open-research 1.1.2 → 1.2.1

package/dist/context-manager-2FA5ANQN.js

@@ -0,0 +1,28 @@
+import {
+  compactConversation,
+  createSessionUsage,
+  estimateConversationTokens,
+  estimateMessageTokens,
+  estimateTokens,
+  getCompactThreshold,
+  getContextWindow,
+  manualCompact,
+  maybeCompact,
+  pruneToolOutputs,
+  updateUsageFromApi
+} from "./chunk-EW27OWCA.js";
+import "./chunk-GVEVKDGV.js";
+import "./chunk-3RG5ZIWI.js";
+export {
+  compactConversation,
+  createSessionUsage,
+  estimateConversationTokens,
+  estimateMessageTokens,
+  estimateTokens,
+  getCompactThreshold,
+  getContextWindow,
+  manualCompact,
+  maybeCompact,
+  pruneToolOutputs,
+  updateUsageFromApi
+};

package/dist/finish-subagent-NCDLMSBT.js

@@ -0,0 +1,22 @@
+import "./chunk-3RG5ZIWI.js";
+
+// src/lib/agent/tools/finish-subagent.ts
+var FINISH_SUBAGENT_SENTINEL = "__FINISH_SUBAGENT__";
+function executeFinishSubagent(args) {
+  const handoff = {
+    summary: args.summary || "Task completed.",
+    filesCreated: args.files_created ?? [],
+    filesModified: args.files_modified ?? [],
+    keyFindings: args.key_findings ?? [],
+    status: args.status || "completed",
+    blockedReason: args.blocked_reason
+  };
+  return {
+    result: FINISH_SUBAGENT_SENTINEL,
+    handoff
+  };
+}
+export {
+  FINISH_SUBAGENT_SENTINEL,
+  executeFinishSubagent
+};

package/dist/{manager-queue-FBAUCAGI.js → manager-queue-RWWN2TU3.js}

@@ -1,13 +1,13 @@
-import {
-  loadOntology,
-  saveOntology
-} from "./chunk-3WM33M3O.js";
 import {
   DEFAULT_CONFIDENCE
 } from "./chunk-KJHM7ZW2.js";
 import {
   getProviderCatalog
 } from "./chunk-GVEVKDGV.js";
+import {
+  loadOntology,
+  saveOntology
+} from "./chunk-3WM33M3O.js";
 import {
   getConnections,
   getNote,
@@ -576,7 +576,7 @@ async function runOntologyManager(input) {
         args,
         ontology
       );
-      if (updated !== ontology) mutated = true;
+      if (!READ_ONLY_TOOLS.has(toolCall.name)) mutated = true;
       ontology = updated;
       messages.push({
         role: "tool",

package/dist/server/serve.js

@@ -0,0 +1,20 @@
+import {
+  createApp
+} from "../chunk-YFDZRMPM.js";
+import "../chunk-G7IOFPGG.js";
+import "../chunk-EW27OWCA.js";
+import "../chunk-KOBMIIQM.js";
+import "../chunk-3GZIDCV2.js";
+import "../chunk-XOSPMXYH.js";
+import "../chunk-CRSHN3PQ.js";
+import "../chunk-77Q5B5H7.js";
+import "../chunk-4HCPHCC2.js";
+import "../chunk-GVEVKDGV.js";
+import "../chunk-3RG5ZIWI.js";
+
+// src/server/serve.ts
+import { serve } from "@hono/node-server";
+var port = parseInt(process.env.PORT ?? "3210", 10);
+var { app } = createApp();
+console.log(`Open Research server listening on http://localhost:${port}`);
+serve({ fetch: app.fetch, port });

package/dist/server-7CSQEGRQ.js

@@ -0,0 +1,16 @@
+import {
+  createApp
+} from "./chunk-YFDZRMPM.js";
+import "./chunk-G7IOFPGG.js";
+import "./chunk-EW27OWCA.js";
+import "./chunk-KOBMIIQM.js";
+import "./chunk-3GZIDCV2.js";
+import "./chunk-XOSPMXYH.js";
+import "./chunk-CRSHN3PQ.js";
+import "./chunk-77Q5B5H7.js";
+import "./chunk-4HCPHCC2.js";
+import "./chunk-GVEVKDGV.js";
+import "./chunk-3RG5ZIWI.js";
+export {
+  createApp
+};

package/dist/{sessions-KL4LUGD7.js → sessions-SDED5HVO.js}

@@ -2,7 +2,7 @@ import {
   appendSessionEvent,
   listSessions,
   loadSessionHistory
-} from "./chunk-HRVDYJEC.js";
+} from "./chunk-KOBMIIQM.js";
 import "./chunk-4HCPHCC2.js";
 import "./chunk-3RG5ZIWI.js";
 export {

package/dist/traverse-citations-CPKPE33Y.js

@@ -0,0 +1,90 @@
+import {
+  getSemanticScholarApiKey,
+  loadOpenResearchConfig
+} from "./chunk-CRSHN3PQ.js";
+import "./chunk-77Q5B5H7.js";
+import "./chunk-4HCPHCC2.js";
+import "./chunk-3RG5ZIWI.js";
+
+// src/lib/agent/tools/traverse-citations.ts
+var S2_BASE = "https://api.semanticscholar.org/graph/v1";
+var FIELDS = "title,url,year,venue,citationCount,externalIds,abstract";
+async function executeTraverseCitations(args) {
+  const { paper_id, direction, limit = 10 } = args;
+  if (!paper_id) return "Error: paper_id is required.";
+  if (direction !== "references" && direction !== "citations") {
+    return 'Error: direction must be "references" or "citations".';
+  }
+  const config = await loadOpenResearchConfig().catch(() => null);
+  const apiKey = getSemanticScholarApiKey(config);
+  let resolvedId = paper_id;
+  if (paper_id.startsWith("10.")) {
+    resolvedId = `DOI:${paper_id}`;
+  } else if (/^\d{4}\.\d{4,5}/.test(paper_id)) {
+    resolvedId = `ArXiv:${paper_id}`;
+  }
+  const endpoint = `${S2_BASE}/paper/${encodeURIComponent(resolvedId)}/${direction}`;
+  const url = new URL(endpoint);
+  url.searchParams.set("fields", FIELDS);
+  url.searchParams.set("limit", String(Math.min(limit, 50)));
+  const headers = {
+    "Accept": "application/json"
+  };
+  if (apiKey) headers["x-api-key"] = apiKey;
+  try {
+    const response = await fetch(url.toString(), {
+      headers,
+      signal: AbortSignal.timeout(15e3)
+    });
+    if (!response.ok) {
+      if (response.status === 404) return `Paper not found: ${paper_id}`;
+      return `Semantic Scholar API error: ${response.status}`;
+    }
+    const body = await response.json();
+    const edges = body.data ?? [];
+    const papers = [];
+    for (const edge of edges) {
+      const paper = direction === "citations" ? edge.citingPaper : edge.citedPaper;
+      if (!paper?.title) continue;
+      papers.push({
+        title: paper.title,
+        year: paper.year ?? void 0,
+        venue: paper.venue || void 0,
+        citationCount: paper.citationCount ?? 0,
+        url: paper.url ?? `https://www.semanticscholar.org/paper/${paper.paperId}`,
+        doi: paper.externalIds?.DOI,
+        arxivId: paper.externalIds?.ArXiv,
+        abstract: paper.abstract?.slice(0, 300)
+      });
+    }
+    papers.sort((a, b) => b.citationCount - a.citationCount);
+    if (papers.length === 0) {
+      return `No ${direction} found for paper ${paper_id}.`;
+    }
+    const dirLabel = direction === "citations" ? "Cited by" : "References";
+    const lines = [`${dirLabel} (${papers.length} papers, sorted by citation count):
+`];
+    for (let i = 0; i < papers.length; i++) {
+      const p = papers[i];
+      const meta = [];
+      if (p.year) meta.push(String(p.year));
+      if (p.venue) meta.push(p.venue);
+      meta.push(`${p.citationCount} citations`);
+      if (p.doi) meta.push(`DOI:${p.doi}`);
+      if (p.arxivId) meta.push(`arXiv:${p.arxivId}`);
+      lines.push(`${i + 1}. "${p.title}"`);
+      lines.push(`   ${meta.join(" | ")}`);
+      lines.push(`   ${p.url}`);
+      if (p.abstract) {
+        lines.push(`   ${p.abstract}${p.abstract.length >= 300 ? "..." : ""}`);
+      }
+      lines.push("");
+    }
+    return lines.join("\n");
+  } catch (error) {
+    return `Error traversing citations: ${error instanceof Error ? error.message : String(error)}`;
+  }
+}
+export {
+  executeTraverseCitations
+};

package/dist/{web-search-IBZ6UAXL.js → web-search-OBNKKXV7.js}

@@ -2,12 +2,16 @@ import {
   USER_AGENT,
   extractBatch,
   fetchAndParseContent,
-  formatExtractionResults,
+  formatExtractionResults
+} from "./chunk-XOSPMXYH.js";
+import {
   loadOpenResearchConfig
-} from "./chunk-TJA4CAZE.js";
+} from "./chunk-CRSHN3PQ.js";
 import "./chunk-77Q5B5H7.js";
 import "./chunk-4HCPHCC2.js";
-import "./chunk-GVEVKDGV.js";
+import {
+  getProviderCatalog
+} from "./chunk-GVEVKDGV.js";
 import "./chunk-3RG5ZIWI.js";
 
 // src/lib/search/duckduckgo.ts
@@ -98,6 +102,48 @@ async function searchBrave(query, apiKey, numResults = 10) {
 }
 
 // src/lib/agent/tools/web-search.ts
+var ADVERSARIAL_QUERY_PROMPT = `You generate search queries that find evidence AGAINST a research target. Your queries should surface:
+- Direct contradictions or negative results
+- Methodological limitations or criticisms
+- Alternative explanations for the same phenomena
+- Boundary conditions where the target claim fails
+
+Do NOT rephrase the target as a question. Generate queries a skeptical reviewer would use to challenge the claim.`;
+var ADVERSARIAL_QUERY_SCHEMA = {
+  name: "adversarial_queries",
+  schema: {
+    type: "object",
+    properties: {
+      queries: {
+        type: "array",
+        items: { type: "string" },
+        description: "1-2 search queries designed to find contradicting or limiting evidence"
+      }
+    },
+    required: ["queries"],
+    additionalProperties: false
+  }
+};
+async function generateAdversarialWebQueries(target, provider) {
+  try {
+    const backgroundModel = getProviderCatalog(provider.kind).backgroundModel;
+    const response = await provider.callLLM({
+      messages: [
+        { role: "system", content: ADVERSARIAL_QUERY_PROMPT },
+        { role: "user", content: target }
+      ],
+      model: backgroundModel,
+      reasoningEffort: "low",
+      temperature: 0,
+      maxTokens: 150,
+      jsonSchema: ADVERSARIAL_QUERY_SCHEMA
+    });
+    const parsed = JSON.parse(response.content);
+    return Array.isArray(parsed.queries) ? parsed.queries.slice(0, 2) : [];
+  } catch {
+    return [];
+  }
+}
 async function discoverWebResults(query, numResults) {
   const config = await loadOpenResearchConfig().catch(() => null);
   const braveKey = config?.apiKeys?.brave;
@@ -117,21 +163,46 @@ async function discoverWebResults(query, numResults) {
   };
 }
 async function executeWebSearch(args, provider) {
-  if (!args.target || !args.query) {
-    return { result: "Error: both target and query are required." };
+  const userQueries = args.queries ?? (args.query ? [args.query] : []);
+  if (!args.target || userQueries.length === 0) {
+    return { result: "Error: both target and query/queries are required." };
   }
   const numResults = Math.min(args.num_results ?? 5, 8);
-  const { results: searchResults, backend } = await discoverWebResults(args.query, numResults);
-  if (searchResults.length === 0) {
+  const adversarialPromise = provider ? generateAdversarialWebQueries(args.target, provider) : Promise.resolve([]);
+  const allSearchPromises = userQueries.map((q) => discoverWebResults(q, numResults));
+  const searchResultSets = await Promise.allSettled(allSearchPromises);
+  const seenUrls = /* @__PURE__ */ new Set();
+  const allHits = [];
+  for (const resultSet of searchResultSets) {
+    if (resultSet.status === "fulfilled") {
+      for (const hit of resultSet.value.results) {
+        if (!seenUrls.has(hit.url)) {
+          seenUrls.add(hit.url);
+          allHits.push({ ...hit, queryIntent: "primary" });
+        }
+      }
+    }
+  }
+  const adversarialQueries = await adversarialPromise;
+  for (const aq of adversarialQueries) {
+    const { results } = await discoverWebResults(aq, 3);
+    for (const hit of results) {
+      if (!seenUrls.has(hit.url)) {
+        seenUrls.add(hit.url);
+        allHits.push({ ...hit, queryIntent: "adversarial" });
+      }
+    }
+  }
+  if (allHits.length === 0) {
     return { result: "No web results found. Try a different query." };
   }
   if (!provider) {
-    const summary = searchResults.slice(0, numResults).map((r, i) => `${i + 1}. ${r.title}
+    const summary = allHits.slice(0, numResults).map((r, i) => `${i + 1}. ${r.title}
    ${r.url}
    ${r.snippet}`).join("\n\n");
-    return { result: `[${backend}] ${summary}` };
+    return { result: summary };
   }
-  const toFetch = searchResults.slice(0, numResults);
+  const toFetch = allHits.slice(0, numResults + 3);
   const contentResults = await Promise.allSettled(
     toFetch.map(async (hit) => {
       const content = await fetchAndParseContent(hit.url);
@@ -140,7 +211,7 @@ async function executeWebSearch(args, provider) {
     })
   );
   const extractionInputs = [];
-  const titleMap = /* @__PURE__ */ new Map();
+  const hitMap = /* @__PURE__ */ new Map();
   for (const result of contentResults) {
     if (result.status === "fulfilled" && result.value) {
       const { hit, text } = result.value;
@@ -150,7 +221,7 @@ async function executeWebSearch(args, provider) {
         url: hit.url,
         target: args.target
       });
-      titleMap.set(hit.url, hit.title);
+      hitMap.set(hit.url, hit);
     }
   }
   if (extractionInputs.length === 0) {
@@ -165,10 +236,12 @@ ${summary}` };
   const extracted = [];
   for (const [url, extraction] of extractions) {
     if (extraction.relevanceScore >= 2) {
+      const hit = hitMap.get(url);
       extracted.push({
-        title: titleMap.get(url) ?? url,
+        title: hit?.title ?? url,
         url,
-        extraction
+        extraction,
+        queryIntent: hit?.queryIntent
       });
     }
   }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "open-research",
-  "version": "1.1.2",
+  "version": "1.2.1",
   "description": "Local-first research CLI agent — discover papers, synthesize notes, run analysis, and draft artifacts from your terminal.",
   "type": "module",
   "license": "MIT",
@@ -37,10 +37,12 @@
     "semantic-scholar"
   ],
   "dependencies": {
+    "@hono/node-server": "^1.19.13",
     "cheerio": "^1.1.2",
     "commander": "^14.0.1",
     "diff": "^8.0.4",
     "gray-matter": "^4.0.3",
+    "hono": "^4.12.12",
     "ink": "^6.3.1",
     "ink-text-input": "^6.0.0",
     "open": "^10.2.0",

package/dist/{query-agent-WM6UNZ37.js → query-agent-HINWAVC5.js}

@@ -1,9 +1,9 @@
-import {
-  loadOntology
-} from "./chunk-3WM33M3O.js";
 import {
   getProviderCatalog
 } from "./chunk-GVEVKDGV.js";
+import {
+  loadOntology
+} from "./chunk-3WM33M3O.js";
 import {
   getConnections,
   getNote,