Merge pull request #17 from Coding-Autopilot-System/harden-antigravity-integrations-20260623

Harden autonomy dashboard and Obsidian integration

Author: OgeonX-Ai

universal-refiner/.gemini-refiner.example.json

@@ -0,0 +1,13 @@
+{
+  "_comment_usage": "Legacy example only. Prefer .universal-refiner.example.json and copy that file to .universal-refiner.json. This file is safe to commit.",
+  "_comment_fields": "All fields are optional. Omit a section to use built-in defaults.",
+  "semantic": {
+    "_comment": "Configure the local OpenAI-compatible provider (Ollama, LM Studio, etc.)",
+    "localEnabled": true,
+    "baseUrl": "http://localhost:11434/v1",
+    "models": ["gemma3:12b", "gemma3"],
+    "mcpSamplingEnabled": true,
+    "timeoutMs": 120000,
+    "temperature": 0.2
+  }
+}

universal-refiner/package-lock.json

@@ -45,9 +45,10 @@
     "dependencies": {
         "@hono/node-server": "^1.19.13",
         "@modelcontextprotocol/sdk": "^1.29.0",
+        "@lancedb/lancedb": "^0.30.0",
         "better-sqlite3": "^12.8.0",
         "chokidar": "^5.0.0",
-        "flexsearch": "^0.7.43",
+        "flexsearch": "^0.8.212",
         "hono": "^4.12.25",
         "typescript": "^5.9.3",
         "zod": "^4.3.6"

universal-refiner/package.json

@@ -0,0 +1,77 @@
+import { EventStore } from "../src/history/event-store.js";
+import { ObsidianOrchestrator } from "../src/integrations/obsidian/obsidian-orchestrator.js";
+import { ConfigManager } from "../src/core/config.js";
+import * as path from "path";
+import * as fs from "fs";
+
+/**
+ * Historical Migration Script
+ * Sweeps the EventStore (events.db) and pushes all old session data to the Obsidian Vault.
+ */
+async function migrate() {
+  console.log("Starting Historical Migration to Obsidian...");
+  
+  // Force the orchestrator to use the global obsidian vault
+  ConfigManager.getObsidianConfig = () => ({ vaultPath: "C:\\repo\\global.obsidian" });
+
+  const store = EventStore.getInstance();
+  const db = (store as any).db;
+
+  // 1. Get all unique projects (repo_ids)
+  const repos = db.prepare("SELECT DISTINCT repo_id FROM prompts WHERE repo_id IS NOT NULL").all() as { repo_id: string }[];
+  console.log(`Found ${repos.length} projects with history.`);
+
+  for (const { repo_id } of repos) {
+    console.log(`\nMigrating project: ${repo_id}...`);
+    
+    // Simulate a rootPath for the orchestrator (it uses basename(rootPath) as repoId)
+    // We'll use a dummy path that ends with the repo_id
+    const dummyRootPath = `C:\\repo\\${repo_id}`;
+
+    // 2. Fetch all successful executions for this repo
+    const executions = db.prepare(`
+      SELECT p.raw_prompt, e.result_summary, e.ended_at, e.executor_name
+      FROM prompts p
+      JOIN executions e ON p.id = e.prompt_id
+      WHERE p.repo_id = ? AND e.status = 'completed'
+      ORDER BY e.ended_at ASC
+    `).all(repo_id) as any[];
+
+    console.log(`- Found ${executions.length} historical executions.`);
+
+    for (const exec of executions) {
+      const summary = `Historical: ${exec.result_summary || "Agent execution"}`;
+      const rationale = `Prompt: ${exec.raw_prompt}\n\nExecutor: ${exec.executor_name}\nDate: ${new Date(exec.ended_at).toLocaleString()}`;
+      
+      await ObsidianOrchestrator.logActivity(dummyRootPath, summary, rationale);
+    }
+
+    // 3. Fetch all commits for this repo
+    const commits = db.prepare(`
+      SELECT message, committed_at, author, sha
+      FROM commits
+      WHERE repo_id = ?
+      ORDER BY committed_at ASC
+    `).all(repo_id) as any[];
+
+    console.log(`- Found ${commits.length} historical commits.`);
+
+    for (const commit of commits) {
+      const summary = `Historical Commit: ${commit.sha.substring(0, 7)} - ${commit.message}`;
+      const rationale = `Author: ${commit.author}\nDate: ${new Date(commit.committed_at).toLocaleString()}`;
+      
+      await ObsidianOrchestrator.logActivity(dummyRootPath, summary, rationale);
+    }
+
+    // 4. Sync lessons (Engineering Mandates)
+    await ObsidianOrchestrator.syncToWiki(dummyRootPath);
+  }
+
+  console.log("\nMigration Complete!");
+  process.exit(0);
+}
+
+migrate().catch(err => {
+  console.error("Migration failed:", err);
+  process.exit(1);
+});

universal-refiner/scripts/obsidian-sync.ts

@@ -7,6 +7,9 @@ import { AutoPilotStatus } from "./autopilot-status.js";
 import { RuntimeLogger } from "./logger.js";
 import { CommandCenterDashboard } from "./dashboard.js";
 import { SerializedJobQueue } from "./job-queue.js";
+import { ExecutionOrchestrator } from "./execution-orchestrator.js";
+import { EventStore } from "../history/event-store.js";
+import { ConfigManager } from "./config.js";
 
 export class BackgroundAutonomyService {
   private watcher: chokidar.FSWatcher | null = null;
@@ -100,14 +103,21 @@ export class BackgroundAutonomyService {
       const engine = new CorrelationEngine();
       const extractor = new LessonExtractor(this.requestModelText);
       const lessonsBefore = AutoPilotStatus.getSnapshot().stats.lessonsExtracted;
+      const orchestrator = new ExecutionOrchestrator(EventStore.getInstance(), this.requestModelText);
+      
       const results = await Promise.allSettled([
         engine.correlateAll(),
         extractor.extractNewLessons(),
+        extractor.extractFailureLessons(),
       ]);
+
       const rejected = results.find((result): result is PromiseRejectedResult => result.status === "rejected");
       if (rejected) {
         throw rejected.reason;
       }
+
+      await this.attemptSelfHealing(orchestrator);
+
       const lessonsAfter = AutoPilotStatus.getSnapshot().stats.lessonsExtracted;
       if (lessonsAfter > lessonsBefore) {
         AutoPilotStatus.record(`Extracted ${lessonsAfter - lessonsBefore} lesson(s)`, "lesson");
@@ -116,7 +126,9 @@ export class BackgroundAutonomyService {
       AutoPilotStatus.incrementCycles();
       AutoPilotStatus.setActive();
       AutoPilotStatus.record("Cycle complete", "cycle_complete");
-      CommandCenterDashboard.log("Background Autonomy: Correlation and lesson extraction complete.");
+      CommandCenterDashboard.log("Background Autonomy: Correlation, lesson extraction, and self-healing complete.");
+
+      await this.syncObsidian();
 
     } catch (error) {
       AutoPilotStatus.setIdle();
@@ -127,6 +139,36 @@ export class BackgroundAutonomyService {
     }
   }
 
+  private async attemptSelfHealing(orchestrator: ExecutionOrchestrator) {
+    try {
+      const lessons = EventStore.getInstance().getApprovedLessonsWithExecutions(10);
+
+      for (const lesson of lessons) {
+        // Heal and retry
+        await orchestrator.healAndRetry(lesson.execution_id, lesson.id);
+      }
+    } catch (error) {
+      RuntimeLogger.error("Self-healing failed", error);
+    }
+  }
+
+  private async syncObsidian() {
+    const obsidianConfig = ConfigManager.getObsidianConfig(this.rootPath);
+    if (!obsidianConfig?.syncLessons) {
+      return;
+    }
+
+    try {
+      const { ObsidianOrchestrator } = await import("../integrations/obsidian/obsidian-orchestrator.js");
+      await ObsidianOrchestrator.syncToWiki(this.rootPath);
+      CommandCenterDashboard.log("Background Autonomy: Synced to Obsidian Vault.");
+      AutoPilotStatus.record("Synced to Obsidian Vault", "cycle_complete");
+    } catch (syncError) {
+      RuntimeLogger.error("Failed to sync to Obsidian", syncError);
+      CommandCenterDashboard.log("Background Autonomy: Failed to sync to Obsidian Vault.");
+    }
+  }
+
   public stop() {
     if (this.watcher) {
       this.watcher.close();

universal-refiner/src/core/background-service.ts

@@ -6,6 +6,8 @@ export interface RefinerConfig {
   mandates?: string[];
   ignoredPaths?: string[];
   semantic?: Partial<SemanticConfig>;
+  atlassian?: any;
+  obsidian?: any;
 }
 
 export interface SemanticConfig {
@@ -88,6 +90,14 @@ export class ConfigManager {
     };
   }
 
+  static getAtlassianConfig(rootPath: string = "."): any | null {
+    return this.loadConfig(rootPath).atlassian || null;
+  }
+
+  static getObsidianConfig(rootPath: string = "."): any | null {
+    return this.loadConfig(rootPath).obsidian || null;
+  }
+
   static getPredictiveMandates(): string[] {
     const logs = AgenticBlackboard.getLogs();
     const recent = logs.slice(0, 10).map(l => l.message.toLowerCase());

universal-refiner/src/core/config.ts

@@ -179,6 +179,10 @@ <h2>Provider Metrics</h2>
     const escapeHtml = (v) => String(v ?? '').replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;');
     const encodeCandidateId = (v) => encodeURIComponent(String(v)).replace(/'/g, '%27');
     const projectName = (p) => p.split(/[\\\/]/).filter(Boolean).pop() || 'ROOT';
+    const selectProject = (encodedProject) => {
+      currentProject = decodeURIComponent(encodedProject);
+      refreshData();
+    };
 
     function switchView(viewId) {
       document.querySelectorAll('.main-view').forEach(v => v.classList.add('hidden'));
@@ -199,13 +203,13 @@ <h2>Provider Metrics</h2>
 
       document.getElementById('project-badge').textContent = projectName(currentProject).toUpperCase();
       document.getElementById('project-dna').innerHTML = `
-        <div class="stat-row"><span class="stat-label">STACK</span><span>${state.stack}</span></div>
-        <div class="stat-row"><span class="stat-label">FRAMEWORK</span><span>${state.framework}</span></div>
-        <div class="stat-row"><span class="stat-label">PATTERN</span><span>${state.pattern}</span></div>
+        <div class="stat-row"><span class="stat-label">STACK</span><span>${escapeHtml(state.stack)}</span></div>
+        <div class="stat-row"><span class="stat-label">FRAMEWORK</span><span>${escapeHtml(state.framework)}</span></div>
+        <div class="stat-row"><span class="stat-label">PATTERN</span><span>${escapeHtml(state.pattern)}</span></div>
       `;
 
       document.getElementById('project-list').innerHTML = state.projects.map(p => 
-        `<div class="nav-item ${p === currentProject ? 'active' : ''}" onclick="currentProject='${p}';refreshData();" style="font-size: 0.7rem; margin-left: 0.5rem;">📂 ${projectName(p)}</div>`
+        `<div class="nav-item ${p === currentProject ? 'active' : ''}" onclick="selectProject('${encodeCandidateId(p)}')" style="font-size: 0.7rem; margin-left: 0.5rem;">📂 ${escapeHtml(projectName(p))}</div>`
       ).join('');
 
       // 2. View Specific Refresh
@@ -214,14 +218,46 @@ <h2>Provider Metrics</h2>
         const data = await res.json();
         document.getElementById('timeline-terminal').innerHTML = data.map(e => {
           let icon = 'EVT', color = 'var(--text)';
-          if (e.type === 'prompt') { icon = 'PRM'; color = 'var(--accent)'; }
+          let extraHtml = '';
+
+          if (e.type === 'prompt') { 
+            icon = 'PRM'; color = 'var(--accent)'; 
+            if (e.details && e.details.intent === 'self-heal') {
+              icon = 'HEAL'; color = '#10b981';
+              extraHtml += `<div class="badge" style="background: rgba(16, 185, 129, 0.15); color: #6ee7b7; border-color: rgba(16, 185, 129, 0.3); margin-top: 8px; display: inline-block;">AUTONOMOUS SELF-HEALING RETRY</div>`;
+            }
+            if (e.details && e.details.normalized_prompt) {
+              extraHtml += `<div style="margin-top: 8px; padding: 10px; background: rgba(56, 189, 248, 0.05); border-left: 2px solid var(--accent); border-radius: 0 4px 4px 0; font-size: 0.75rem; white-space: pre-wrap; color: var(--dim);"><strong>IMPROVED PROMPT:</strong><br/>${escapeHtml(e.details.normalized_prompt)}</div>`;
+            }
+          }
           else if (e.type === 'commit') { icon = 'GIT'; color = '#f472b6'; }
           else if (e.type === 'log') { icon = 'LOG'; color = 'var(--dim)'; }
+          else if (e.type === 'execution') { 
+            icon = 'EXEC'; 
+            color = e.event_type === 'failed' ? '#ef4444' : '#22c55e';
+            let execBadge = e.event_type === 'failed' 
+              ? `<span class="badge" style="background: rgba(239, 68, 68, 0.15); color: #fca5a5; border-color: rgba(239, 68, 68, 0.3);">AI ERROR</span>`
+              : `<span class="badge" style="background: rgba(34, 197, 94, 0.15); color: #86efac; border-color: rgba(34, 197, 94, 0.3);">SUCCESS</span>`;
+            
+            extraHtml = `<div style="margin-top: 8px;">
+              ${execBadge} <span style="color: var(--dim); font-size: 0.7rem; margin-left: 6px;">EXECUTOR: ${escapeHtml(e.author || 'unknown')}</span>
+            </div>`;
+
+            if (e.event_type === 'failed' && e.details && e.details.error) {
+              extraHtml += `<div style="margin-top: 8px; padding: 10px; background: rgba(239, 68, 68, 0.05); border-left: 2px solid #ef4444; border-radius: 0 4px 4px 0; font-size: 0.75rem; white-space: pre-wrap; color: #fca5a5; font-family: monospace;"><strong>RAW ERROR:</strong><br/>${escapeHtml(typeof e.details.error === 'object' ? JSON.stringify(e.details.error, null, 2) : String(e.details.error))}</div>`;
+            } else if (e.event_type === 'completed' && e.details && e.details.healedResponse) {
+               extraHtml += `<div style="margin-top: 8px; padding: 10px; background: rgba(34, 197, 94, 0.05); border-left: 2px solid #22c55e; border-radius: 0 4px 4px 0; font-size: 0.75rem; white-space: pre-wrap; color: #86efac;"><strong>HEALED RESPONSE:</strong><br/>${escapeHtml(e.details.healedResponse)}</div>`;
+            }
+          }
+
           return `
             <div class="log-line">
               <span class="log-ts">${new Date(e.timestamp).toLocaleTimeString()}</span>
               <span class="log-icon" style="color:${color}">${icon}</span>
-              <span>${escapeHtml(e.summary)}</span>
+              <div style="flex-grow: 1;">
+                <div style="white-space: pre-wrap; font-family: monospace; font-size: 0.85rem;">${escapeHtml(e.summary)}</div>
+                ${extraHtml}
+              </div>
             </div>
           `;
         }).join('');
@@ -235,14 +271,14 @@ <h2>Provider Metrics</h2>
             <div style="display:flex; justify-content:space-between; align-items:flex-start;">
               <div>
                 <code style="color:var(--accent)">${c.sha.substring(0, 7)}</code> <strong>${escapeHtml(c.message)}</strong>
-                <div style="font-size:0.7rem; color:var(--dim); margin-top:4px;">by ${c.author} • ${new Date(c.committed_at).toLocaleString()}</div>
+                <div style="font-size:0.7rem; color:var(--dim); margin-top:4px;">by ${escapeHtml(c.author)} • ${new Date(c.committed_at).toLocaleString()}</div>
               </div>
               <div style="text-align:right">
                 <span class="diff-add">+${JSON.parse(c.diff_stats_json).insertions || 0}</span> 
                 <span class="diff-del">-${JSON.parse(c.diff_stats_json).deletions || 0}</span>
               </div>
             </div>
-            ${c.prompt_id ? `<div class="badge" style="margin-top:10px; display:inline-block">Linked to Prompt: ${c.prompt_id}</div>` : ''}
+            ${c.prompt_id ? `<div class="badge" style="margin-top:10px; display:inline-block">Linked to Prompt: ${escapeHtml(c.prompt_id)}</div>` : ''}
           </div>
         `).join('') || '<p style="color:var(--dim)">No commits ingested for this project.</p>';
       }
@@ -328,9 +364,13 @@ <h2>Provider Metrics</h2>
       }
     }
 
+    // Auto-poll every 3 seconds so the user never has to click anything
+    setInterval(() => {
+      refreshData().catch(err => console.error("Auto-refresh failed:", err));
+    }, 3000);
+
     // Initial Load
     refreshData();
-    setInterval(refreshData, 10000);
   </script>
 </body>
 </html>

universal-refiner/src/core/dashboard.html

@@ -17,7 +17,12 @@ import { AutoPilotStatus } from "./autopilot-status.js";
 const __dirname = path.dirname(fileURLToPath(import.meta.url));
 
 export function resolveDashboardHost(configuredHost = process.env.PROMPT_REFINER_DASHBOARD_HOST): string {
-  return configuredHost?.trim() || "127.0.0.1";
+  const host = configuredHost?.trim() || "127.0.0.1";
+  if (isLoopbackHost(host) || process.env.PROMPT_REFINER_DASHBOARD_ALLOW_REMOTE === "true") {
+    return host;
+  }
+  RuntimeLogger.warn("Ignoring non-loopback dashboard host without PROMPT_REFINER_DASHBOARD_ALLOW_REMOTE=true", { host });
+  return "127.0.0.1";
 }
 
 interface DashboardState {
@@ -60,7 +65,7 @@ function sanitizeEndpoint(rawUrl: string): string {
 
 export function isSameOriginRequest(origin: string | undefined, requestUrl: string): boolean {
   if (!origin) {
-    return true;
+    return false;
   }
 
   try {
@@ -70,6 +75,23 @@ export function isSameOriginRequest(origin: string | undefined, requestUrl: stri
   }
 }
 
+export function isJsonContentType(contentType: string | undefined): boolean {
+  const mediaType = contentType?.split(";")[0]?.trim().toLowerCase();
+  return mediaType === "application/json" || Boolean(mediaType?.endsWith("+json"));
+}
+
+function isLoopbackHost(host: string): boolean {
+  const normalized = host.toLowerCase();
+  return normalized === "localhost" || normalized === "127.0.0.1" || normalized === "::1" || normalized === "[::1]";
+}
+
+function redactSensitive(value: string): string {
+  return value
+    .replace(/(ghp_|github_pat_|sk-|xox[baprs]-)[a-z0-9_\-]+/gi, "$1[REDACTED]")
+    .replace(/(token|api[_-]?key|password|secret|authorization)\s*[:=]\s*["']?[^"'\s,;]+/gi, "$1=[REDACTED]")
+    .slice(0, 2_000);
+}
+
 export class CommandCenterDashboard {
   private static rootPath: string = ".";
   private static server: { close: (callback?: (error?: Error) => void) => void } | null = null;
@@ -92,7 +114,7 @@ export class CommandCenterDashboard {
   }
 
   private static logRouteError(routeName: string, error: unknown, selectedPath?: string) {
-    const message = error instanceof Error ? error.stack || error.message : String(error);
+    const message = redactSensitive(error instanceof Error ? error.stack || error.message : String(error));
     RuntimeLogger.error(`Dashboard route failed: ${routeName}`, {
       selectedPath: selectedPath || this.rootPath,
       error: message,
@@ -241,8 +263,10 @@ export class CommandCenterDashboard {
 
     app.get("/api/timeline", async (c) => {
       try {
+        const store = EventStore.getInstance();
+        const repoId = store.ensureRepository(this.resolveSelectedPath(c.req.query("project"))).id;
         const provider = new TimelineProvider();
-        const timeline = provider.getUnifiedTimeline(50);
+        const timeline = provider.getUnifiedTimeline(50, repoId);
         return c.json(timeline);
       } catch (error) {
         this.logRouteError("api/timeline", error);
@@ -302,7 +326,7 @@ export class CommandCenterDashboard {
         if (!isSameOriginRequest(c.req.header("origin"), c.req.url)) {
           return c.json({ error: "Cross-origin review requests are not allowed" }, 403);
         }
-        if (!c.req.header("content-type")?.toLowerCase().startsWith("application/json")) {
+        if (!isJsonContentType(c.req.header("content-type"))) {
           return c.json({ error: "Review requests must use application/json" }, 415);
         }