research-copilot 0.1.2 → 0.1.3

package/README.md

@@ -41,6 +41,28 @@ Then reload your shell: `source ~/.zshrc`
 
 ---
 
+## How is Research Copilot different from Claude Cowork?
+
+[Claude Cowork](https://www.anthropic.com/product/claude-cowork) is Anthropic's general-purpose autonomous agent for knowledge workers — it handles file organization, document drafting, and data extraction across everyday desktop tasks.
+
+Research Copilot is a **vertical tool built specifically for academic research**. The two differ in depth, not surface:
+
+| | Claude Cowork | Research Copilot |
+|---|---|---|
+| **Scope** | Horizontal — any knowledge work | Vertical — academic research lifecycle |
+| **Literature** | No academic search | Multi-source search (Semantic Scholar, arXiv, OpenAlex, DBLP) with relevance scoring, coverage tracking, and citation tracing |
+| **Paper management** | Processes files you already have | Structured artifact system with DOI, bibtex, citeKey, citation counts, and relevance metadata |
+| **Academic writing** | Generic document drafting | Venue-specific templates (NeurIPS, ICML, journals), IMRAD structure, LaTeX, citation verification (never hallucinated) |
+| **Grant writing** | None | Agency-specific guidance (NSF, NIH, DOE, DARPA, NSTC) with compliance checklists |
+| **Data analysis** | Extracts data from documents | LLM-generated Python scripts with statistical modeling, matplotlib/seaborn visualization, and output manifests |
+| **Domain skills** | General capabilities | 13 pluggable research skills (scientific writing, visualization, scholar evaluation, etc.) — extensible via Markdown |
+| **Knowledge persistence** | Not specified | Artifact store, session summaries, cross-session memory, @-mention references |
+| **Openness** | Closed-source commercial product | Open source (MIT) — fully customizable |
+
+**In short**: Claude Cowork is like a smart office assistant. Research Copilot is like a lab partner who knows how to search literature, run stats, write papers, and apply for grants.
+
+---
+
 ## Features
 
 ### AI Chat with Coding & Writing Tools

package/app/out/main/index.mjs

@@ -1244,11 +1244,56 @@ function createArtifactSearchTool(projectPath) {
     }
   };
 }
+function createUpdateMemoryTool(projectPath) {
+  return {
+    name: "update-memory",
+    description: 'Write to the "## Agent Memory" section of agent.md — your persistent memory across sessions. Use this to save: user preferences, project context, key decisions, important findings. The content you provide REPLACES the entire Agent Memory section (User Instructions section is preserved automatically). Keep it concise (<5000 chars total). Consolidate and remove outdated entries rather than appending.',
+    parameters: {
+      type: "object",
+      properties: {
+        memory: {
+          type: "string",
+          description: 'The full content for the "## Agent Memory" section. Markdown format.'
+        }
+      },
+      required: ["memory"]
+    },
+    execute: async (input) => {
+      const args = input;
+      const memory = String(args.memory || "").trim();
+      if (!memory) return toolError("MISSING_PARAMETER", "memory content is required.", {
+        suggestions: ["Provide the content to save in the Agent Memory section."]
+      });
+      const record = findArtifactById(projectPath, AGENT_MD_ID);
+      const currentContent = record?.artifact?.type === "note" ? record.artifact.content || "" : "";
+      const agentMemoryMarker = "## Agent Memory";
+      const markerIdx = currentContent.indexOf(agentMemoryMarker);
+      const userInstructions = markerIdx >= 0 ? currentContent.slice(0, markerIdx).trimEnd() : currentContent.split("\n").filter((l) => !l.startsWith("## Agent Memory")).join("\n").trimEnd();
+      const newContent = `${userInstructions}
+
+${agentMemoryMarker}
+
+${memory}
+`;
+      const updated = updateArtifact(projectPath, AGENT_MD_ID, { content: newContent });
+      if (!updated) {
+        return toolError("UPDATE_FAILED", "Failed to update agent.md.", {
+          suggestions: ["agent.md may not exist. Try opening a project folder first."]
+        });
+      }
+      return {
+        success: true,
+        data: { message: "Agent memory updated.", charCount: newContent.length }
+      };
+    }
+  };
+}
 function createResearchMemoryTools(params) {
   return [
     createArtifactCreateTool(params.sessionId, params.projectPath),
     createArtifactUpdateTool(params.projectPath),
-    createArtifactSearchTool(params.projectPath)
+    createArtifactSearchTool(params.projectPath),
+    createUpdateMemoryTool(params.projectPath)
   ];
 }
 const WEB_DEFAULTS = {
@@ -1696,12 +1741,11 @@ Memory model:
 - Session context is maintained automatically via periodic summaries.
 - For quick-reference info, create a note via artifact-create({ type: "note", ... }).
 
-Long-term memory (agent.md):
-- agent.md is your persistent memory across sessions. Its content is injected into your context every turn, so anything written there will be remembered.
-- agent.md has two sections: "## User Instructions" (written by the user — NEVER modify this section) and "## Agent Memory" (written by you — update freely).
-- Use artifact-update on agent.md to save important cross-session information to the "## Agent Memory" section: user preferences, ongoing project context, key decisions, important findings.
-- agent.md has a ~5000 character limit. Do NOT blindly append — rewrite and consolidate the "## Agent Memory" section to keep it concise and up-to-date. Remove outdated entries. Think of it as a living summary, not a log.
-- Only persist genuinely valuable information that you would need in a future session. Do not save trivial or ephemeral details.
+Long-term memory:
+- Use the update-memory tool to persist information across sessions. It writes to the "## Agent Memory" section of agent.md, which is injected into your context every turn.
+- WHEN to save: user states a preference ("always do X", "I prefer Y"), a key project decision is made, you discover something important about the project that future sessions need.
+- WHEN NOT to save: routine task results, things already visible in files/git, ephemeral conversation details.
+- Keep it concise — consolidate and remove outdated entries. It's a living summary, not a log.
 
 Coding tasks:
 - For code implementation, follow test-first workflow: write/update test → confirm it fails → implement → confirm it passes.
@@ -5054,7 +5098,7 @@ async function enrichPaperArtifacts(options) {
       onProgress?.({ paperId: paper.id, status: "done" });
     } catch (err) {
       const errorMsg = err instanceof Error ? err.message : String(err);
-      {
+      if (debug) {
         console.error(`[enrich] Error enriching "${paper.title?.slice(0, 60)}":`, err);
       }
       failed++;
@@ -5066,7 +5110,7 @@ async function enrichPaperArtifacts(options) {
       onProgress?.({ paperId: paper.id, status: "failed" });
     }
   }
-  {
+  if (debug) {
     console.log(`[enrich] Done: ${enriched} enriched, ${skipped} skipped, ${failed} failed`);
   }
   return {
@@ -5813,7 +5857,7 @@ function initializeProject(path2) {
   }
   ensureAgentMd(path2);
   const migration = migrateLegacyArtifacts(path2);
-  if (migration.updatedFiles > 0) {
+  if (migration.updatedFiles > 0 && process.env.RESEARCH_COPILOT_DEBUG) {
     console.log(`[ResearchPilot] migrated legacy artifacts: files=${migration.updatedFiles}, literature->paper=${migration.convertedLiteratureType}, data.name removed=${migration.removedDataNameField}`);
   }
 }
@@ -5840,7 +5884,7 @@ async function ensureCoordinator(state, win, model, options) {
       reasoningEffort: state.currentReasoningEffort,
       projectPath: state.projectPath,
       sessionId: state.sessionId,
-      debug: true,
+      debug: !!process.env.RESEARCH_COPILOT_DEBUG,
       onStream: (chunk) => {
         state.realtimeBuffer.appendChunk(chunk);
         safeSend(win, "agent:stream-chunk", chunk);
@@ -6098,23 +6142,17 @@ function registerIpcHandlers() {
       sessionId: state.sessionId,
       projectPath: state.projectPath,
       paperIds,
-      debug: true,
+      debug: !!process.env.RESEARCH_COPILOT_DEBUG,
       onProgress: (event) => {
         safeSend(win, "enrich:progress", event);
       }
     });
   });
   handleWindow("mention:candidates", ({ state }, query, type) => {
-    if (!state.projectPath) {
-      console.warn("[mention:candidates] No projectPath set");
-      return [];
-    }
+    if (!state.projectPath) return [];
     try {
-      const result = getCandidates(state.projectPath, type, query);
-      console.log(`[mention:candidates] query="${query}" type=${type} → ${result.length} candidates (project: ${state.projectPath})`);
-      return result;
-    } catch (err) {
-      console.error("[mention:candidates] Error:", err);
+      return getCandidates(state.projectPath, type, query);
+    } catch {
       return [];
     }
   });

package/bin/cli.mjs

@@ -62,8 +62,11 @@ const nodePath = process.env.NODE_PATH
   : pkgNodeModules
 
 // Launch Electron with the app directory
+// Suppress Electron's debug output (GPU warnings, CSP notices, etc.) in production.
+// Set ELECTRON_ENABLE_LOGGING=1 to see them.
+const quiet = !process.env.ELECTRON_ENABLE_LOGGING
 const child = spawn(electronPath, [appDir], {
-  stdio: ['inherit', 'inherit', 'inherit'],
+  stdio: quiet ? ['ignore', 'ignore', 'ignore'] : 'inherit',
   env: { ...process.env, NODE_PATH: nodePath },
 })
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "research-copilot",
-  "version": "0.1.2",
+  "version": "0.1.3",
   "description": "AI-powered research assistant for scientists — literature search, data analysis, academic writing, and project management",
   "type": "module",
   "bin": {