parser here.\n /\nfunction snippetRange(\n startLine: number,\n fileLineCount: number,\n entityStartsInFile: number[],\n maxLines: number,\n): { start: number; end: number } {\n const nextStart = entityStartsInFile.find((l) => l > startLine);\n const hardEnd = nextStart !== undefined ? nextStart - 1 : fileLineCount;\n return { start: startLine, end: Math.min(hardEnd, startLine + maxLines - 1) };\n}\n\nexport async function buildContextPack(\n graph: Graph,\n task: string,\n readFile: FileReader,\n options: ContextOptions = {},\n): Promise<ContextPack> {\n const tokenBudget = options.tokenBudget ?? DEFAULT_CONTEXT_BUDGET;\n const maxSnippetLines = options.maxSnippetLines ?? DEFAULT_MAX_SNIPPET_LINES;\n const ranked = rankForTask(graph, task, options.maxSeeds);\n\n // Every known entity start line per file — used to end snippets at the\n // next declaration instead of an arbitrary window.\n const entityStarts = new Map<string, number[]>();\n graph.forEachNode((_id, attrs) => {\n const file = attrs.sourceFile as string \| undefined;\n const line = lineNumberOf((attrs.sourceLocation as string \| undefined) ?? '');\n if (file && line !== null) {\n const starts = entityStarts.get(file) ?? [];\n starts.push(line);\n entityStarts.set(file, starts);\n }\n });\n for (const starts of entityStarts.values()) starts.sort((a, b) => a - b);\n\n const fileCache = new Map<string, string[] \| null>();\n const readLines = async (file: string): Promise<string[] \| null> => {\n const cached = fileCache.get(file);\n if (cached !== undefined) return cached;\n let lines: string[] \| null;\n try {\n lines = (await readFile(file)).split('\\n');\n } catch {\n lines = null;\n }\n fileCache.set(file, lines);\n return lines;\n };\n\n const snippets: ContextSnippet[] = [];\n const overflow: Array<{ nodeId: string; file: string }> = [];\n const coveredRanges = new Map<string, Array<{ start: number; end: number }>>();\n let tokens = 0;\n\n for (const node of ranked) {\n const attrs = graph.getNodeAttributes(node.id);\n const file = (attrs.sourceFile as string \| undefined) ?? '';\n const startLine = lineNumberOf((attrs.sourceLocation as string \| undefined) ?? '');\n if (!isReadableFile(file) \|\| startLine === null) continue;\n\n const lines = await readLines(file);\n if (lines === null) continue;\n\n const { start, end } = snippetRange(startLine, lines.length, entityStarts.get(file) ?? [], maxSnippetLines);\n\n // Skip if an already-packed snippet from the same file covers this range.\n const covered = (coveredRanges.get(file) ?? []).some((r) => start >= r.start && end <= r.end);\n if (covered) continue;\n\n const code = lines.slice(start - 1, end).join('\\n');\n const cost = tokensOf(code) + 15; // header overhead\n if (tokens + cost > tokenBudget) {\n overflow.push({ nodeId: node.id, file: `${file}:L${startLine}` });\n continue;\n }\n\n tokens += cost;\n snippets.push({\n nodeId: node.id,\n label: (attrs.label as string \| undefined) ?? node.id,\n file,\n startLine: start,\n endLine: end,\n code,\n reason: node.reason,\n score: node.score,\n });\n const ranges = coveredRanges.get(file) ?? [];\n ranges.push({ start, end });\n coveredRanges.set(file, ranges);\n }\n\n return { task, snippets, tokens, tokenBudget, overflow };\n}\n\n/* Render a pack as agent-ready markdown. /\nexport function renderContextPack(pack: ContextPack): string {\n const lines: string[] = [\n `# Context pack: ${pack.task}`,\n '',\n `_~${pack.tokens} of ${pack.tokenBudget} token budget, ${pack.snippets.length} snippet(s)._`,\n '',\n ];\n\n if (pack.snippets.length === 0) {\n lines.push('No matching code found — try different keywords.');\n return lines.join('\\n');\n }\n\n for (const snippet of pack.snippets) {\n lines.push(`## ${snippet.label} — \\`${snippet.file}:L${snippet.startLine}-L${snippet.endLine}\\``);\n lines.push(`_${snippet.reason}_`);\n lines.push('```');\n lines.push(snippet.code);\n lines.push('```');\n lines.push('');\n }\n\n if (pack.overflow.length > 0) {\n lines.push(`## Didn't fit the budget (${pack.overflow.length})`);\n for (const item of pack.overflow.slice(0, 15)) {\n lines.push(`- ${item.nodeId} (${item.file})`);\n }\n lines.push('');\n }\n\n return lines.join('\\n');\n}\n","import as path from 'node:path';\nimport type Graph from 'graphology';\nimport { LocalFileGraphStore } from './store/localFile.js';\n\n/*\n Load a previously-exported graph.json back into a graphology Graph.\n * Thin wrapper over LocalFileGraphStore (which enforces the path-traversal\n * guard — see SECURITY.md) that throws when no graph exists, because every\n * CLI/MCP caller treats \"no graph yet\" as a hard error. Library callers who\n * want the null-on-missing contract should use a GraphStore directly.\n /\nexport async function loadGraph(outDir: string = path.join(process.cwd(), 'graphify-out')): Promise<Graph> {\n const graph = await new LocalFileGraphStore().load(outDir);\n if (graph === null) {\n throw new Error(`No graph found in ${outDir} — run \\`graphify <path>\\` to build one first.`);\n }\n return graph;\n}\n","import as fs from 'node:fs/promises';\nimport type Graph from 'graphology';\nimport { validateGraphPath } from '../security.js';\nimport { deserializeGraph, serializeGraph } from './serialize.js';\nimport type { GraphStore, SerializedGraph } from './types.js';\n\n/*\n The reference GraphStore: one graph.json per directory, `ref` = the\n * outDir path. Reproduces the classic graphify-out/ behavior byte-for-byte\n * (same pretty-printed JSON exportGraph() writes) and routes every path\n * through security.validateGraphPath(), so a caller-supplied ref — or a\n * symlinked graph.json — can never read or write outside the directory it\n * resolves to.\n /\nexport class LocalFileGraphStore implements GraphStore {\n async load(ref: string): Promise<Graph \| null> {\n let jsonPath: string;\n try {\n jsonPath = validateGraphPath('graph.json', ref);\n } catch (error) {\n // A ref whose directory doesn't exist simply has no graph yet;\n // traversal/symlink-escape rejections must still propagate.\n if ((error as Error).message.startsWith('Base directory does not exist')) return null;\n throw error;\n }\n\n let raw: string;\n try {\n raw = await fs.readFile(jsonPath, 'utf-8');\n } catch (error) {\n if ((error as NodeJS.ErrnoException).code === 'ENOENT') return null;\n throw error;\n }\n return deserializeGraph(JSON.parse(raw) as SerializedGraph);\n }\n\n async save(ref: string, graph: Graph): Promise<void> {\n await fs.mkdir(ref, { recursive: true });\n const jsonPath = validateGraphPath('graph.json', ref);\n await fs.writeFile(jsonPath, JSON.stringify(serializeGraph(graph), null, 2), 'utf-8');\n }\n}\n","/\n Security helpers — URL validation, SSRF-guarded fetch, path guards, label\n * sanitization, prompt-injection defenses. Every control listed in\n * SECURITY.md must have a corresponding function here and a unit test in\n * tests/security.test.ts. See the master prompt §5 for the full checklist.\n /\n\nimport { createHash } from 'node:crypto';\nimport as dns from 'node:dns';\nimport * as http from 'node:http';\nimport * as https from 'node:https';\nimport * as fs from 'node:fs';\nimport * as net from 'node:net';\nimport * as nodePath from 'node:path';\n\nconst ALLOWED_SCHEMES = new Set(['http:', 'https:']);\nconst MAX_FETCH_BYTES = 50 * 1024 * 1024;\nconst MAX_TEXT_BYTES = 10 * 1024 * 1024;\nconst MAX_LABEL_LEN = 256;\nconst MAX_REDIRECTS = 5;\nconst REQUEST_TIMEOUT_MS = 15_000;\n\n/** Hostnames that must never be reachable, regardless of what they resolve to. /\nconst BLOCKED_HOSTNAMES = new Set([\n 'metadata.google.internal',\n 'metadata.internal',\n 'metadata',\n 'metadata.azure.com',\n 'instance-data',\n 'instance-data.ec2.internal',\n]);\n\n// ---------------------------------------------------------------------------\n// IP range checks (SSRF guard core). Implemented without extra dependencies.\n// ---------------------------------------------------------------------------\n\nfunction ipv4ToInt(ip: string): number \| null {\n const parts = ip.split('.');\n if (parts.length !== 4) return null;\n let result = 0;\n for (const part of parts) {\n if (!/^\\d{1,3}$/.test(part)) return null;\n const n = Number(part);\n if (n > 255) return null;\n result = (result << 8) \| n;\n }\n return result >>> 0;\n}\n\nfunction ipv4InCidr(ipInt: number, cidr: string): boolean {\n const [base, prefixStr] = cidr.split('/');\n const prefix = Number(prefixStr);\n const baseInt = ipv4ToInt(base ?? '');\n if (baseInt === null) return false;\n const mask = prefix === 0 ? 0 : (~0 << (32 - prefix)) >>> 0;\n return (ipInt & mask) >>> 0 === (baseInt & mask) >>> 0;\n}\n\n/* IPv4 ranges that must never be connected to from a server-side fetch. /\nconst BLOCKED_IPV4_CIDRS = [\n '0.0.0.0/8', // \"this\" network\n '10.0.0.0/8', // private\n '100.64.0.0/10', // carrier-grade NAT (CGN)\n '127.0.0.0/8', // loopback\n '169.254.0.0/16', // link-local (covers 169.254.169.254 cloud metadata)\n '172.16.0.0/12', // private\n '192.0.0.0/24', // IETF protocol assignments\n '192.0.2.0/24', // TEST-NET-1\n '192.168.0.0/16', // private\n '198.18.0.0/15', // benchmarking\n '198.51.100.0/24', // TEST-NET-2\n '203.0.113.0/24', // TEST-NET-3\n '224.0.0.0/4', // multicast\n '240.0.0.0/4', // reserved\n '255.255.255.255/32', // broadcast\n];\n\nexport function isForbiddenIpv4(ip: string): boolean {\n const ipInt = ipv4ToInt(ip);\n if (ipInt === null) return true; // malformed -> treat as forbidden, fail closed\n return BLOCKED_IPV4_CIDRS.some((cidr) => ipv4InCidr(ipInt, cidr));\n}\n\n/* Expand a (possibly `::`-compressed) IPv6 address into 8 16-bit groups. /\nfunction expandIpv6(ip: string): number[] \| null {\n const withoutZone = ip.split('%')[0] ?? '';\n const parts = withoutZone.split('::');\n if (parts.length > 2) return null;\n\n const head = parts[0] ? parts[0].split(':').filter((s) => s.length > 0) : [];\n const tail = parts.length === 2 && parts[1] ? parts[1].split(':').filter((s) => s.length > 0) : [];\n\n let missing = 0;\n if (parts.length === 2) {\n missing = 8 - head.length - tail.length;\n if (missing < 0) return null;\n } else if (head.length + tail.length !== 8) {\n return null;\n }\n\n const groupsHex = [...head, ...Array(missing).fill('0'), ...tail];\n if (groupsHex.length !== 8) return null;\n\n const groups: number[] = [];\n for (const g of groupsHex) {\n if (!/^[0-9a-fA-F]{1,4}$/.test(g)) return null;\n groups.push(parseInt(g, 16));\n }\n return groups;\n}\n\nexport function isForbiddenIpv6(ip: string): boolean {\n const lower = ip.toLowerCase();\n if (lower === '::1' \|\| lower === '::') return true;\n\n const mapped = /^::ffff:(\\d+\\.\\d+\\.\\d+\\.\\d+)$/.exec(lower);\n if (mapped) return isForbiddenIpv4(mapped[1] as string);\n\n const groups = expandIpv6(lower);\n if (groups === null) return true; // unparsable -> fail closed\n const first = groups[0] as number;\n if ((first & 0xffc0) === 0xfe80) return true; // fe80::/10 link-local\n if ((first & 0xfe00) === 0xfc00) return true; // fc00::/7 unique local\n if ((first & 0xff00) === 0xff00) return true; // ff00::/8 multicast\n if (groups.every((g) => g === 0)) return true; // unspecified/all-zero\n return false;\n}\n\nexport function isForbiddenIp(ip: string): boolean {\n return net.isIPv6(ip) ? isForbiddenIpv6(ip) : isForbiddenIpv4(ip);\n}\n\n// ---------------------------------------------------------------------------\n// URL validation\n// ---------------------------------------------------------------------------\n\n/\n Validate a URL is http/https and, when the hostname is itself a literal\n * IP or a known cloud-metadata hostname, reject it synchronously. DNS-bound\n * hostnames are re-validated at connect time by safeFetch() (see below) —\n * this function alone cannot rule out DNS rebinding for a hostname that\n * currently resolves to a public IP.\n /\nexport function validateUrl(url: string): string {\n let parsed: URL;\n try {\n parsed = new URL(url);\n } catch {\n throw new Error(`Invalid URL: ${url}`);\n }\n\n if (!ALLOWED_SCHEMES.has(parsed.protocol)) {\n throw new Error(\n `URL scheme not allowed: \"${parsed.protocol}\" (allowed: ${[...ALLOWED_SCHEMES].join(', ')})`,\n );\n }\n\n const hostname = parsed.hostname.toLowerCase();\n if (BLOCKED_HOSTNAMES.has(hostname)) {\n throw new Error(`URL targets a blocked host: ${hostname}`);\n }\n\n // WHATWG URL keeps the brackets on an IPv6 literal host (e.g. \"[::1]\") —\n // strip them before checking net.isIP()/isForbiddenIp().\n const bareHost =\n hostname.startsWith('[') && hostname.endsWith(']') ? hostname.slice(1, -1) : hostname;\n if (net.isIP(bareHost) && isForbiddenIp(bareHost)) {\n throw new Error(`URL targets a forbidden IP address: ${bareHost}`);\n }\n\n return parsed.toString();\n}\n\n// ---------------------------------------------------------------------------\n// safeFetch — SSRF-guarded, size-capped, redirect-revalidating fetch\n// ---------------------------------------------------------------------------\n\nexport type LookupFn = (hostname: string) => Promise<{ address: string; family: number }>;\n\n/\n Resolve a hostname (or pass through a literal IP) and validate the\n * result. `lookup` defaults to the real `dns.promises.lookup` — tests\n * substitute a fake to exercise the rebind guard deterministically without\n * making a real DNS query.\n /\nexport async function resolveAndValidate(\n hostname: string,\n lookup: LookupFn = dns.promises.lookup,\n): Promise<{ address: string; family: number }> {\n if (net.isIP(hostname)) {\n if (isForbiddenIp(hostname)) {\n throw new Error(`Refusing to connect to forbidden IP: ${hostname}`);\n }\n return { address: hostname, family: net.isIPv6(hostname) ? 6 : 4 };\n }\n const result = await lookup(hostname);\n if (isForbiddenIp(result.address)) {\n throw new Error(`Refusing to connect to forbidden IP: ${hostname} -> ${result.address}`);\n }\n return result;\n}\n\nexport interface RawResponse {\n statusCode: number;\n headers: http.IncomingHttpHeaders;\n body: Buffer;\n}\n\n/* Minimal shape of the `http`/`https` modules that requestOnce() needs — narrow on purpose so tests can substitute a fake transport instead of mocking network I/O. /\nexport type RequestTransport = Pick<typeof http, 'request'>;\n\n/\n Issue a single HTTP(S) request, connecting to `resolvedAddress` directly\n * (via a `lookup` override) rather than re-resolving DNS at connect time —\n * this is what prevents a DNS-rebind attacker from swapping the target\n * between validation and connection (TOCTOU). Streams the body and aborts\n * once it exceeds the byte cap for its declared content type.\n /\nexport function requestOnce(\n target: URL,\n resolvedAddress: string,\n resolvedFamily: number,\n transport: RequestTransport = target.protocol === 'https:' ? https : http,\n): Promise<RawResponse> {\n return new Promise((resolve, reject) => {\n const req = transport.request(\n {\n protocol: target.protocol,\n hostname: target.hostname,\n host: target.hostname,\n port: target.port \|\| (target.protocol === 'https:' ? 443 : 80),\n path: `${target.pathname}${target.search}`,\n method: 'GET',\n timeout: REQUEST_TIMEOUT_MS,\n headers: { 'user-agent': 'graphify/0.1', accept: '/' },\n // Force the connection to the address we already validated — do not\n // let Node re-resolve `target.hostname` at connect time.\n lookup: (\n _hostname: string,\n options: unknown,\n callback: (err: NodeJS.ErrnoException \| null, address: string, family: number) => void,\n ) => {\n callback(null, resolvedAddress, resolvedFamily);\n },\n } as http.RequestOptions,\n (res) => {\n const statusCode = res.statusCode ?? 0;\n const contentType = String(res.headers['content-type'] ?? '');\n const isTextual = /^text\\/\|json\|xml\|html\|charset=/i.test(contentType);\n const cap = isTextual ? MAX_TEXT_BYTES : MAX_FETCH_BYTES;\n\n const chunks: Buffer[] = [];\n let total = 0;\n let aborted = false;\n\n res.on('data', (chunk: Buffer) => {\n total += chunk.length;\n if (total > cap) {\n aborted = true;\n res.destroy();\n req.destroy();\n reject(new Error(`Response exceeded ${cap} byte cap (content-type: ${contentType})`));\n return;\n }\n chunks.push(chunk);\n });\n res.on('end', () => {\n if (aborted) return;\n resolve({ statusCode, headers: res.headers, body: Buffer.concat(chunks) });\n });\n res.on('error', (err) => {\n if (!aborted) reject(err);\n });\n },\n );\n\n req.on('timeout', () => {\n req.destroy(new Error(`Request timed out after ${REQUEST_TIMEOUT_MS}ms`));\n });\n req.on('error', reject);\n req.end();\n });\n}\n\nexport interface SafeFetchDeps {\n /* Override DNS resolution + IP validation (default: resolveAndValidate). /\n resolve?: (hostname: string) => Promise<{ address: string; family: number }>;\n /* Override the actual request (default: requestOnce against real http/https). /\n request?: (target: URL, address: string, family: number) => Promise<RawResponse>;\n}\n\n/\n Fetch a URL with the SSRF guards from validateUrl() plus streaming size\n * caps (MAX_FETCH_BYTES / MAX_TEXT_BYTES) and a hard error on non-2xx\n * status. Every redirect hop is independently validated and re-resolved —\n * a redirect to a private/loopback/metadata address is rejected exactly\n * like a direct request would be.\n \n `deps` exists so tests can substitute the DNS/network collaborators with\n * deterministic fakes (see tests/security.test.ts) instead of mocking\n * Node's core modules or hitting real sockets — production callers should\n * never need to pass it.\n /\nexport async function safeFetch(url: string, deps: SafeFetchDeps = {}): Promise<Buffer> {\n const resolve = deps.resolve ?? resolveAndValidate;\n const doRequest = deps.request ?? requestOnce;\n\n let current = validateUrl(url);\n for (let hop = 0; hop <= MAX_REDIRECTS; hop++) {\n const target = new URL(current);\n const { address, family } = await resolve(target.hostname);\n const response = await doRequest(target, address, family);\n\n if (response.statusCode >= 300 && response.statusCode < 400) {\n const location = response.headers.location;\n if (!location) {\n throw new Error(`Redirect response (${response.statusCode}) missing Location header`);\n }\n const next = new URL(location, target).toString();\n current = validateUrl(next);\n continue;\n }\n\n if (response.statusCode < 200 \|\| response.statusCode >= 300) {\n throw new Error(`Non-2xx response: ${response.statusCode}`);\n }\n\n return response.body;\n }\n throw new Error(`Too many redirects (> ${MAX_REDIRECTS}) while fetching ${url}`);\n}\n\n// ---------------------------------------------------------------------------\n// Database DSN validation (MySQL schema extraction)\n// ---------------------------------------------------------------------------\n\nexport interface ValidatedDsn {\n /\n Credential-free rendering (`mysql://host:port/db`). This is the ONLY\n * form that may ever appear in graph nodes, reports, logs, or errors —\n * the password exists solely inside `connection`.\n /\n safeDisplay: string;\n connection: {\n host: string;\n port: number;\n user: string;\n password: string;\n database: string;\n };\n}\n\nconst DEFAULT_MYSQL_PORT = 3306;\n\n/\n Parse and validate a `mysql://user:pass@host:port/database` DSN.\n \n Deliberately does NOT apply the SSRF IP blocklist that safeFetch()\n * enforces: connecting to a localhost/private-network database is the\n * primary legitimate use of an explicitly user-supplied DSN, unlike a URL\n * scraped out of corpus content. The security property that matters here\n * is credential containment — see ValidatedDsn.safeDisplay.\n /\nexport function validateDsn(dsn: string): ValidatedDsn {\n let parsed: URL;\n try {\n parsed = new URL(dsn);\n } catch {\n throw new Error('Invalid DSN — expected mysql://user:pass@host:port/database');\n }\n\n if (parsed.protocol !== 'mysql:') {\n throw new Error(`DSN scheme not supported: \"${parsed.protocol}\" (only mysql: is supported)`);\n }\n\n const database = decodeURIComponent(parsed.pathname.replace(/^\\//, ''));\n if (!database \|\| database.includes('/')) {\n throw new Error('DSN must name exactly one database, e.g. mysql://localhost:3306/mydb');\n }\n if (!parsed.hostname) {\n throw new Error('DSN must include a host, e.g. mysql://localhost:3306/mydb');\n }\n\n const port = parsed.port ? Number(parsed.port) : DEFAULT_MYSQL_PORT;\n return {\n safeDisplay: `mysql://${parsed.hostname}:${port}/${database}`,\n connection: {\n host: parsed.hostname,\n port,\n user: decodeURIComponent(parsed.username) \|\| 'root',\n password: decodeURIComponent(parsed.password),\n database,\n },\n };\n}\n\n// ---------------------------------------------------------------------------\n// Path traversal guard\n// ---------------------------------------------------------------------------\n\n/\n Resolve `path` and require it stays inside `base` (defaults to\n * `<cwd>/graphify-out`). `base` must already exist. Throws on traversal\n * attempts (`../`, absolute escapes, symlink-resolved escapes).\n /\nexport function validateGraphPath(path: string, base?: string): string {\n const baseDir = base ?? nodePath.join(process.cwd(), 'graphify-out');\n\n let resolvedBase: string;\n try {\n resolvedBase = fs.realpathSync(baseDir);\n } catch {\n throw new Error(`Base directory does not exist: ${baseDir}`);\n }\n\n const candidate = nodePath.isAbsolute(path) ? path : nodePath.join(resolvedBase, path);\n const resolvedCandidate = nodePath.resolve(candidate);\n\n // Resolve symlinks for whichever is the deepest existing ancestor, so a\n // symlink inside an otherwise-valid path can't escape the base dir either.\n let realCandidate = resolvedCandidate;\n try {\n realCandidate = fs.realpathSync(resolvedCandidate);\n } catch {\n // Path (or part of it) may not exist yet (e.g. a file we're about to\n // write) — fall back to the lexically-resolved path for the check.\n }\n\n const relative = nodePath.relative(resolvedBase, realCandidate);\n const escapes = relative === '..' \|\| relative.startsWith(`..${nodePath.sep}`) \|\| nodePath.isAbsolute(relative);\n if (escapes) {\n throw new Error(`Path escapes graphify-out/: ${path}`);\n }\n\n return realCandidate;\n}\n\n// ---------------------------------------------------------------------------\n// Label sanitization (unchanged reference implementation) + HTML escaping\n// ---------------------------------------------------------------------------\n\n/* Strip control characters, cap length. Apply to every node/edge label. /\nexport function sanitizeLabel(text: string \| null \| undefined): string {\n if (text == null) return '';\n // eslint-disable-next-line no-control-regex -- intentional: stripping raw control chars\n const stripped = String(text).replace(/[\\x00-\\x1f\\x7f]/g, '');\n return stripped.slice(0, MAX_LABEL_LEN);\n}\n\n/\n HTML-escape a string. Callers must run sanitizeLabel() first for\n * length/control-char stripping, then escapeHtml() immediately before\n * embedding into graph.html (XSS control, see SECURITY.md).\n /\nexport function escapeHtml(text: string): string {\n return text\n .replace(/&/g, '&')\n .replace(/</g, '<')\n .replace(/>/g, '>')\n .replace(/\"/g, '"')\n .replace(/'/g, ''');\n}\n\n// ---------------------------------------------------------------------------\n// Prompt-injection defenses for LLM-bound file content\n// ---------------------------------------------------------------------------\n\n/\n Known jailbreak / chat-template sentinels that must never reach a prompt\n * unescaped, whether they occur in source files or are forged to spoof our\n * own <untrusted_source> delimiter.\n /\nconst SENTINEL_PATTERNS: RegExp[] = [\n /<\\\|im_start\\\|>/gi,\n /<\\\|im_end\\\|>/gi,\n /<\\\|system\\\|>/gi,\n /\\[INST\\]/gi,\n /\\[\\/INST\\]/gi,\n /<<SYS>>/gi,\n /<<\\/SYS>>/gi,\n /<\\/untrusted_source>/gi,\n /<untrusted_source/gi,\n];\n\n/\n Render brackets as fullwidth lookalikes (＜＞［］) so the defanged\n * echo is human-visible but no longer byte-identical to the original\n * sentinel — a naive downstream scan for the literal delimiter/sentinel\n * text will not re-match our own \"we found one\" marker.\n /\nfunction toFullwidthBrackets(text: string): string {\n return text\n .replace(/</g, '＜')\n .replace(/>/g, '＞')\n .replace(/\\[/g, '［')\n .replace(/\\]/g, '］');\n}\n\n/\n Replace known jailbreak/chat-template sentinels with a visibly defanged\n * form — never silently stripped (silent stripping can itself be an\n * injection vector if it changes meaning unexpectedly).\n /\nfunction defangSentinels(content: string): string {\n let result = content;\n for (const pattern of SENTINEL_PATTERNS) {\n result = result.replace(pattern, (match) => `[DEFANGED:${toFullwidthBrackets(match)}]`);\n }\n return result;\n}\n\n/\n Wrap file content for LLM prompts in a hash-stamped untrusted-source\n * delimiter and neutralize known jailbreak/chat-template sentinels. This\n * raises the bar against prompt injection; it does not eliminate it —\n * document that plainly wherever this is referenced.\n /\nexport function wrapUntrustedSource(path: string, content: string): string {\n const sha256 = createHash('sha256').update(content, 'utf8').digest('hex');\n const safePath = escapeHtml(sanitizeLabel(path));\n const defanged = defangSentinels(content);\n return `<untrusted_source path=\"${safePath}\" sha256=\"${sha256}\">\\n${defanged}\\n</untrusted_source>`;\n}\n","import Graph from 'graphology';\nimport type { SerializedGraph } from './types.js';\n\n/\n The stable serialization contract for graphs at rest: graphology's\n * node-link JSON. exportGraph() has always written exactly this shape to\n * graph.json, so anything serialized here stays loadable by every existing\n * consumer (and vice versa).\n /\nexport function serializeGraph(graph: Graph): SerializedGraph {\n return graph.export();\n}\n\nexport function deserializeGraph(data: SerializedGraph): Graph {\n return Graph.from(data);\n}\n","import type Graph from 'graphology';\nimport { resolveNode, type NodeMatch } from './query.js';\nimport type { Confidence, Relation } from './types.js';\n\n/\n Reverse impact analysis — \"what breaks if I change X\". Walks incoming\n * dependency edges (who calls / imports / inherits from the target)\n * transitively, so depth 1 is the direct blast radius and deeper levels are\n * ripple effects. Like everything in query.ts this is lexical + structural,\n * fully offline and deterministic.\n /\n\n/\n Relations where `source --rel--> target` means \"source depends on target\",\n * i.e. changing the target can break the source. `contains`/`method` are\n * included because changing an entity plausibly affects its container file\n * or class signature consumers see.\n /\nconst DEPENDENCY_RELATIONS: ReadonlySet<Relation> = new Set([\n 'calls',\n 'imports',\n 'imports_from',\n 'inherits',\n 'implements',\n 'mixes_in',\n 'embeds',\n 'references',\n 're_exports',\n 'method',\n 'contains',\n] satisfies Relation[]);\n\nexport interface AffectedNode {\n id: string;\n label: string;\n sourceFile: string;\n sourceLocation: string;\n /* 1 = depends on the target directly, 2 = one step removed, ... /\n depth: number;\n /* The dependency edge that pulled this node in (this node -> something already affected). /\n via: {\n relation: Relation;\n confidence: Confidence;\n /* The already-affected node this one depends on. /\n dependsOn: string;\n };\n}\n\nexport interface ImpactResult {\n target: NodeMatch;\n affected: AffectedNode[];\n /* How many affected nodes there are per confidence tier of the edge that pulled each one in. /\n byConfidence: Record<Confidence, number>;\n maxDepth: number;\n truncated: boolean;\n}\n\nexport interface ImpactOptions {\n /* How many reverse hops to follow (default 3). /\n maxDepth?: number;\n /* Hard cap on affected nodes reported (default 200). /\n limit?: number;\n /* Restrict the traversal to these relations (default: every dependency-carrying relation). /\n relations?: Relation[];\n}\n\nconst DEFAULT_IMPACT_DEPTH = 3;\nconst DEFAULT_IMPACT_LIMIT = 200;\n\nconst CONFIDENCE_RANK: Record<Confidence, number> = { EXTRACTED: 3, INFERRED: 2, AMBIGUOUS: 1 };\n\n/\n Resolve `nodeQuery` to its best-matching node, then reverse-BFS over\n * incoming dependency edges. Returns null when nothing in the graph matches\n * the query at all (same contract as explainNode()).\n /\nexport function affectedBy(graph: Graph, nodeQuery: string, options: ImpactOptions = {}): ImpactResult \| null {\n const target = resolveNode(graph, nodeQuery);\n if (!target) return null;\n\n const maxDepth = options.maxDepth ?? DEFAULT_IMPACT_DEPTH;\n const limit = options.limit ?? DEFAULT_IMPACT_LIMIT;\n const followed: ReadonlySet<Relation> = options.relations ? new Set(options.relations) : DEPENDENCY_RELATIONS;\n\n const affected: AffectedNode[] = [];\n const visited = new Set<string>([target.id]);\n let frontier: string[] = [target.id];\n let truncated = false;\n\n for (let depth = 1; depth <= maxDepth && frontier.length > 0 && !truncated; depth++) {\n // Collect every dependent of the current frontier before descending, so\n // each node's reported depth is its shortest* reverse distance.\n const nextFrontier = new Map<string, AffectedNode>();\n\n for (const current of [...frontier].sort((a, b) => a.localeCompare(b))) {\n graph.forEachInEdge(current, (_edge, edgeAttrs, source) => {\n if (visited.has(source)) return;\n const relation = edgeAttrs.relation as Relation;\n if (!followed.has(relation)) return;\n\n const confidence = edgeAttrs.confidence as Confidence;\n const existing = nextFrontier.get(source);\n // Same node reachable via several edges this round: keep the\n // strongest-confidence one, mirroring buildGraph()'s merge rule.\n if (existing && CONFIDENCE_RANK[existing.via.confidence] >= CONFIDENCE_RANK[confidence]) return;\n\n const attrs = graph.getNodeAttributes(source);\n nextFrontier.set(source, {\n id: source,\n label: (attrs.label as string \| undefined) ?? source,\n sourceFile: (attrs.sourceFile as string \| undefined) ?? '',\n sourceLocation: (attrs.sourceLocation as string \| undefined) ?? '',\n depth,\n via: { relation, confidence, dependsOn: current },\n });\n });\n }\n\n const roundNodes = [...nextFrontier.values()].sort((a, b) => a.id.localeCompare(b.id));\n for (const node of roundNodes) {\n if (affected.length >= limit) {\n truncated = true;\n break;\n }\n visited.add(node.id);\n affected.push(node);\n }\n frontier = roundNodes.filter((n) => visited.has(n.id)).map((n) => n.id);\n }\n\n const byConfidence: Record<Confidence, number> = { EXTRACTED: 0, INFERRED: 0, AMBIGUOUS: 0 };\n for (const node of affected) byConfidence[node.via.confidence] += 1;\n\n return { target, affected, byConfidence, maxDepth, truncated };\n}\n","import type Graph from 'graphology';\nimport { affectedBy } from './impact.js';\nimport { resolveNode } from './query.js';\nimport type { Relation } from './types.js';\n\n/*\n `graphify tests` — structural test selection. Coverage tools need\n * instrumentation and a full test run to know what covers what; the graph\n * already knows, statically: a test file imports/calls the code it\n * exercises, so the test files inside a change's reverse blast radius are\n * exactly the ones worth running. Cross-language, no instrumentation.\n /\n\n/* Test-file naming conventions across the supported languages. /\nconst TEST_FILE_PATTERNS: RegExp[] = [\n /(^\|\\/)tests?\\//, // tests/ or test/ directory\n /(^\|\\/)__tests__\\//,\n /(^\|\\/)spec\\//,\n /\\.test\\.[cm]?[jt]sx?$/,\n /\\.spec\\.[cm]?[jt]sx?$/,\n /(^\|\\/)test_[^/]+\\.py$/,\n /_test\\.py$/,\n /_test\\.go$/,\n /Tests?\\.(java\|cs)$/,\n /_spec\\.rb$/,\n /_test\\.rb$/,\n];\n\nexport function isTestFile(path: string): boolean {\n return TEST_FILE_PATTERNS.some((p) => p.test(path));\n}\n\nexport interface TestSelection {\n /* What the selection was computed for (resolved node id, or the changed files). /\n target: string;\n /* Unique test files, most directly affected first. /\n testFiles: Array<{ file: string; depth: number; via: string }>;\n /* How many non-test nodes were in the blast radius (context for confidence). /\n affectedNodeCount: number;\n /\n `usage` — selected by following actual use (calls/inheritance), tight;\n * `import-reachability` — the broad fallback: anything that can reach the\n * target through imports/re-exports, which over-includes files that share\n * a barrel entry with the target.\n /\n precision: 'usage' \| 'import-reachability';\n}\n\nconst TEST_REACH_DEPTH = 4;\nconst TEST_REACH_LIMIT = 2000;\n\n/* Relations that mean \"actually uses it\", as opposed to \"can merely reach it through an import\". /\nconst USAGE_RELATIONS: Relation[] = ['calls', 'inherits', 'implements', 'mixes_in', 'embeds', 'references'];\n\nfunction selectionFromImpact(\n graph: Graph,\n targetIds: string[],\n targetLabel: string,\n relations?: Relation[],\n): TestSelection {\n const best = new Map<string, { depth: number; via: string }>();\n let affectedNodeCount = 0;\n\n for (const id of targetIds) {\n const impact = affectedBy(graph, id, { maxDepth: TEST_REACH_DEPTH, limit: TEST_REACH_LIMIT, relations });\n if (!impact) continue;\n affectedNodeCount += impact.affected.length;\n for (const node of impact.affected) {\n if (!isTestFile(node.sourceFile)) continue;\n const existing = best.get(node.sourceFile);\n if (!existing \|\| node.depth < existing.depth) {\n best.set(node.sourceFile, { depth: node.depth, via: node.via.dependsOn });\n }\n }\n }\n\n const testFiles = [...best.entries()]\n .map(([file, info]) => ({ file, depth: info.depth, via: info.via }))\n .sort((a, b) => a.depth - b.depth \|\| a.file.localeCompare(b.file));\n\n return {\n target: targetLabel,\n testFiles,\n affectedNodeCount,\n precision: relations ? 'usage' : 'import-reachability',\n };\n}\n\n/* A file node's entities (so a usage-relation traversal has call targets to start from). /\nfunction entityRootsOf(graph: Graph, id: string): string[] {\n if (id.includes('::')) return [id];\n const roots: string[] = [];\n graph.forEachOutEdge(id, (_edge, attrs, _source, target) => {\n if (String(attrs.relation) === 'contains') roots.push(target);\n });\n roots.sort((a, b) => a.localeCompare(b));\n return roots.length > 0 ? roots : [id];\n}\n\n/\n Test files reachable (reverse) from the node best matching `nodeQuery`.\n * Tries a tight usage-relation pass first (tests that actually CALL the\n * target — precise even when many files share a barrel entry point); falls\n * back to full import-reachability when usage finds nothing. Null if\n * nothing matches the query.\n /\nexport function testsForNode(graph: Graph, nodeQuery: string): TestSelection \| null {\n const match = resolveNode(graph, nodeQuery);\n if (!match) return null;\n\n const precise = selectionFromImpact(graph, entityRootsOf(graph, match.id), match.id, USAGE_RELATIONS);\n if (precise.testFiles.length > 0) return precise;\n\n return selectionFromImpact(graph, [match.id], match.id);\n}\n\n/\n Test files reachable from any of the given changed files (as reported by\n * `git diff --name-only`). Changed test files select themselves. Unknown\n * files (not in the graph) are skipped.\n */\nexport function testsForChangedFiles(graph: Graph, changedFiles: string[]): TestSelection {\n const fileIds: string[] = [];\n const selfSelected = new Map<string, { depth: number; via: string }>();\n\n for (const file of changedFiles) {\n if (isTestFile(file)) {\n selfSelected.set(file, { depth: 0, via: '(changed directly)' });\n continue;\n }\n if (graph.hasNode(file)) fileIds.push(file);\n }\n\n const label = changedFiles.join(', ');\n const preciseRoots = fileIds.flatMap((f) => entityRootsOf(graph, f));\n let selection = selectionFromImpact(graph, preciseRoots, label, USAGE_RELATIONS);\n if (selection.testFiles.length === 0) {\n selection = selectionFromImpact(graph, fileIds, label);\n }\n for (const [file, info] of selfSelected) {\n if (!selection.testFiles.some((t) => t.file === file)) {\n selection.testFiles.push({ file, depth: info.depth, via: info.via });\n }\n }\n selection.testFiles.sort((a, b) => a.depth - b.depth \|\| 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package/dist/mcp/server.js CHANGED Viewed

@@ -7,7 +7,7 @@ import {
   renderContextPack,
   shortestPath,
   testsForNode
-} from "../chunk-K322XB4U.js";
+} from "../chunk-7LTO76UD.js";
 import {
   validateGraphPath
 } from "../chunk-6JLEILYF.js";

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@dreamtree-org/graphify",
-  "version": "1.3.0",
+  "version": "1.4.0",
   "description": "Turn a folder of code/docs/papers into a queryable, persistent knowledge graph for AI coding assistants.",
   "type": "module",
   "license": "MIT",

package/dist/chunk-K322XB4U.js.map DELETED Viewed

@@ -1 +0,0 @@

- {"version":3,"sources":["../src/store/serialize.ts","../src/store/localFile.ts","../src/graphStore.ts","../src/query.ts","../src/impact.ts","../src/context.ts","../src/testmap.ts"],"sourcesContent":["import Graph from 'graphology';\nimport type { SerializedGraph } from './types.js';\n\n/**\n * The stable serialization contract for graphs at rest: graphology's\n * node-link JSON. exportGraph() has always written exactly this shape to\n * graph.json, so anything serialized here stays loadable by every existing\n * consumer (and vice versa).\n */\nexport function serializeGraph(graph: Graph): SerializedGraph {\n return graph.export();\n}\n\nexport function deserializeGraph(data: SerializedGraph): Graph {\n return Graph.from(data);\n}\n","import * as fs from 'node:fs/promises';\nimport type Graph from 'graphology';\nimport { validateGraphPath } from '../security.js';\nimport { deserializeGraph, serializeGraph } from './serialize.js';\nimport type { GraphStore, SerializedGraph } from './types.js';\n\n/**\n * The reference GraphStore: one graph.json per directory, `ref` = the\n * outDir path. Reproduces the classic graphify-out/ behavior byte-for-byte\n * (same pretty-printed JSON exportGraph() writes) and routes every path\n * through security.validateGraphPath(), so a caller-supplied ref — or a\n * symlinked graph.json — can never read or write outside the directory it\n * resolves to.\n */\nexport class LocalFileGraphStore implements GraphStore {\n async load(ref: string): Promise<Graph | null> {\n let jsonPath: string;\n try {\n jsonPath = validateGraphPath('graph.json', ref);\n } catch (error) {\n // A ref whose directory doesn't exist simply has no graph yet;\n // traversal/symlink-escape rejections must still propagate.\n if ((error as Error).message.startsWith('Base directory does not exist')) return null;\n throw error;\n }\n\n let raw: string;\n try {\n raw = await fs.readFile(jsonPath, 'utf-8');\n } catch (error) {\n if ((error as NodeJS.ErrnoException).code === 'ENOENT') return null;\n throw error;\n }\n return deserializeGraph(JSON.parse(raw) as SerializedGraph);\n }\n\n async save(ref: string, graph: Graph): Promise<void> {\n await fs.mkdir(ref, { recursive: true });\n const jsonPath = validateGraphPath('graph.json', ref);\n await fs.writeFile(jsonPath, JSON.stringify(serializeGraph(graph), null, 2), 'utf-8');\n }\n}\n","import * as path from 'node:path';\nimport type Graph from 'graphology';\nimport { LocalFileGraphStore } from './store/localFile.js';\n\n/**\n * Load a previously-exported graph.json back into a graphology Graph.\n * Thin wrapper over LocalFileGraphStore (which enforces the path-traversal\n * guard — see SECURITY.md) that throws when no graph exists, because every\n * CLI/MCP caller treats \"no graph yet\" as a hard error. Library callers who\n * want the null-on-missing contract should use a GraphStore directly.\n */\nexport async function loadGraph(outDir: string = path.join(process.cwd(), 'graphify-out')): Promise<Graph> {\n const graph = await new LocalFileGraphStore().load(outDir);\n if (graph === null) {\n throw new Error(`No graph found in ${outDir} — run \\`graphify <path>\\` to build one first.`);\n }\n return graph;\n}\n","import type Graph from 'graphology';\n\n/**\n * Library-level graph queries shared by the CLI (`graphify query/path/\n * explain`) and the MCP server tools of the same name. None of this is an\n * LLM call — it's lexical node matching + graph traversal, so it works\n * fully offline and deterministically.\n */\n\nconst STOPWORDS = new Set([\n 'a', 'an', 'the', 'is', 'are', 'was', 'were', 'do', 'does', 'did', 'how',\n 'what', 'where', 'when', 'why', 'who', 'which', 'to', 'of', 'in', 'on',\n 'for', 'and', 'or', 'this', 'that', 'it', 'does', 'that\\'s',\n]);\n\n/** Insert spaces at camelCase boundaries so identifier words become separate tokens. */\nfunction splitCamelCase(text: string): string {\n return text\n .replace(/([a-z0-9])([A-Z])/g, '$1 $2')\n .replace(/([A-Z]+)([A-Z][a-z])/g, '$1 $2');\n}\n\nfunction tokenize(text: string): string[] {\n return splitCamelCase(text)\n .toLowerCase()\n .split(/[^a-z0-9]+/)\n .filter((token) => token.length > 1 && !STOPWORDS.has(token));\n}\n\n/**\n * Split an identifier-ish string (node label/id) into its word subtokens:\n * camelCase, snake_case, kebab-case, dots, and path separators all become\n * boundaries, so `src/a/fileStorage.js::saveAttachment` yields\n * `src, file, storage, js, save, attachment`.\n */\nfunction subtokenize(text: string): string[] {\n return splitCamelCase(text)\n .toLowerCase()\n .split(/[^a-z0-9]+/)\n .filter((token) => token.length > 1);\n}\n\n/** Don't run the fuzzy tier on tokens this short — too many false positives. */\nconst FUZZY_MIN_TOKEN_LEN = 3;\n/** Minimum similarity for a fuzzy match to count at all. */\nconst FUZZY_THRESHOLD = 0.7;\nconst SUBTOKEN_MATCH_SCORE = 1;\nconst SUBSTRING_MATCH_SCORE = 0.6;\nconst FUZZY_MATCH_WEIGHT = 0.5;\n\n/**\n * Optimal-string-alignment Damerau-Levenshtein distance. Chosen over\n * bigram-set similarity because the common code-search typo is a\n * transposition (\"sorceNodes\"), which OSA counts as one edit but bigram\n * overlap punishes brutally.\n */\nfunction osaDistance(a: string, b: string): number {\n let prev2: number[] = [];\n let prev: number[] = Array.from({ length: b.length + 1 }, (_, j) => j);\n let curr: number[] = new Array<number>(b.length + 1).fill(0);\n\n for (let i = 1; i <= a.length; i++) {\n curr[0] = i;\n for (let j = 1; j <= b.length; j++) {\n const substitution = a[i - 1] === b[j - 1] ? 0 : 1;\n let best = Math.min(\n (prev[j] as number) + 1,\n (curr[j - 1] as number) + 1,\n (prev[j - 1] as number) + substitution,\n );\n if (i > 1 && j > 1 && a[i - 1] === b[j - 2] && a[i - 2] === b[j - 1]) {\n best = Math.min(best, (prev2[j - 2] as number) + 1);\n }\n curr[j] = best;\n }\n [prev2, prev, curr] = [prev, curr, new Array<number>(b.length + 1).fill(0)];\n }\n return prev[b.length] as number;\n}\n\n/** Normalized similarity in [0, 1]; short-circuits pairs whose length gap alone puts them under FUZZY_THRESHOLD. */\nfunction fuzzySimilarity(a: string, b: string): number {\n if (a === b) return 1;\n const maxLen = Math.max(a.length, b.length);\n if (maxLen === 0) return 1;\n if (Math.abs(a.length - b.length) / maxLen > 1 - FUZZY_THRESHOLD) return 0;\n return 1 - osaDistance(a, b) / maxLen;\n}\n\nexport interface NodeMatch {\n id: string;\n label: string;\n score: number;\n}\n\n/**\n * Score every node against the query's tokens. Identifier-aware and\n * typo-tolerant, in three tiers per token (best tier wins):\n *\n * 1. exact subtoken match (camelCase/snake_case-split word of the label\n * or id) — \"storage\" matches `fileStorage.js`;\n * 2. plain substring of the label/id (the original v1 behavior);\n * 3. fuzzy (Damerau-Levenshtein) match against a subtoken — \"sorce\"\n * still finds `scoreNodes`.\n *\n * Still fully lexical and deterministic — no LLM, no randomness.\n */\nexport function scoreNodes(graph: Graph, query: string): NodeMatch[] {\n const tokens = tokenize(query);\n const matches: NodeMatch[] = [];\n\n graph.forEachNode((id, attributes) => {\n const label = (attributes.label as string | undefined) ?? id;\n const haystack = `${label} ${id}`.toLowerCase();\n const subtokens = new Set(subtokenize(`${label} ${id}`));\n let score = 0;\n for (const token of tokens) {\n if (subtokens.has(token)) {\n score += SUBTOKEN_MATCH_SCORE;\n continue;\n }\n if (haystack.includes(token)) {\n score += SUBSTRING_MATCH_SCORE;\n continue;\n }\n if (token.length >= FUZZY_MIN_TOKEN_LEN) {\n let best = 0;\n for (const subtoken of subtokens) {\n const similarity = fuzzySimilarity(token, subtoken);\n if (similarity > best) best = similarity;\n }\n if (best >= FUZZY_THRESHOLD) score += best * FUZZY_MATCH_WEIGHT;\n }\n }\n if (score > 0) matches.push({ id, label, score });\n });\n\n // On equal score, real source nodes beat module:/external: placeholders —\n // \"devtools\" should resolve to the devtools middleware, not the\n // @redux-devtools package node that happens to share a subtoken.\n const placeholderRank = (id: string): number =>\n id.startsWith('module:') || id.startsWith('external:') ? 1 : 0;\n matches.sort(\n (a, b) =>\n b.score - a.score || placeholderRank(a.id) - placeholderRank(b.id) || a.id.localeCompare(b.id),\n );\n return matches;\n}\n\n/**\n * Best-effort single-node resolution: the highest-scoring lexical match,\n * or null if nothing in the graph matches at all. Deliberately does *not*\n * fall back to \"the most connected node\" — path/explain name a specific\n * node by intent, and silently substituting an unrelated one would be\n * more misleading than clearly saying \"no match\".\n */\nexport function resolveNode(graph: Graph, query: string): NodeMatch | null {\n const matches = scoreNodes(graph, query);\n return matches[0] ?? null;\n}\n\nexport interface VisitedNode {\n id: string;\n label: string;\n sourceFile: string;\n sourceLocation: string;\n depth: number;\n}\n\nexport interface TraversalEdge {\n source: string;\n target: string;\n relation: string;\n confidence: string;\n}\n\nexport interface QueryResult {\n seeds: NodeMatch[];\n visited: VisitedNode[];\n edges: TraversalEdge[];\n}\n\nexport interface QueryOptions {\n dfs?: boolean;\n /** Hard cap on how many nodes to include. Defaults to a generous ceiling derived from `tokenBudget`. */\n budget?: number;\n /** Approximate cap, in tokens (~4 chars each), on the serialized size of the result. Default 2000. */\n tokenBudget?: number;\n maxDepth?: number;\n maxSeeds?: number;\n}\n\nconst DEFAULT_MAX_DEPTH = 2;\nconst DEFAULT_MAX_SEEDS = 5;\nconst DEFAULT_BUDGET = 40;\nconst DEFAULT_TOKEN_BUDGET = 2000;\n/** When only tokenBudget is given, allow up to this many nodes per budgeted token-decile as a safety ceiling. */\nconst NODES_PER_TOKEN = 1 / 10;\n\n/**\n * Estimated token contribution of one node to the rendered result: its own\n * line (label, file, location) plus a rough allowance for the edge lines\n * that mention its id. Chars/4 is the usual serviceable approximation.\n */\nfunction nodeTokenCost(graph: Graph, id: string): number {\n const attrs = graph.getNodeAttributes(id);\n const label = (attrs.label as string | undefined) ?? id;\n const sourceFile = (attrs.sourceFile as string | undefined) ?? '';\n return Math.ceil((id.length * 2 + label.length + sourceFile.length + 24) / 4);\n}\n\n/**\n * BFS (default, broad context) or DFS (--dfs, trace a specific path)\n * traversal from the nodes whose label best matches `question`'s\n * keywords. This is lexical retrieval, not natural-language\n * understanding — it surfaces the neighborhood of the graph an agent (or\n * a human) should look at to answer the question, it does not itself\n * compose an answer.\n */\nexport function queryGraph(graph: Graph, question: string, options: QueryOptions = {}): QueryResult {\n const maxDepth = options.maxDepth ?? DEFAULT_MAX_DEPTH;\n const maxSeeds = options.maxSeeds ?? DEFAULT_MAX_SEEDS;\n const tokenBudget = options.tokenBudget ?? DEFAULT_TOKEN_BUDGET;\n const budget = options.budget ?? Math.max(DEFAULT_BUDGET, Math.ceil(tokenBudget * NODES_PER_TOKEN));\n\n const allMatches = scoreNodes(graph, question);\n const seeds = allMatches.length > 0 ? allMatches.slice(0, maxSeeds) : [];\n\n const visited = new Map<string, number>(); // id -> depth\n const frontier: Array<{ id: string; depth: number }> = seeds.map((s) => ({ id: s.id, depth: 0 }));\n let spentTokens = 0;\n for (const seed of seeds) {\n visited.set(seed.id, 0);\n spentTokens += nodeTokenCost(graph, seed.id);\n }\n\n while (frontier.length > 0 && visited.size < budget && spentTokens < tokenBudget) {\n const current = options.dfs ? (frontier.pop() as { id: string; depth: number }) : (frontier.shift() as { id: string; depth: number });\n if (current.depth >= maxDepth) continue;\n\n const neighbors = [...graph.neighbors(current.id)].sort((a, b) => a.localeCompare(b));\n for (const neighbor of neighbors) {\n if (visited.has(neighbor) || visited.size >= budget || spentTokens >= tokenBudget) continue;\n visited.set(neighbor, current.depth + 1);\n spentTokens += nodeTokenCost(graph, neighbor);\n frontier.push({ id: neighbor, depth: current.depth + 1 });\n }\n }\n\n const visitedNodes: VisitedNode[] = [...visited.entries()]\n .map(([id, depth]) => {\n const attrs = graph.getNodeAttributes(id);\n return {\n id,\n label: (attrs.label as string | undefined) ?? id,\n sourceFile: (attrs.sourceFile as string | undefined) ?? '',\n sourceLocation: (attrs.sourceLocation as string | undefined) ?? '',\n depth,\n };\n })\n .sort((a, b) => a.depth - b.depth || a.id.localeCompare(b.id));\n\n const edges: TraversalEdge[] = [];\n graph.forEachEdge((_edge, attrs, source, target) => {\n if (visited.has(source) && visited.has(target)) {\n edges.push({\n source,\n target,\n relation: String(attrs.relation),\n confidence: String(attrs.confidence),\n });\n }\n });\n edges.sort(\n (a, b) => a.source.localeCompare(b.source) || a.target.localeCompare(b.target) || a.relation.localeCompare(b.relation),\n );\n\n return enforceTokenBudget({ seeds, visited: visitedNodes, edges }, tokenBudget);\n}\n\n/**\n * The traversal-time cost estimate can't see how densely connected the\n * visited neighborhood is — a hub-heavy subgraph induces far more edge\n * lines than nodes. Enforce the budget on the *actual* result: drop the\n * deepest/last nodes (and the edges that touched them) until the\n * serialized size fits. Seeds are never dropped.\n */\nfunction enforceTokenBudget(result: QueryResult, tokenBudget: number): QueryResult {\n const cost = (value: unknown): number => Math.ceil(JSON.stringify(value).length / 4);\n\n const visited = [...result.visited];\n let edges = [...result.edges];\n let total = cost(result.seeds) + visited.reduce((s, n) => s + cost(n), 0) + edges.reduce((s, e) => s + cost(e), 0);\n\n const seedIds = new Set(result.seeds.map((s) => s.id));\n // visited is sorted by (depth, id) — pop from the end so the deepest,\n // least-central context goes first and the result stays deterministic.\n while (total > tokenBudget && visited.length > 0) {\n const last = visited[visited.length - 1] as VisitedNode;\n if (seedIds.has(last.id)) break;\n visited.pop();\n total -= cost(last);\n const remaining: TraversalEdge[] = [];\n for (const edge of edges) {\n if (edge.source === last.id || edge.target === last.id) {\n total -= cost(edge);\n } else {\n remaining.push(edge);\n }\n }\n edges = remaining;\n }\n\n return { seeds: result.seeds, visited, edges };\n}\n\nexport interface PathResult {\n from: NodeMatch;\n to: NodeMatch;\n found: boolean;\n path: string[];\n edges: TraversalEdge[];\n}\n\n/** Shortest path between the nodes that best match `fromQuery` and `toQuery` (undirected BFS — connectivity, not call direction). */\nexport function shortestPath(graph: Graph, fromQuery: string, toQuery: string): PathResult | null {\n const from = resolveNode(graph, fromQuery);\n const to = resolveNode(graph, toQuery);\n if (!from || !to) return null;\n\n if (from.id === to.id) {\n return { from, to, found: true, path: [from.id], edges: [] };\n }\n\n const predecessor = new Map<string, string>();\n const visited = new Set<string>([from.id]);\n const queue: string[] = [from.id];\n\n while (queue.length > 0) {\n const current = queue.shift() as string;\n if (current === to.id) break;\n const neighbors = [...graph.neighbors(current)].sort((a, b) => a.localeCompare(b));\n for (const neighbor of neighbors) {\n if (visited.has(neighbor)) continue;\n visited.add(neighbor);\n predecessor.set(neighbor, current);\n queue.push(neighbor);\n }\n }\n\n if (!visited.has(to.id)) {\n return { from, to, found: false, path: [], edges: [] };\n }\n\n const path: string[] = [to.id];\n let cursor = to.id;\n while (cursor !== from.id) {\n const prev = predecessor.get(cursor);\n if (!prev) break;\n path.unshift(prev);\n cursor = prev;\n }\n\n const edges: TraversalEdge[] = [];\n for (let i = 0; i < path.length - 1; i++) {\n const a = path[i] as string;\n const b = path[i + 1] as string;\n const key = graph.edges(a, b)[0] ?? graph.edges(b, a)[0];\n if (key) {\n const attrs = graph.getEdgeAttributes(key);\n edges.push({ source: a, target: b, relation: String(attrs.relation), confidence: String(attrs.confidence) });\n }\n }\n\n return { from, to, found: true, path, edges };\n}\n\nexport interface ExplainResult {\n id: string;\n label: string;\n sourceFile: string;\n sourceLocation: string;\n communityLabel?: string;\n outgoing: TraversalEdge[];\n incoming: TraversalEdge[];\n}\n\n/** Plain-language-ready explanation of the node that best matches `query`. */\nexport function explainNode(graph: Graph, query: string): ExplainResult | null {\n const match = resolveNode(graph, query);\n if (!match) return null;\n\n const attrs = graph.getNodeAttributes(match.id);\n const outgoing: TraversalEdge[] = [];\n const incoming: TraversalEdge[] = [];\n\n graph.forEachOutEdge(match.id, (_edge, edgeAttrs, source, target) => {\n outgoing.push({ source, target, relation: String(edgeAttrs.relation), confidence: String(edgeAttrs.confidence) });\n });\n graph.forEachInEdge(match.id, (_edge, edgeAttrs, source, target) => {\n incoming.push({ source, target, relation: String(edgeAttrs.relation), confidence: String(edgeAttrs.confidence) });\n });\n\n outgoing.sort((a, b) => a.target.localeCompare(b.target) || a.relation.localeCompare(b.relation));\n incoming.sort((a, b) => a.source.localeCompare(b.source) || a.relation.localeCompare(b.relation));\n\n return {\n id: match.id,\n label: match.label,\n sourceFile: (attrs.sourceFile as string | undefined) ?? '',\n sourceLocation: (attrs.sourceLocation as string | undefined) ?? '',\n communityLabel: attrs.communityLabel as string | undefined,\n outgoing,\n incoming,\n };\n}\n","import type Graph from 'graphology';\nimport { resolveNode, type NodeMatch } from './query.js';\nimport type { Confidence, Relation } from './types.js';\n\n/**\n * Reverse impact analysis — \"what breaks if I change X\". Walks *incoming*\n * dependency edges (who calls / imports / inherits from the target)\n * transitively, so depth 1 is the direct blast radius and deeper levels are\n * ripple effects. Like everything in query.ts this is lexical + structural,\n * fully offline and deterministic.\n */\n\n/**\n * Relations where `source --rel--> target` means \"source depends on target\",\n * i.e. changing the target can break the source. `contains`/`method` are\n * included because changing an entity plausibly affects its container file\n * or class signature consumers see.\n */\nconst DEPENDENCY_RELATIONS: ReadonlySet<Relation> = new Set([\n 'calls',\n 'imports',\n 'imports_from',\n 'inherits',\n 'implements',\n 'mixes_in',\n 'embeds',\n 'references',\n 're_exports',\n 'method',\n 'contains',\n] satisfies Relation[]);\n\nexport interface AffectedNode {\n id: string;\n label: string;\n sourceFile: string;\n sourceLocation: string;\n /** 1 = depends on the target directly, 2 = one step removed, ... */\n depth: number;\n /** The dependency edge that pulled this node in (this node -> something already affected). */\n via: {\n relation: Relation;\n confidence: Confidence;\n /** The already-affected node this one depends on. */\n dependsOn: string;\n };\n}\n\nexport interface ImpactResult {\n target: NodeMatch;\n affected: AffectedNode[];\n /** How many affected nodes there are per confidence tier of the edge that pulled each one in. */\n byConfidence: Record<Confidence, number>;\n maxDepth: number;\n truncated: boolean;\n}\n\nexport interface ImpactOptions {\n /** How many reverse hops to follow (default 3). */\n maxDepth?: number;\n /** Hard cap on affected nodes reported (default 200). */\n limit?: number;\n /** Restrict the traversal to these relations (default: every dependency-carrying relation). */\n relations?: Relation[];\n}\n\nconst DEFAULT_IMPACT_DEPTH = 3;\nconst DEFAULT_IMPACT_LIMIT = 200;\n\nconst CONFIDENCE_RANK: Record<Confidence, number> = { EXTRACTED: 3, INFERRED: 2, AMBIGUOUS: 1 };\n\n/**\n * Resolve `nodeQuery` to its best-matching node, then reverse-BFS over\n * incoming dependency edges. Returns null when nothing in the graph matches\n * the query at all (same contract as explainNode()).\n */\nexport function affectedBy(graph: Graph, nodeQuery: string, options: ImpactOptions = {}): ImpactResult | null {\n const target = resolveNode(graph, nodeQuery);\n if (!target) return null;\n\n const maxDepth = options.maxDepth ?? DEFAULT_IMPACT_DEPTH;\n const limit = options.limit ?? DEFAULT_IMPACT_LIMIT;\n const followed: ReadonlySet<Relation> = options.relations ? new Set(options.relations) : DEPENDENCY_RELATIONS;\n\n const affected: AffectedNode[] = [];\n const visited = new Set<string>([target.id]);\n let frontier: string[] = [target.id];\n let truncated = false;\n\n for (let depth = 1; depth <= maxDepth && frontier.length > 0 && !truncated; depth++) {\n // Collect every dependent of the current frontier before descending, so\n // each node's reported depth is its *shortest* reverse distance.\n const nextFrontier = new Map<string, AffectedNode>();\n\n for (const current of [...frontier].sort((a, b) => a.localeCompare(b))) {\n graph.forEachInEdge(current, (_edge, edgeAttrs, source) => {\n if (visited.has(source)) return;\n const relation = edgeAttrs.relation as Relation;\n if (!followed.has(relation)) return;\n\n const confidence = edgeAttrs.confidence as Confidence;\n const existing = nextFrontier.get(source);\n // Same node reachable via several edges this round: keep the\n // strongest-confidence one, mirroring buildGraph()'s merge rule.\n if (existing && CONFIDENCE_RANK[existing.via.confidence] >= CONFIDENCE_RANK[confidence]) return;\n\n const attrs = graph.getNodeAttributes(source);\n nextFrontier.set(source, {\n id: source,\n label: (attrs.label as string | undefined) ?? source,\n sourceFile: (attrs.sourceFile as string | undefined) ?? '',\n sourceLocation: (attrs.sourceLocation as string | undefined) ?? '',\n depth,\n via: { relation, confidence, dependsOn: current },\n });\n });\n }\n\n const roundNodes = [...nextFrontier.values()].sort((a, b) => a.id.localeCompare(b.id));\n for (const node of roundNodes) {\n if (affected.length >= limit) {\n truncated = true;\n break;\n }\n visited.add(node.id);\n affected.push(node);\n }\n frontier = roundNodes.filter((n) => visited.has(n.id)).map((n) => n.id);\n }\n\n const byConfidence: Record<Confidence, number> = { EXTRACTED: 0, INFERRED: 0, AMBIGUOUS: 0 };\n for (const node of affected) byConfidence[node.via.confidence] += 1;\n\n return { target, affected, byConfidence, maxDepth, truncated };\n}\n","import type Graph from 'graphology';\nimport { scoreNodes } from './query.js';\n\n/**\n * `graphify context` — the working-set pack. Instead of returning node\n * names for the agent to chase (query -> then read whole files anyway),\n * this fuses the two steps: the graph knows every entity's file and line,\n * so rank the nodes relevant to the task, read just the relevant line\n * ranges, and pack the actual code into a token budget. One call returns\n * the code an agent needs to start a task.\n */\n\nexport interface ContextSnippet {\n nodeId: string;\n label: string;\n file: string;\n startLine: number;\n endLine: number;\n code: string;\n /** Why this snippet is in the pack (lexical match / neighbor-of relation). */\n reason: string;\n score: number;\n}\n\nexport interface ContextPack {\n task: string;\n snippets: ContextSnippet[];\n /** Approximate tokens used out of the budget. */\n tokens: number;\n tokenBudget: number;\n /** Ranked nodes that didn't fit the budget — the agent can pull them explicitly. */\n overflow: Array<{ nodeId: string; file: string }>;\n}\n\nexport interface ContextOptions {\n /** Approximate token cap for the pack (default 4000). */\n tokenBudget?: number;\n maxSeeds?: number;\n /** Cap on snippet length in lines (default 60). */\n maxSnippetLines?: number;\n}\n\nexport type FileReader = (path: string) => Promise<string>;\n\nconst DEFAULT_CONTEXT_BUDGET = 4000;\nconst DEFAULT_MAX_SEEDS = 8;\nconst DEFAULT_MAX_SNIPPET_LINES = 60;\n/** A neighbor inherits this fraction of the score of the node that pulled it in. */\nconst NEIGHBOR_DECAY = 0.4;\n\nconst tokensOf = (text: string): number => Math.ceil(text.length / 4);\n\nfunction lineNumberOf(sourceLocation: string): number | null {\n const match = /^L(\\d+)$/.exec(sourceLocation);\n return match ? Number(match[1]) : null;\n}\n\nfunction isReadableFile(sourceFile: string): boolean {\n return sourceFile !== '' && !sourceFile.startsWith('<') && !sourceFile.includes('://');\n}\n\ninterface RankedNode {\n id: string;\n score: number;\n reason: string;\n}\n\n/**\n * Rank nodes for the task: lexical seeds first (their match score), then\n * their graph neighbors at a decayed score, labeled with the relation that\n * connects them. Deterministic (score desc, id asc).\n */\nexport function rankForTask(graph: Graph, task: string, maxSeeds = DEFAULT_MAX_SEEDS): RankedNode[] {\n const seeds = scoreNodes(graph, task).slice(0, maxSeeds);\n const ranked = new Map<string, RankedNode>();\n for (const seed of seeds) {\n ranked.set(seed.id, { id: seed.id, score: seed.score, reason: 'matches the task' });\n }\n\n for (const seed of seeds) {\n graph.forEachEdge(seed.id, (_edge, attrs, source, target) => {\n const neighbor = source === seed.id ? target : source;\n if (ranked.has(neighbor)) return;\n const relation = String(attrs.relation);\n const direction = source === seed.id ? `${relation} ->` : `<- ${relation}`;\n ranked.set(neighbor, {\n id: neighbor,\n score: seed.score * NEIGHBOR_DECAY,\n reason: `${direction} ${seed.label}`,\n });\n });\n }\n\n return [...ranked.values()].sort((a, b) => b.score - a.score || a.id.localeCompare(b.id));\n}\n\n/**\n * Extract the snippet for a node: from its declaration line to just before\n * the next known entity in the same file (capped), so snippets align with\n * real code block boundaries without needing a parser here.\n */\nfunction snippetRange(\n startLine: number,\n fileLineCount: number,\n entityStartsInFile: number[],\n maxLines: number,\n): { start: number; end: number } {\n const nextStart = entityStartsInFile.find((l) => l > startLine);\n const hardEnd = nextStart !== undefined ? nextStart - 1 : fileLineCount;\n return { start: startLine, end: Math.min(hardEnd, startLine + maxLines - 1) };\n}\n\nexport async function buildContextPack(\n graph: Graph,\n task: string,\n readFile: FileReader,\n options: ContextOptions = {},\n): Promise<ContextPack> {\n const tokenBudget = options.tokenBudget ?? DEFAULT_CONTEXT_BUDGET;\n const maxSnippetLines = options.maxSnippetLines ?? DEFAULT_MAX_SNIPPET_LINES;\n const ranked = rankForTask(graph, task, options.maxSeeds);\n\n // Every known entity start line per file — used to end snippets at the\n // next declaration instead of an arbitrary window.\n const entityStarts = new Map<string, number[]>();\n graph.forEachNode((_id, attrs) => {\n const file = attrs.sourceFile as string | undefined;\n const line = lineNumberOf((attrs.sourceLocation as string | undefined) ?? '');\n if (file && line !== null) {\n const starts = entityStarts.get(file) ?? [];\n starts.push(line);\n entityStarts.set(file, starts);\n }\n });\n for (const starts of entityStarts.values()) starts.sort((a, b) => a - b);\n\n const fileCache = new Map<string, string[] | null>();\n const readLines = async (file: string): Promise<string[] | null> => {\n const cached = fileCache.get(file);\n if (cached !== undefined) return cached;\n let lines: string[] | null;\n try {\n lines = (await readFile(file)).split('\\n');\n } catch {\n lines = null;\n }\n fileCache.set(file, lines);\n return lines;\n };\n\n const snippets: ContextSnippet[] = [];\n const overflow: Array<{ nodeId: string; file: string }> = [];\n const coveredRanges = new Map<string, Array<{ start: number; end: number }>>();\n let tokens = 0;\n\n for (const node of ranked) {\n const attrs = graph.getNodeAttributes(node.id);\n const file = (attrs.sourceFile as string | undefined) ?? '';\n const startLine = lineNumberOf((attrs.sourceLocation as string | undefined) ?? '');\n if (!isReadableFile(file) || startLine === null) continue;\n\n const lines = await readLines(file);\n if (lines === null) continue;\n\n const { start, end } = snippetRange(startLine, lines.length, entityStarts.get(file) ?? [], maxSnippetLines);\n\n // Skip if an already-packed snippet from the same file covers this range.\n const covered = (coveredRanges.get(file) ?? []).some((r) => start >= r.start && end <= r.end);\n if (covered) continue;\n\n const code = lines.slice(start - 1, end).join('\\n');\n const cost = tokensOf(code) + 15; // header overhead\n if (tokens + cost > tokenBudget) {\n overflow.push({ nodeId: node.id, file: `${file}:L${startLine}` });\n continue;\n }\n\n tokens += cost;\n snippets.push({\n nodeId: node.id,\n label: (attrs.label as string | undefined) ?? node.id,\n file,\n startLine: start,\n endLine: end,\n code,\n reason: node.reason,\n score: node.score,\n });\n const ranges = coveredRanges.get(file) ?? [];\n ranges.push({ start, end });\n coveredRanges.set(file, ranges);\n }\n\n return { task, snippets, tokens, tokenBudget, overflow };\n}\n\n/** Render a pack as agent-ready markdown. */\nexport function renderContextPack(pack: ContextPack): string {\n const lines: string[] = [\n `# Context pack: ${pack.task}`,\n '',\n `_~${pack.tokens} of ${pack.tokenBudget} token budget, ${pack.snippets.length} snippet(s)._`,\n '',\n ];\n\n if (pack.snippets.length === 0) {\n lines.push('No matching code found — try different keywords.');\n return lines.join('\\n');\n }\n\n for (const snippet of pack.snippets) {\n lines.push(`## ${snippet.label} — \\`${snippet.file}:L${snippet.startLine}-L${snippet.endLine}\\``);\n lines.push(`_${snippet.reason}_`);\n lines.push('```');\n lines.push(snippet.code);\n lines.push('```');\n lines.push('');\n }\n\n if (pack.overflow.length > 0) {\n lines.push(`## Didn't fit the budget (${pack.overflow.length})`);\n for (const item of pack.overflow.slice(0, 15)) {\n lines.push(`- ${item.nodeId} (${item.file})`);\n }\n lines.push('');\n }\n\n return lines.join('\\n');\n}\n","import type Graph from 'graphology';\nimport { affectedBy } from './impact.js';\nimport { resolveNode } from './query.js';\nimport type { Relation } from './types.js';\n\n/**\n * `graphify tests` — structural test selection. Coverage tools need\n * instrumentation and a full test run to know what covers what; the graph\n * already knows, statically: a test file imports/calls the code it\n * exercises, so the test files inside a change's reverse blast radius are\n * exactly the ones worth running. Cross-language, no instrumentation.\n */\n\n/** Test-file naming conventions across the supported languages. */\nconst TEST_FILE_PATTERNS: RegExp[] = [\n /(^|\\/)tests?\\//, // tests/ or test/ directory\n /(^|\\/)__tests__\\//,\n /(^|\\/)spec\\//,\n /\\.test\\.[cm]?[jt]sx?$/,\n /\\.spec\\.[cm]?[jt]sx?$/,\n /(^|\\/)test_[^/]+\\.py$/,\n /_test\\.py$/,\n /_test\\.go$/,\n /Tests?\\.(java|cs)$/,\n /_spec\\.rb$/,\n /_test\\.rb$/,\n];\n\nexport function isTestFile(path: string): boolean {\n return TEST_FILE_PATTERNS.some((p) => p.test(path));\n}\n\nexport interface TestSelection {\n /** What the selection was computed for (resolved node id, or the changed files). */\n target: string;\n /** Unique test files, most directly affected first. */\n testFiles: Array<{ file: string; depth: number; via: string }>;\n /** How many non-test nodes were in the blast radius (context for confidence). */\n affectedNodeCount: number;\n /**\n * `usage` — selected by following actual use (calls/inheritance), tight;\n * `import-reachability` — the broad fallback: anything that can reach the\n * target through imports/re-exports, which over-includes files that share\n * a barrel entry with the target.\n */\n precision: 'usage' | 'import-reachability';\n}\n\nconst TEST_REACH_DEPTH = 4;\nconst TEST_REACH_LIMIT = 2000;\n\n/** Relations that mean \"actually uses it\", as opposed to \"can merely reach it through an import\". */\nconst USAGE_RELATIONS: Relation[] = ['calls', 'inherits', 'implements', 'mixes_in', 'embeds', 'references'];\n\nfunction selectionFromImpact(\n graph: Graph,\n targetIds: string[],\n targetLabel: string,\n relations?: Relation[],\n): TestSelection {\n const best = new Map<string, { depth: number; via: string }>();\n let affectedNodeCount = 0;\n\n for (const id of targetIds) {\n const impact = affectedBy(graph, id, { maxDepth: TEST_REACH_DEPTH, limit: TEST_REACH_LIMIT, relations });\n if (!impact) continue;\n affectedNodeCount += impact.affected.length;\n for (const node of impact.affected) {\n if (!isTestFile(node.sourceFile)) continue;\n const existing = best.get(node.sourceFile);\n if (!existing || node.depth < existing.depth) {\n best.set(node.sourceFile, { depth: node.depth, via: node.via.dependsOn });\n }\n }\n }\n\n const testFiles = [...best.entries()]\n .map(([file, info]) => ({ file, depth: info.depth, via: info.via }))\n .sort((a, b) => a.depth - b.depth || a.file.localeCompare(b.file));\n\n return {\n target: targetLabel,\n testFiles,\n affectedNodeCount,\n precision: relations ? 'usage' : 'import-reachability',\n };\n}\n\n/** A file node's entities (so a usage-relation traversal has call targets to start from). */\nfunction entityRootsOf(graph: Graph, id: string): string[] {\n if (id.includes('::')) return [id];\n const roots: string[] = [];\n graph.forEachOutEdge(id, (_edge, attrs, _source, target) => {\n if (String(attrs.relation) === 'contains') roots.push(target);\n });\n roots.sort((a, b) => a.localeCompare(b));\n return roots.length > 0 ? roots : [id];\n}\n\n/**\n * Test files reachable (reverse) from the node best matching `nodeQuery`.\n * Tries a tight usage-relation pass first (tests that actually CALL the\n * target — precise even when many files share a barrel entry point); falls\n * back to full import-reachability when usage finds nothing. Null if\n * nothing matches the query.\n */\nexport function testsForNode(graph: Graph, nodeQuery: string): TestSelection | null {\n const match = resolveNode(graph, nodeQuery);\n if (!match) return null;\n\n const precise = selectionFromImpact(graph, entityRootsOf(graph, match.id), match.id, USAGE_RELATIONS);\n if (precise.testFiles.length > 0) return precise;\n\n return selectionFromImpact(graph, [match.id], match.id);\n}\n\n/**\n * Test files reachable from any of the given changed files (as reported by\n * `git diff --name-only`). Changed test files select themselves. 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