Merge main into coding-style-fixes, resolving conflicts

Resolved conflicts in favor of main's nullish coalescing (??) and
AI SDK v6 reasoning-start/reasoning-end streaming approach.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

.gitignore

@@ -135,6 +135,9 @@ dist
 .yarn/install-state.gz
 .pnp.*
 
+# Test vault chat files
+test-vault/coi/chat_*.md
+
 #macos
 .DS_Store
 

README.md

@@ -107,6 +107,35 @@ I am an idependent software developer. If you find Co-Intelligence to be useful,
 
 [<img style='border:0px;height:36px;' src='https://storage.ko-fi.com/cdn/kofi6.png?v=6' border='0' alt='Buy Me a Coffee at ko-fi.com' />](https://ko-fi.com/X8X71G7YSI)
 
+## Development
+
+### Setup
+
+```bash
+npm install
+npm run dev      # Watch mode — rebuilds on file changes
+npm run build    # Production build (also validates TypeScript types)
+npm test         # Run tests with Vitest
+```
+
+### Manual Testing
+
+A test vault is included at `test-vault/` so you can test the plugin in Obsidian without affecting your personal vault. To build and open it:
+
+```bash
+./scripts/open-test-vault.sh
+```
+
+The first time you open the vault, you'll need to enable community plugins in Settings > Community plugins. After that, the Co-Intelligence AI plugin will be pre-enabled.
+
+The script symlinks the build output (`dist/`) into the test vault's plugin directory, so rebuilds are picked up automatically. For a live development workflow:
+
+1. Run `npm run dev` in one terminal
+2. Run `./scripts/open-test-vault.sh` to open the vault
+3. After changes rebuild, reload Obsidian (Cmd/Ctrl+P > "Reload app without saving")
+
+The test vault includes sample folders and system prompts for exercising plugin features.
+
 ## Contributing, Feedback, and Help
 
 This is an open source project, using the [MIT License](LICENSE). Pull requests for bug fixes or small improvements are welcome. If you want to get involved in a more substantial way, please [Contact me](https://epistemic.technology/contact/).

package.json

@@ -14,18 +14,20 @@
   "author": "Epistemic Technology",
   "license": "MIT",
   "dependencies": {
-    "@ai-sdk/anthropic": "^3.0.37",
-    "@ai-sdk/google": "^3.0.21",
-    "@ai-sdk/openai": "^3.0.25",
-    "@ai-sdk/perplexity": "^3.0.17",
-    "ai": "^6.0.73",
+    "@ai-sdk/anthropic": "^3.0.41",
+    "@ai-sdk/google": "^3.0.24",
+    "@ai-sdk/openai": "^3.0.26",
+    "@ai-sdk/perplexity": "^3.0.18",
+    "ai": "^6.0.79",
     "monkey-around": "^2.3.0",
     "solid-js": "^1.9.11",
     "zod": "^3.25.76"
   },
   "pnpm": {
     "overrides": {
-      "vitest>vite": "^6.4.1"
+      "vitest>vite": "^6.4.1",
+      "seroval": "^1.4.1",
+      "jsondiffpatch": "^0.7.2"
     }
   },
   "devDependencies": {

scripts/open-test-vault.sh

@@ -0,0 +1,48 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+PROJECT_DIR="$(dirname "$SCRIPT_DIR")"
+VAULT_DIR="$PROJECT_DIR/test-vault"
+PLUGIN_DIR="$VAULT_DIR/.obsidian/plugins/co-intelligence"
+OBSIDIAN_CONFIG="$HOME/Library/Application Support/obsidian/obsidian.json"
+
+# Create plugin directory and symlinks
+mkdir -p "$PLUGIN_DIR"
+ln -sf "$PROJECT_DIR/dist/main.js" "$PLUGIN_DIR/main.js"
+ln -sf "$PROJECT_DIR/dist/styles.css" "$PLUGIN_DIR/styles.css"
+ln -sf "$PROJECT_DIR/manifest.json" "$PLUGIN_DIR/manifest.json"
+
+# Build latest
+echo "Building plugin..."
+npm --prefix "$PROJECT_DIR" run build
+
+# Register the vault with Obsidian if not already registered
+if [ -f "$OBSIDIAN_CONFIG" ]; then
+  if ! python3 -c "
+import json, sys
+with open('$OBSIDIAN_CONFIG') as f:
+    config = json.load(f)
+sys.exit(0 if any(v.get('path') == '$VAULT_DIR' for v in config.get('vaults', {}).values()) else 1)
+"; then
+    echo "Registering test vault with Obsidian..."
+    python3 -c "
+import json, hashlib, time
+config_path = '$OBSIDIAN_CONFIG'
+vault_path = '$VAULT_DIR'
+with open(config_path) as f:
+    config = json.load(f)
+vault_id = hashlib.md5(vault_path.encode()).hexdigest()[:16]
+config.setdefault('vaults', {})[vault_id] = {'path': vault_path, 'ts': int(time.time() * 1000)}
+with open(config_path, 'w') as f:
+    json.dump(config, f)
+"
+  fi
+fi
+
+# Open the test vault in Obsidian
+echo "Opening test vault in Obsidian..."
+ENCODED_PATH=$(python3 -c "import urllib.parse; print(urllib.parse.quote('$VAULT_DIR'))")
+open "obsidian://open?path=$ENCODED_PATH"
+
+echo "Done. If this is the first time, enable the plugin in Settings > Community plugins."

src/components/BotMessage.tsx

@@ -14,7 +14,7 @@ export const BotMessage: Component<BotMessageProps> = ({
 }: BotMessageProps) => {
   const file = useContext(FileContext);
   const filePath = file?.path || "";
-  const content = (message.content as string) || "";
+  const content = (message.content as string) ?? "";
   // Perplexity models use <think> tags to indicate the reasoning section.
   // OpenAI models use chunk types instead. These are translated into <think>
   // tags by handleSendMessage in ChatInterface.tsx

src/components/ChatInterface.tsx

@@ -176,34 +176,31 @@ export const ChatInterface = ({
             console.error("Error:", chunk.error);
             new Notice("Unknown error occurred. See console log for details.");
           }
-          if (
-            chunk.type !== "text-delta" &&
-            chunk.type !== "reasoning-delta"
-          ) {
+          if (chunk.type === "reasoning-start") {
+            doingReasoning = true;
+            accumulatedContent += "<think>";
             continue;
           }
-          if (!chunk.text) {
+          if (chunk.type === "reasoning-end") {
+            doingReasoning = false;
+            accumulatedContent += "</think>";
             continue;
           }
+          if (chunk.type !== "text-delta" && chunk.type !== "reasoning-delta") {
+            continue;
+          }
+          const text = chunk.text;
           if (isFirstChunk) {
             const assistantMessage: ModelChatMessage = {
               role: "assistant",
-              content: chunk.text,
+              content: text,
             };
             setMessages([...messages(), assistantMessage]);
-            if (chunk.type === "reasoning-delta") {
-              accumulatedContent = "<think>";
-              doingReasoning = true;
-            }
-            accumulatedContent += chunk.text;
+            accumulatedContent += text;
             isFirstChunk = false;
             setIsProcessing(false);
           } else {
-            if (doingReasoning && chunk.type !== "reasoning-delta") {
-              accumulatedContent += "</think>";
-              doingReasoning = false;
-            }
-            accumulatedContent += chunk.text;
+            accumulatedContent += text;
             setMessages((prevMessages) => {
               const updatedMessages = [...prevMessages];
               updatedMessages[updatedMessages.length - 1] = {
@@ -252,7 +249,7 @@ export const ChatInterface = ({
 
         // Replace source reference numbers [n] with [n+offset]
         const offset = lastSourceLinkNumber();
-        const updatedContent = (lastMessage.content as string).replace(
+        const updatedContent = ((lastMessage.content as string) ?? "").replace(
           /\[(\d+)\]/g,
           (match, num) => {
             const source = uniqueNewSources[parseInt(num) - 1];
@@ -280,7 +277,9 @@ export const ChatInterface = ({
       if (!hasProcessedSources) {
         const currentMessage = messages()[messages().length - 1];
         const newLinks =
-          (currentMessage.content as string).match(/\[(.*?)\]\((.*?)\)/g) || [];
+          ((currentMessage.content as string) ?? "").match(
+            /\[(.*?)\]\((.*?)\)/g,
+          ) || [];
         newLinks.forEach((link) => {
           const [text, url] = link.slice(1, -1).split("](");
           const existingSource = sources().find((source) => source.url === url);

src/utils/notes.ts

@@ -182,7 +182,7 @@ export function serializeCoiNoteContent(
 ): string {
   const serializedMessages = messages
     .map(({ role, content }) => {
-      const contentStr = (content as string) || "";
+      const contentStr = (content as string) ?? "";
 
       // Find the highest level header in the content
       const headerMatches = contentStr.match(/^#+/gm);

test-vault/.gitignore

@@ -0,0 +1,7 @@
+# Obsidian generates config files when the vault is opened.
+# Only community-plugins.json is checked in (to pre-enable the plugin).
+.obsidian/*
+!.obsidian/community-plugins.json
+
+# Plugin symlinks are machine-specific; the script recreates them.
+.obsidian/plugins/

test-vault/.obsidian/community-plugins.json

@@ -0,0 +1,3 @@
+[
+  "co-intelligence"
+]

test-vault/coi/prompts/Code reviewer.md

@@ -0,0 +1 @@
+You are a code reviewer. Review code for bugs, style issues, and potential improvements. Be constructive and specific.

test-vault/coi/prompts/Helpful assistant.md

@@ -0,0 +1 @@
+You are a helpful assistant. Be concise and clear in your responses.

test-vault/notes/Sample note.md

@@ -0,0 +1,13 @@
+This is a sample note for testing context linking in Co-Intelligence AI.
+
+## Key points
+
+- First point with **bold** and *italic* formatting
+- Second point with a `code snippet`
+- Third point with a [[link to nowhere]]
+
+```javascript
+function hello() {
+  console.log("Hello from a code block");
+}
+```