@triedotdev/mcp 1.0.149 → 1.0.154

package/dist/index.js

@@ -1,10 +1,7 @@
 #!/usr/bin/env node
 import {
   GitHubIngester
-} from "./chunk-YOJGSRZK.js";
-import {
-  CodebaseIndex
-} from "./chunk-V7AY2EJO.js";
+} from "./chunk-CBAMZERA.js";
 import {
   appendToSection,
   completeBootstrap,
@@ -22,15 +19,12 @@ import {
   needsBootstrap,
   projectInfoExists,
   updateProjectSection
-} from "./chunk-7OJ6JIPL.js";
+} from "./chunk-OVSYTWUU.js";
 import {
   LinearIngester
-} from "./chunk-LD7ZEFNY.js";
+} from "./chunk-FXZAABXO.js";
 import {
-  ExtractionPipeline,
   GitHubBranchesTool,
-  InteractiveDashboard,
-  StreamingManager,
   TrieCheckTool,
   TrieCloudFixTool,
   TrieExplainTool,
@@ -44,79 +38,68 @@ import {
   TriePipelineTool,
   TrieQueryContextTool,
   TrieTellTool,
+  TrieWatchTool,
   getPrompt,
   getSystemPrompt,
   handleCheckpointTool
-} from "./chunk-HYNDXZAU.js";
-import "./chunk-23RJT5WT.js";
-import "./chunk-GAL7OIYU.js";
+} from "./chunk-QAM5X5HM.js";
+import "./chunk-3CYMLM35.js";
+import "./chunk-LJISDV3A.js";
 import {
-  getOutputManager
-} from "./chunk-TIMIKBY2.js";
-import "./chunk-ILGMFND2.js";
-import "./chunk-72KSLD7A.js";
-import "./chunk-OTQEFXHU.js";
+  CodebaseIndex
+} from "./chunk-YEQXKKZQ.js";
+import "./chunk-KLMJKM63.js";
+import "./chunk-LFNH3CSN.js";
+import "./chunk-NVZZUUEU.js";
+import "./chunk-T7UAH7GE.js";
 import {
   exportToJson,
   formatFriendlyError,
   importFromJson,
   isTrieInitialized
-} from "./chunk-53KUI7RQ.js";
+} from "./chunk-EMJ7RVWB.js";
 import {
   loadConfig
-} from "./chunk-NKHO34UZ.js";
-import "./chunk-4C67GV3O.js";
+} from "./chunk-FTOF3FHT.js";
+import "./chunk-KYKADM7P.js";
 import "./chunk-ZV2K6M7T.js";
 import {
   findCrossProjectPatterns,
   getGlobalMemoryStats,
   listTrackedProjects,
   searchGlobalPatterns
-} from "./chunk-B2AHQ2IR.js";
-import {
-  getStorage
-} from "./chunk-FG467PDD.js";
+} from "./chunk-OWSGJUUR.js";
 import {
   ContextGraph
-} from "./chunk-FH335WL5.js";
-import "./chunk-ZDDE442Q.js";
-import {
-  isAIAvailable,
-  runAIAnalysis
-} from "./chunk-FPEMP54L.js";
-import "./chunk-CU5VDH6F.js";
+} from "./chunk-JYWGYUKX.js";
+import "./chunk-Z2E7X4WI.js";
+import "./chunk-UL337UDQ.js";
+import "./chunk-L4FODDDB.js";
+import "./chunk-WO7CC5FH.js";
+import "./chunk-2LAJKFWU.js";
+import "./chunk-6NLHFIYA.js";
+import "./chunk-ALSCZ7WR.js";
+import "./chunk-XD2HKZVB.js";
 import {
   findSimilarIssues,
   getMemoryStats,
   getRecentIssues,
   markIssueResolved,
   purgeIssues,
-  searchIssues,
-  storeIssues
-} from "./chunk-QH77RQB3.js";
+  searchIssues
+} from "./chunk-4ZAFQEP6.js";
 import "./chunk-EFWVF6TI.js";
-import "./chunk-F4NJ4CBP.js";
-import "./chunk-IXO4G4D3.js";
-import "./chunk-6NLHFIYA.js";
 import {
-  getSkillRegistry
-} from "./chunk-G76DYVGX.js";
-import {
-  getAutonomyConfig
-} from "./chunk-5KJ4UJOY.js";
-import {
-  getChangedFilesSinceTimestamp,
-  getGitChangedFiles,
   runShellCommandSync
-} from "./chunk-ZUEAHFSY.js";
+} from "./chunk-HD5H7YSW.js";
 import "./chunk-43X6JBEM.js";
 import {
   getTrieDirectory,
   getWorkingDirectory
-} from "./chunk-SH7H3WRU.js";
+} from "./chunk-7F2R2ITA.js";
 import {
   isInteractiveMode
-} from "./chunk-APMV77PU.js";
+} from "./chunk-JKEEQAG2.js";
 import "./chunk-DGUM43GV.js";
 
 // src/server/mcp-server.ts
@@ -795,1436 +778,29 @@ trie_test action:"run" files:["src/utils.test.ts"]
   }
 };
 
-// src/tools/watch.ts
-import { watch, existsSync as existsSync2, readFileSync } from "fs";
-import { stat, readFile as readFile2 } from "fs/promises";
-import { join as join2, extname as extname2, basename as basename2 } from "path";
-import { createHash } from "crypto";
-var WATCH_EXTENSIONS = /* @__PURE__ */ new Set([
-  ".ts",
-  ".tsx",
-  ".js",
-  ".jsx",
-  ".mjs",
-  ".vue",
-  ".svelte",
-  ".astro",
-  ".py",
-  ".go",
-  ".rs"
-]);
-var SKIP_DIRS = /* @__PURE__ */ new Set([
-  "node_modules",
-  ".git",
-  "dist",
-  "build",
-  ".next",
-  ".nuxt",
-  "coverage",
-  ".turbo",
-  ".cache"
-]);
-var TrieWatchTool = class _TrieWatchTool {
-  extractionPipeline = null;
-  watchedDirectory = "";
-  codebaseIndex = null;
-  state = {
-    isRunning: false,
-    lastScan: /* @__PURE__ */ new Map(),
-    pendingFiles: /* @__PURE__ */ new Set(),
-    scanDebounceTimer: null,
-    issueCache: /* @__PURE__ */ new Map(),
-    totalIssuesFound: 0,
-    filesScanned: 0,
-    nudgedFiles: /* @__PURE__ */ new Set(),
-    nudges: [],
-    lastAutoScan: 0,
-    autoScanInProgress: false,
-    tokenBudget: {
-      used: 0,
-      windowStart: Date.now(),
-      hourlyLimit: 5e4,
-      scansSaved: 0
-    },
-    cleanFiles: /* @__PURE__ */ new Map()
-  };
-  watchers = /* @__PURE__ */ new Map();
-  streamingManager = void 0;
-  dashboard = void 0;
-  lastHypothesisCheck = 0;
-  pipelineSyncTimer = null;
-  static HYPOTHESIS_CHECK_INTERVAL_MS = 3e5;
-  // Check every 5 minutes
-  static PIPELINE_SYNC_INTERVAL_MS = 30 * 60 * 1e3;
-  // 30 minutes
-  async execute(args) {
-    const { action, directory, debounceMs = 1e3 } = args;
-    switch (action) {
-      case "start":
-        return this.startWatching(getWorkingDirectory(directory), debounceMs);
-      case "stop":
-        return await this.stopWatching();
-      case "status":
-        return await this.getStatus();
-      case "issues":
-        return this.getCurrentIssues();
-      case "nudges":
-        return this.getNudges();
-      default:
-        return {
-          content: [{
-            type: "text",
-            text: `Unknown action: ${action}. Use 'start', 'stop', 'status', or 'issues'.`
-          }]
-        };
-    }
-  }
-  async startWatching(directory, debounceMs) {
-    if (this.state.isRunning) {
-      return {
-        content: [{
-          type: "text",
-          text: "[!] Watch mode is already running. Use `trie_watch stop` to stop it first."
-        }]
-      };
-    }
-    if (!isTrieInitialized(directory)) {
-      return {
-        content: [{
-          type: "text",
-          text: "Trie is not initialized for this project. Run `trie init` first."
-        }]
-      };
-    }
-    const anthropicApiKey = process.env.ANTHROPIC_API_KEY;
-    if (anthropicApiKey) {
-      this.extractionPipeline = new ExtractionPipeline({
-        workingDirectory: directory,
-        anthropicApiKey
-      });
-      await this.extractionPipeline.initialize();
-    }
-    this.codebaseIndex = new CodebaseIndex(directory);
-    this.state.isRunning = true;
-    this.watchedDirectory = directory;
-    this.state.issueCache.clear();
-    this.state.totalIssuesFound = 0;
-    this.state.filesScanned = 0;
-    this.state.nudgedFiles.clear();
-    this.state.nudges = [];
-    try {
-      const storage = getStorage(directory);
-      await storage.initialize();
-      const unresolvedNudges = await storage.queryNudges({ resolved: false });
-      console.debug(`[Watch] Found ${unresolvedNudges.length} unresolved nudges in storage`);
-      for (const nudge of unresolvedNudges) {
-        let mappedSeverity = "high";
-        if (nudge.severity === "critical") {
-          mappedSeverity = "critical";
-        } else if (nudge.severity === "high") {
-          mappedSeverity = "high";
-        }
-        this.state.nudges.push({
-          file: nudge.file || "unknown",
-          // Keep full path, don't use basename
-          message: nudge.message,
-          severity: mappedSeverity,
-          timestamp: new Date(nudge.timestamp).toLocaleTimeString("en-US", { hour12: false })
-        });
-        console.debug(`[Watch] Loaded nudge: ${nudge.message.slice(0, 60)}... (${nudge.severity} -> ${mappedSeverity})`);
-      }
-      if (unresolvedNudges.length > 0) {
-        console.log(`[Watch] \u2713 Loaded ${unresolvedNudges.length} unresolved nudges from storage`);
-      } else {
-        console.debug(`[Watch] No unresolved nudges found in storage`);
-      }
-    } catch (error) {
-      console.error("[Watch] Failed to load nudges from storage:", error);
-    }
-    try {
-      const graph = new ContextGraph(directory);
-      const allNodes = await graph.listNodes();
-      const unresolvedIncidents = allNodes.filter(
-        (n) => n.type === "incident" && !n.data.resolved
-      );
-      console.debug(`[Watch] Found ${unresolvedIncidents.length} unresolved incidents in context graph`);
-      for (const incident of unresolvedIncidents) {
-        const incidentData = incident.data;
-        let mappedSeverity = "high";
-        if (incidentData.severity === "critical") {
-          mappedSeverity = "critical";
-        } else if (incidentData.severity === "major") {
-          mappedSeverity = "critical";
-        } else if (incidentData.severity === "minor") {
-          mappedSeverity = "high";
-        }
-        const edges = await graph.getEdges(incident.id);
-        const linkedFiles = edges.filter((e) => e.type === "causedBy" || e.type === "affects").map((e) => {
-          const node = allNodes.find((n) => n.id === e.to_id || n.id === e.from_id);
-          if (node?.type === "file") {
-            return node.data.path;
-          }
-          return null;
-        }).filter((f) => f !== null);
-        const file = linkedFiles[0] || "unknown";
-        const message = `INCIDENT: ${incidentData.description}`;
-        this.state.nudges.push({
-          file,
-          message,
-          severity: mappedSeverity,
-          timestamp: new Date(incidentData.timestamp).toLocaleTimeString("en-US", { hour12: false })
-        });
-        console.debug(`[Watch] Loaded incident: ${incidentData.description.slice(0, 60)}... (${incidentData.severity} -> ${mappedSeverity})`);
-      }
-      if (unresolvedIncidents.length > 0) {
-        console.log(`[Watch] \u2713 Loaded ${unresolvedIncidents.length} unresolved incidents from context graph`);
-      } else {
-        console.debug(`[Watch] No unresolved incidents found in context graph`);
-      }
-    } catch (error) {
-      console.error("[Watch] Failed to load incidents from context graph:", error);
-    }
-    if (!isInteractiveMode()) {
-      console.error("\n\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501");
-      console.error("TRIE AGENT - NOW WATCHING");
-      console.error("\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\n");
-      console.error("Your Trie agent is now watching over your codebase.");
-      console.error("Signal extraction: ENABLED (building governance ledger)");
-      console.error(`Watching: ${directory}`);
-      console.error(`Debounce: ${debounceMs}ms`);
-      console.error("");
-    }
-    if (isInteractiveMode()) {
-      this.streamingManager = new StreamingManager();
-      this.dashboard = new InteractiveDashboard();
-      this.streamingManager.subscribe((update) => this.dashboard?.handleStreamUpdate(update));
-      const outputManager = getOutputManager();
-      outputManager.setMode("tui");
-      outputManager.setStreamingManager(this.streamingManager);
-      await this.dashboard.start();
-      this.streamingManager.reportWatchStatus({ watching: true, directories: 0, debounceMs });
-    } else {
-      getOutputManager().setMode("console");
-    }
-    await this.watchDirectory(directory, debounceMs);
-    await this.watchContextGraph(directory);
-    if (this.streamingManager) {
-      this.streamingManager.reportWatchStatus({
-        watching: true,
-        directories: this.watchers.size,
-        debounceMs
-      });
-    }
-    setTimeout(() => {
-      void this.initialGoalComplianceScan();
-      void this.initialHypothesisGeneration();
-      void this.syncPipelineIntegrations();
-    }, 1e3);
-    this.pipelineSyncTimer = setInterval(() => {
-      void this.syncPipelineIntegrations();
-    }, _TrieWatchTool.PIPELINE_SYNC_INTERVAL_MS);
-    const indexStatus = this.codebaseIndex?.isEmpty() ? "BUILDING (one-time, speeds up goal checks)" : "READY";
-    return {
-      content: [{
-        type: "text",
-        text: `**TRIE AGENT ACTIVATED** 
-
-Your Trie agent is now autonomously watching and learning from your codebase.
-
-**Watching:** \`${directory}\`
-**Debounce:** ${debounceMs}ms (waits for you to stop typing)
-**Signal Extraction:** ${process.env.ANTHROPIC_API_KEY ? "ENABLED" : "LIMITED (set ANTHROPIC_API_KEY for full extraction)"}
-**Codebase Index:** ${indexStatus}
-
-### How the agent works:
-1. You write/edit code
-2. Agent detects the change
-3. Extracts governance, facts, blockers -> stores in ledger
-4. Predicts risks based on historical patterns
-5. Nudges you if something looks risky
-
-### The agent learns:
-- Every commit builds the governance ledger
-- \`trie gotcha\` queries the ledger for predictions
-- \`trie ok\` / \`trie bad\` teach the agent what matters
-
-### Commands:
-- \`trie_watch status\` - See agent status
-- \`trie_watch stop\` - Stop the agent
-- \`trie_index status\` - Check codebase index`
-      }]
-    };
-  }
-  shouldSkipPath(filePath) {
-    const parts = filePath.split("/");
-    return parts.some((p) => SKIP_DIRS.has(p) || p.startsWith(".") && p !== ".");
-  }
-  async watchDirectory(dir, debounceMs) {
-    if (!existsSync2(dir)) return;
-    try {
-      const dirStat = await stat(dir);
-      if (!dirStat.isDirectory()) return;
-      const watcher = watch(dir, { persistent: true, recursive: true }, (_eventType, filename) => {
-        if (!filename) return;
-        if (this.shouldSkipPath(filename)) return;
-        const ext = extname2(filename).toLowerCase();
-        if (!WATCH_EXTENSIONS.has(ext)) return;
-        const fullPath = join2(dir, filename);
-        if (!existsSync2(fullPath)) return;
-        this.state.pendingFiles.add(fullPath);
-        if (this.state.scanDebounceTimer) {
-          clearTimeout(this.state.scanDebounceTimer);
-        }
-        this.state.scanDebounceTimer = setTimeout(() => {
-          this.processPendingFiles();
-        }, debounceMs);
-      });
-      watcher.on("error", (err) => {
-        if (!isInteractiveMode()) {
-          console.error(`[!] Watcher error: ${err.message}`);
-        }
-        watcher.close();
-        this.watchers.delete(dir);
-      });
-      this.watchers.set(dir, watcher);
-      if (this.streamingManager) {
-        this.streamingManager.reportWatchStatus({
-          watching: true,
-          directories: 1,
-          debounceMs
-        });
-      }
-    } catch {
-    }
-  }
-  /**
-   * Watch .trie/context.json for incident changes
-   */
-  async watchContextGraph(directory) {
-    const contextPath = join2(getTrieDirectory(directory), "context.json");
-    if (!existsSync2(contextPath)) {
-      console.debug("[Watch] No context.json found, skipping incident watcher");
-      return;
-    }
-    try {
-      const watcher = watch(contextPath, { persistent: true }, async (_eventType, _filename) => {
-        console.debug("[Watch] context.json changed, reloading incidents...");
-        await this.reloadIncidents(directory);
-      });
-      watcher.on("error", (err) => {
-        console.error(`[Watch] Context watcher error: ${err.message}`);
-        watcher.close();
-      });
-      this.watchers.set("context.json", watcher);
-      console.debug("[Watch] \u2713 Watching context.json for incident changes");
-    } catch (error) {
-      console.error("[Watch] Failed to set up context.json watcher:", error);
-    }
-  }
-  /**
-   * Reload incidents from context graph
-   */
-  async reloadIncidents(directory) {
-    try {
-      const graph = new ContextGraph(directory);
-      const allNodes = await graph.listNodes();
-      const unresolvedIncidents = allNodes.filter(
-        (n) => n.type === "incident" && !n.data.resolved
-      );
-      this.state.nudges = this.state.nudges.filter((n) => !n.message.startsWith("INCIDENT:"));
-      for (const incident of unresolvedIncidents) {
-        const incidentData = incident.data;
-        let mappedSeverity = "high";
-        if (incidentData.severity === "critical") {
-          mappedSeverity = "critical";
-        } else if (incidentData.severity === "major") {
-          mappedSeverity = "critical";
-        } else if (incidentData.severity === "minor") {
-          mappedSeverity = "high";
-        }
-        const edges = await graph.getEdges(incident.id);
-        const linkedFiles = edges.filter((e) => e.type === "causedBy" || e.type === "affects").map((e) => {
-          const node = allNodes.find((n) => n.id === e.to_id || n.id === e.from_id);
-          if (node?.type === "file") {
-            return node.data.path;
-          }
-          return null;
-        }).filter((f) => f !== null);
-        const file = linkedFiles[0] || "unknown";
-        const message = `INCIDENT: ${incidentData.description}`;
-        this.state.nudges.push({
-          file,
-          message,
-          severity: mappedSeverity,
-          timestamp: new Date(incidentData.timestamp).toLocaleTimeString("en-US", { hour12: false })
-        });
-      }
-      console.log(`[Watch] \u2713 Reloaded ${unresolvedIncidents.length} unresolved incidents`);
-    } catch (error) {
-      console.error("[Watch] Failed to reload incidents:", error);
-    }
-  }
-  async processPendingFiles() {
-    if (this.state.pendingFiles.size === 0) return;
-    const files = Array.from(this.state.pendingFiles);
-    this.state.pendingFiles.clear();
-    if (!isInteractiveMode()) {
-      console.error(`
-Detected changes in ${files.length} file(s):`);
-      for (const file of files) {
-        console.error(`   - ${basename2(file)}`);
-      }
-      console.error("");
-    }
-    try {
-      const projectPath = this.watchedDirectory || getWorkingDirectory(void 0, true);
-      if (this.extractionPipeline) {
-        try {
-          const fileContents = await Promise.all(
-            files.map(async (file) => {
-              try {
-                const content = await readFile2(file, "utf-8");
-                return { file, content };
-              } catch {
-                return null;
-              }
-            })
-          );
-          const validFiles = fileContents.filter((f) => f !== null);
-          if (validFiles.length > 0) {
-            const combinedContent = validFiles.map(
-              (f) => `File: ${basename2(f.file)}
-${f.content.slice(0, 1e3)}`
-              // First 1KB of each file
-            ).join("\n\n---\n\n");
-            if (!isInteractiveMode()) {
-              console.error("[*] Extracting signals from changes...");
-            }
-            const signal = await this.extractionPipeline.process(combinedContent, {
-              sourceType: "file",
-              sourceId: `watch-${Date.now()}`
-            });
-            if (signal.governance.length > 0 || signal.facts.length > 0 || signal.blockers.length > 0) {
-              const govCount = signal.governance.length;
-              if (!isInteractiveMode()) {
-                console.error(`   [+] Extracted: ${govCount} governance, ${signal.facts.length} facts, ${signal.blockers.length} blockers`);
-              }
-              if (this.streamingManager) {
-                this.streamingManager.reportSignalExtraction({
-                  governance: govCount,
-                  facts: signal.facts.length,
-                  blockers: signal.blockers.length,
-                  questions: signal.questions.length
-                });
-              }
-            }
-          }
-        } catch (error) {
-          if (!isInteractiveMode()) {
-            console.error(`   [!] Signal extraction failed: ${error}`);
-          }
-        }
-      }
-      void this.autoScanFiles(files).catch((err) => {
-        getOutputManager().log("warn", `Auto scan failed: ${err}`);
-      });
-      await this.discoverPatternsFromIssues(projectPath);
-      const now = Date.now();
-      if (now - this.lastHypothesisCheck > _TrieWatchTool.HYPOTHESIS_CHECK_INTERVAL_MS) {
-        this.checkAndGenerateHypotheses(projectPath);
-        this.lastHypothesisCheck = now;
-      }
-      if (this.streamingManager) {
-        const now2 = Date.now();
-        for (const file of files) {
-          const lastReport = this.state.lastScan.get(file) || 0;
-          if (now2 - lastReport > 2e3) {
-            this.streamingManager.reportWatchChange(file);
-          }
-        }
-      }
-      this.state.filesScanned += files.length;
-      for (const file of files) {
-        this.state.lastScan.set(file, Date.now());
-        if (this.codebaseIndex) {
-          const relativePath = file.replace(projectPath + "/", "");
-          void this.codebaseIndex.indexFile(relativePath).then(() => {
-            void this.codebaseIndex?.save();
-          });
-        }
-      }
-    } catch (error) {
-      if (!isInteractiveMode()) {
-        console.error(`Scan error: ${error}`);
-      }
-    }
-  }
-  isQuiet() {
-    const projectPath = this.watchedDirectory || getWorkingDirectory(void 0, true);
-    const quietPath = join2(getTrieDirectory(projectPath), "quiet.json");
-    try {
-      const raw = readFileSync(quietPath, "utf-8");
-      const data = JSON.parse(raw);
-      const until = new Date(data.until).getTime();
-      return Date.now() < until;
-    } catch {
-      return false;
-    }
-  }
-  /**
-   * Check and generate hypotheses autonomously
-   * Claude observes patterns and creates new hypotheses to test
-   */
-  async checkAndGenerateHypotheses(projectPath) {
-    if (!isAIAvailable()) return;
-    try {
-      const { getHypothesisEngine } = await import("./hypothesis-O72ZLVOW.js");
-      const { getOutputManager: getOutputManager2 } = await import("./output-manager-DZO5LGSG.js");
-      const hypothesisEngine = getHypothesisEngine(projectPath);
-      const recentIssues = Array.from(this.state.issueCache.values()).flat();
-      const patterns = [];
-      const observations = [];
-      if (this.state.nudges.length > 0) {
-        const nudgesByFile = {};
-        for (const nudge of this.state.nudges) {
-          nudgesByFile[nudge.file] = (nudgesByFile[nudge.file] || 0) + 1;
-        }
-        const topFiles = Object.entries(nudgesByFile).sort(([, a], [, b]) => b - a).slice(0, 3);
-        if (topFiles[0] && topFiles[0][1] > 2) {
-          observations.push(`File ${topFiles[0][0]} has ${topFiles[0][1]} repeated issues this session`);
-        }
-      }
-      if (this.state.nudges.length > 5) {
-        observations.push(`High issue detection rate: ${this.state.nudges.length} violations detected in watch session`);
-      }
-      let generated = await hypothesisEngine.generateHypothesesWithAI({
-        recentIssues,
-        patterns,
-        observations
-      });
-      if (generated.length === 0) {
-        generated = await hypothesisEngine.autoGenerateHypotheses();
-      }
-      for (const hypothesis of generated) {
-        const message = `[New Hypothesis] "${hypothesis.statement}" (${Math.round(hypothesis.confidence * 100)}% confidence)`;
-        getOutputManager2().nudge(
-          message,
-          "info",
-          void 0,
-          1e4
-        );
-        if (!isInteractiveMode()) {
-          console.error(`
-   [?] ${message}`);
-          console.error(`       Test: ${hypothesis.testCriteria || "Collecting evidence..."}`);
-        }
-        if (this.streamingManager) {
-          this.streamingManager.reportSignalExtraction({
-            governance: 0,
-            facts: 0,
-            blockers: 0,
-            questions: 1
-            // Hypotheses are questions to answer
-          });
-        }
-      }
-      if (recentIssues.length > 10) {
-        await hypothesisEngine.updateConfidenceFromOutcomes();
-      }
-    } catch (error) {
-      if (!isInteractiveMode()) {
-        console.error(`   [!] Hypothesis check failed: ${error}`);
-      }
-    }
-  }
-  /**
-   * Discover patterns from accumulated issues
-   * Patterns emerge naturally from your coding workflow
-   */
-  async discoverPatternsFromIssues(projectPath) {
-    const totalIssues = Array.from(this.state.issueCache.values()).flat().length;
-    if (totalIssues < 5) return;
-    try {
-      const { ContextGraph: ContextGraph2 } = await import("./graph-J4OGTYCO.js");
-      const { IncidentIndex } = await import("./incident-index-BWW2UEY7.js");
-      const { TriePatternDiscovery } = await import("./pattern-discovery-F7LU5K6E.js");
-      const graph = new ContextGraph2(projectPath);
-      const incidentIndex = await IncidentIndex.build(graph, projectPath);
-      const discovery = new TriePatternDiscovery(graph, incidentIndex);
-      const hotPatterns = discovery.discoverHotPatterns(2);
-      for (const hot of hotPatterns) {
-        const existingPatterns = await graph.listNodes();
-        const alreadyExists = existingPatterns.some(
-          (n) => n.type === "pattern" && n.data.description?.includes(hot.path)
-        );
-        if (!alreadyExists) {
-          await graph.addNode("pattern", {
-            description: `${hot.type === "directory" ? "Directory" : "File"} hot zone: ${hot.path}`,
-            appliesTo: [hot.path],
-            confidence: Math.min(0.95, hot.confidence),
-            occurrences: hot.incidentCount,
-            firstSeen: (/* @__PURE__ */ new Date()).toISOString(),
-            lastSeen: (/* @__PURE__ */ new Date()).toISOString(),
-            isAntiPattern: hot.incidentCount >= 3,
-            // 3+ incidents = anti-pattern
-            source: "local"
-          });
-          if (!isInteractiveMode()) {
-            console.error(`   [+] Pattern discovered: ${hot.path} (${hot.incidentCount} issues)`);
-          }
-          if (this.streamingManager) {
-            this.streamingManager.reportSignalExtraction({
-              governance: 0,
-              facts: 1,
-              // Patterns are facts about the codebase
-              blockers: 0,
-              questions: 0
-            });
-          }
-        }
-      }
-      if (totalIssues >= 10) {
-        const coOccurrences = await discovery.discoverCoOccurrences(2);
-        for (const coOcc of coOccurrences.slice(0, 3)) {
-          const desc = `Files break together: ${coOcc.files[0]} + ${coOcc.files[1]}`;
-          const existingPatterns = await graph.listNodes();
-          const alreadyExists = existingPatterns.some(
-            (n) => n.type === "pattern" && n.data.description === desc
-          );
-          if (!alreadyExists) {
-            await graph.addNode("pattern", {
-              description: desc,
-              appliesTo: [...coOcc.files],
-              confidence: Math.min(0.95, coOcc.confidence),
-              occurrences: coOcc.coOccurrences,
-              firstSeen: (/* @__PURE__ */ new Date()).toISOString(),
-              lastSeen: (/* @__PURE__ */ new Date()).toISOString(),
-              isAntiPattern: coOcc.confidence > 0.7,
-              source: "local"
-            });
-            if (!isInteractiveMode()) {
-              console.error(`   [+] Co-occurrence pattern: ${coOcc.files[0]} + ${coOcc.files[1]}`);
-            }
-          }
-        }
-      }
-    } catch (error) {
-      if (!isInteractiveMode()) {
-        console.error(`   [!] Pattern discovery failed: ${error}`);
-      }
-    }
-  }
-  // Defaults -- overridden by config when loaded
-  aiWatcherCooldownMs = 3e4;
-  cleanFileCooldownMs = 3e5;
-  maxFilesPerScan = 5;
-  maxCharsPerFile = 4e3;
-  /**
-   * Use the trie (context graph) to score how urgently a file needs scanning.
-   * Higher score = more worth spending tokens on.
-   */
-  async scoreScanPriority(file, graph, projectPath) {
-    let score = 1;
-    const lastClean = this.state.cleanFiles.get(file);
-    if (lastClean && Date.now() - lastClean < this.cleanFileCooldownMs) {
-      return 0;
-    }
-    const fileNode = await graph.getNode("file", join2(projectPath, file));
-    if (!fileNode) return score;
-    const data = fileNode.data;
-    const riskScores = { critical: 10, high: 6, medium: 2, low: 1 };
-    score += riskScores[data.riskLevel] ?? 1;
-    score += Math.min(data.incidentCount * 3, 12);
-    if (data.changeCount > 10) score += 2;
-    return score;
-  }
-  /**
-   * Roll the token budget window if an hour has passed.
-   * Returns remaining tokens in the current window.
-   */
-  getRemainingBudget() {
-    const budget = this.state.tokenBudget;
-    const elapsed = Date.now() - budget.windowStart;
-    if (elapsed > 36e5) {
-      budget.used = 0;
-      budget.windowStart = Date.now();
-    }
-    return Math.max(0, budget.hourlyLimit - budget.used);
-  }
-  recordTokenUsage(tokens) {
-    this.state.tokenBudget.used += tokens;
-  }
-  /**
-   * AI-powered watcher -- the primary detection system.
-   * 
-   * This is the single AI call that handles:
-   * 1. Code review (bugs, security, logic errors)
-   * 2. Goal violation detection (user-defined quality goals)
-   * 
-   * When goals are active, files with goal violations bypass priority scoring
-   * so violations are always caught. Throttled by cooldown + token budget.
-   */
-  async autoScanFiles(files) {
-    if (!isAIAvailable()) return;
-    if (this.state.autoScanInProgress) return;
-    const now = Date.now();
-    if (now - this.state.lastAutoScan < this.aiWatcherCooldownMs) return;
-    this.state.autoScanInProgress = true;
-    this.state.lastAutoScan = now;
-    const projectPath = this.watchedDirectory || getWorkingDirectory(void 0, true);
-    try {
-      try {
-        const config = await getAutonomyConfig(projectPath);
-        const wc = config.aiWatcher;
-        if (!wc.enabled) return;
-        this.state.tokenBudget.hourlyLimit = wc.hourlyTokenLimit;
-        this.aiWatcherCooldownMs = wc.scanCooldownSec * 1e3;
-        this.cleanFileCooldownMs = wc.cleanFileCooldownSec * 1e3;
-        this.maxFilesPerScan = wc.maxFilesPerScan;
-        this.maxCharsPerFile = wc.maxCharsPerFile;
-      } catch {
-      }
-      const remaining = this.getRemainingBudget();
-      if (remaining < 500) return;
-      try {
-        const graph = new ContextGraph(projectPath);
-        const { getActiveGoals, recordGoalViolationCaught } = await import("./goal-validator-DV6DRSGF.js");
-        console.debug("[AI Watcher] Loading active goals...");
-        const activeGoals = await getActiveGoals(projectPath);
-        const hasGoals = activeGoals.length > 0;
-        console.debug("[AI Watcher] Goals loaded:", {
-          totalGoals: activeGoals.length,
-          hasGoals,
-          goals: activeGoals.map((g) => ({ id: g.id, description: g.description, status: g.status }))
-        });
-        if (this.isQuiet() && !hasGoals) return;
-        const scored = [];
-        for (const file of files) {
-          const relativePath = file.replace(projectPath + "/", "");
-          const score = await this.scoreScanPriority(relativePath, graph, projectPath);
-          if (hasGoals || score > 0) {
-            scored.push({ file, relativePath, score: Math.max(score, hasGoals ? 1 : 0) });
-          } else {
-            this.state.tokenBudget.scansSaved++;
-          }
-        }
-        if (scored.length === 0) return;
-        scored.sort((a, b) => b.score - a.score);
-        const budgetScale = remaining > 2e4 ? 1 : remaining > 1e4 ? 0.6 : 0.4;
-        const maxFiles = Math.max(1, Math.round(this.maxFilesPerScan * budgetScale));
-        const filesToScan = scored.slice(0, maxFiles);
-        const charLimit = Math.round(this.maxCharsPerFile * (remaining > 15e3 ? 1 : 0.5));
-        const fileContents = await Promise.all(
-          filesToScan.map(async ({ file, relativePath }) => {
-            try {
-              const content = await readFile2(file, "utf-8");
-              return { path: relativePath, content: content.slice(0, charLimit) };
-            } catch {
-              return null;
-            }
-          })
-        );
-        const valid = fileContents.filter(Boolean);
-        if (valid.length === 0) return;
-        const filesBlock = valid.map(
-          (f) => `### ${f.path}
-\`\`\`
-${f.content}
-\`\`\``
-        ).join("\n\n");
-        let goalsSection = "";
-        if (hasGoals) {
-          goalsSection = `
-USER-DEFINED GOALS (IMPORTANT - check EVERY file against ALL goals):
-${activeGoals.map((g, i) => `  ${i + 1}. "${g.description}"`).join("\n")}
-
-Goal violations are HIGH PRIORITY. If a file violates any goal, you MUST report it.
-`;
-        }
-        console.debug("[AI Watcher] Sending files to AI analysis:", {
-          fileCount: valid.length,
-          hasGoals,
-          goalsIncluded: hasGoals,
-          filePaths: valid.map((f) => f.path),
-          goalsSection: goalsSection.slice(0, 200) + (goalsSection.length > 200 ? "..." : "")
-        });
-        const result = await runAIAnalysis({
-          systemPrompt: `You are a code quality watcher. You review code for two things:
-
-1. CODE ISSUES: bugs, security vulnerabilities, logic errors, risky patterns
-2. GOAL VIOLATIONS: check every file against the user's quality goals
-${goalsSection}
-Reply ONLY with a JSON array. Each element must have:
-- "file": relative file path
-- "severity": "critical" | "major" | "minor"
-- "description": 1-sentence description of what you found
-- "confidence": number 0-100, how confident you are this is a real issue
-- "suggestedFix": 1-sentence description of what should change to fix it
-- "isGoalViolation": true if this violates a user goal, false otherwise
-- "goalIndex": 0-based index of the violated goal (only if isGoalViolation is true)
-
-Be thorough with goal checking. If a goal says "no emojis" and you see an emoji anywhere in the file, report it with the exact location. If a goal says "no inline styles" and you see a style attribute, report it.
-
-If no issues or violations found, reply with: []
-Output ONLY the JSON array, no markdown fences, no commentary.`,
-          userPrompt: `Review these changed files:
-
-${filesBlock}`,
-          maxTokens: 2048,
-          temperature: 0.1
-        });
-        if (result.tokensUsed) {
-          this.recordTokenUsage(result.tokensUsed.input + result.tokensUsed.output);
-        }
-        console.debug("[AI Watcher] AI analysis result:", {
-          success: result.success,
-          contentLength: result.content ? result.content.length : 0,
-          tokensUsed: result.tokensUsed,
-          contentPreview: result.content ? result.content.slice(0, 500) : "null"
-        });
-        if (!result.success || !result.content.trim()) {
-          console.debug("[AI Watcher] AI analysis failed or returned empty content");
-          return;
-        }
-        let issues = [];
-        try {
-          const cleaned = result.content.replace(/```json?\n?|\n?```/g, "").trim();
-          console.debug("[AI Watcher] Parsing AI response:", { cleanedContent: cleaned.slice(0, 300) });
-          issues = JSON.parse(cleaned);
-          if (!Array.isArray(issues)) issues = [];
-          console.debug("[AI Watcher] Parsed issues:", {
-            totalIssues: issues.length,
-            goalViolations: issues.filter((i) => i.isGoalViolation).length,
-            issueTypes: issues.map((i) => ({ file: i.file, isGoalViolation: i.isGoalViolation, goalIndex: i.goalIndex }))
-          });
-        } catch (error) {
-          console.debug("[AI Watcher] Failed to parse AI response:", error);
-          return;
-        }
-        const issuedFiles = new Set(issues.map((i) => i.file));
-        for (const { relativePath } of filesToScan) {
-          if (!issuedFiles.has(relativePath)) {
-            this.state.cleanFiles.set(relativePath, Date.now());
-          }
-        }
-        if (issues.length === 0) return;
-        for (const issue of issues.slice(0, 10)) {
-          const severity = issue.severity === "critical" ? "critical" : issue.severity === "major" ? "major" : "minor";
-          if (issue.isGoalViolation && issue.goalIndex != null && issue.goalIndex >= 0 && issue.goalIndex < activeGoals.length) {
-            const goal = activeGoals[issue.goalIndex];
-            if (!goal) continue;
-            const confidence = Math.min(100, Math.max(0, issue.confidence ?? 80));
-            const fixId = `fix-${Date.now()}-${Math.random().toString(36).slice(2, 8)}`;
-            console.debug("[AI Watcher] Goal violation detected:", {
-              goalDescription: goal.description,
-              file: issue.file,
-              violation: issue.description,
-              confidence,
-              goalIndex: issue.goalIndex,
-              totalActiveGoals: activeGoals.length
-            });
-            const goalViolationIssue = {
-              id: fixId,
-              file: issue.file,
-              agent: "goal-violation",
-              severity: severity === "critical" ? "critical" : severity === "major" ? "serious" : "moderate",
-              issue: `Goal "${goal.description}" violated: ${issue.description}`,
-              fix: issue.suggestedFix || "Review and fix",
-              category: "goal-violation",
-              confidence,
-              autoFixable: true
-            };
-            await storeIssues([goalViolationIssue], basename2(projectPath), projectPath);
-            await recordGoalViolationCaught(goal, issue.file, projectPath);
-            const confidenceStr = `${confidence}%`;
-            const nudgeMsg = `Goal "${goal.description}" violated in ${issue.file}: ${issue.description} [${confidenceStr} confidence]`;
-            console.debug("[AI Watcher] Sending nudge:", {
-              message: nudgeMsg,
-              file: issue.file,
-              severity: "warning"
-            });
-            getOutputManager().nudge(nudgeMsg, "warning", issue.file);
-            await this.persistNudge({
-              message: nudgeMsg,
-              severity: "warning",
-              file: issue.file,
-              category: "quality",
-              goalId: goal.id,
-              priority: 7,
-              suggestedAction: issue.suggestedFix || "Review and fix manually",
-              relatedIssues: [fixId]
-            });
-            if (this.streamingManager) {
-              this.streamingManager.reportPendingFix({
-                id: fixId,
-                file: issue.file,
-                description: issue.description,
-                goalDescription: goal.description,
-                confidence,
-                severity: issue.severity,
-                suggestedFix: issue.suggestedFix || "Remove the violating code"
-              });
-            }
-            if (!isInteractiveMode()) {
-              console.error(`   [!] Goal violation (${confidenceStr}): ${issue.description}`);
-              console.error(`       Fix: ${issue.suggestedFix || "Review and fix manually"}`);
-            }
-            continue;
-          }
-          const incident = await graph.addNode("incident", {
-            description: issue.description,
-            severity,
-            affectedUsers: null,
-            duration: null,
-            timestamp: (/* @__PURE__ */ new Date()).toISOString(),
-            resolved: false,
-            resolution: null,
-            fixChangeId: null,
-            reportedVia: "detected"
-          });
-          const filePath = join2(projectPath, issue.file);
-          const fileNode = await graph.getNode("file", filePath);
-          if (fileNode) {
-            await graph.addEdge(fileNode.id, incident.id, "affects");
-            const data = fileNode.data;
-            const newRisk = severity === "critical" ? "critical" : severity === "major" ? "high" : data.riskLevel === "low" ? "medium" : data.riskLevel;
-            await graph.updateNode("file", fileNode.id, {
-              incidentCount: (data.incidentCount ?? 0) + 1,
-              riskLevel: newRisk
-            });
-          }
-          this.state.totalIssuesFound++;
-          if (severity !== "minor") {
-            getOutputManager().nudge(
-              `${issue.description}`,
-              severity === "critical" ? "critical" : "warning",
-              issue.file,
-              severity === "critical" ? void 0 : 15e3
-            );
-            await this.persistNudge({
-              message: issue.description,
-              severity: severity === "critical" ? "critical" : "warning",
-              file: issue.file,
-              category: "quality",
-              priority: severity === "critical" ? 9 : 6,
-              ...issue.suggestedFix && { suggestedAction: issue.suggestedFix }
-            });
-          }
-        }
-        if (this.streamingManager && issues.length > 0) {
-          this.streamingManager.reportSignalExtraction({
-            governance: 0,
-            facts: 0,
-            blockers: issues.length,
-            questions: 0
-          });
-        }
-      } catch (error) {
-        getOutputManager().log("warn", `AI watcher error: ${error}`);
-      }
-    } finally {
-      this.state.autoScanInProgress = false;
-    }
-  }
-  /**
-   * Initial hypothesis generation when watch starts.
-   *
-   * This generates hypotheses from existing patterns and issues to give
-   * users immediate insights about their codebase.
-   */
-  async initialHypothesisGeneration() {
-    if (!isAIAvailable()) {
-      console.debug("[Initial Hypothesis] AI not available, skipping initial hypothesis generation");
-      return;
-    }
-    const projectPath = this.watchedDirectory || getWorkingDirectory(void 0, true);
-    console.debug("[Initial Hypothesis] Starting initial hypothesis generation", { projectPath });
-    try {
-      const { getHypothesisEngine } = await import("./hypothesis-O72ZLVOW.js");
-      const hypothesisEngine = getHypothesisEngine(projectPath);
-      console.debug("[Initial Hypothesis] Running AI-powered hypothesis generation...");
-      const generated = await hypothesisEngine.generateHypothesesWithAI({
-        recentIssues: [],
-        // No recent issues yet on startup
-        patterns: [],
-        observations: ["Initial watch session started", "Analyzing codebase for potential patterns"]
-      });
-      console.debug("[Initial Hypothesis] Generated hypotheses on startup:", {
-        count: generated.length,
-        hypotheses: generated.map((h) => ({ statement: h.statement, confidence: h.confidence }))
-      });
-      if (generated.length > 0) {
-        const { getOutputManager: getOutputManager2 } = await import("./output-manager-DZO5LGSG.js");
-        const outputManager = getOutputManager2();
-        for (const hypothesis of generated.slice(0, 2)) {
-          const message = `[Initial Hypothesis] "${hypothesis.statement}" (${Math.round(hypothesis.confidence * 100)}% confidence)`;
-          outputManager.nudge(message, "info", void 0, 1e4);
-          if (!isInteractiveMode()) {
-            console.error(`   [?] ${message}`);
-          }
-        }
-        if (this.streamingManager) {
-          this.streamingManager.reportSignalExtraction({
-            governance: 0,
-            facts: 0,
-            blockers: 0,
-            questions: generated.length
-          });
-        }
-      }
-    } catch (error) {
-      console.debug("[Initial Hypothesis] Failed to generate initial hypotheses:", error);
-    }
-  }
-  /**
-   * Initial goal compliance scan when watch starts.
-   * 
-   * This checks recently modified files against active goals so the user
-   * gets immediate feedback about goal violations without waiting for files
-   * to be changed.
-   * 
-   * Strategy:
-   * 1. Check if there are any active goals - if not, skip
-   * 2. Find recently modified files (last 24 hours OR uncommitted changes)
-   * 3. Filter to watched file types
-   * 4. Run a quick AI scan focused only on goal violations
-   * 5. Nudge the user about any violations found
-   */
-  async initialGoalComplianceScan() {
-    if (!isAIAvailable()) {
-      console.debug("[Initial Scan] AI not available, skipping initial goal compliance scan");
-      return;
-    }
-    const projectPath = this.watchedDirectory || getWorkingDirectory(void 0, true);
-    console.debug("[Initial Scan] Starting initial goal compliance scan", { projectPath });
-    try {
-      const { getActiveGoals, recordGoalViolationCaught } = await import("./goal-validator-DV6DRSGF.js");
-      const activeGoals = await getActiveGoals(projectPath);
-      console.debug("[Initial Scan] Loaded goals for initial scan:", {
-        goalCount: activeGoals.length,
-        goals: activeGoals.map((g) => ({ id: g.id, description: g.description }))
-      });
-      if (activeGoals.length === 0) {
-        console.debug("[Initial Scan] No active goals found, skipping initial scan");
-        return;
-      }
-      if (!isInteractiveMode()) {
-        console.error("[*] Checking recent files against active goals...");
-      }
-      const recentFiles = /* @__PURE__ */ new Set();
-      const uncommittedFiles = await getGitChangedFiles(projectPath);
-      if (uncommittedFiles) {
-        uncommittedFiles.forEach((f) => recentFiles.add(join2(projectPath, f)));
-      }
-      const oneDayAgo = Date.now() - 24 * 60 * 60 * 1e3;
-      const recentChanges = await getChangedFilesSinceTimestamp(projectPath, oneDayAgo);
-      if (recentChanges) {
-        recentChanges.forEach((f) => recentFiles.add(f));
-      }
-      const filesToCheck = Array.from(recentFiles).filter((file) => {
-        const ext = extname2(file).toLowerCase();
-        return WATCH_EXTENSIONS.has(ext) && existsSync2(file);
-      });
-      console.debug("[Initial Scan] Files discovered for initial scan:", {
-        totalRecentFiles: recentFiles.size,
-        filteredFiles: filesToCheck.length,
-        filePaths: filesToCheck.slice(0, 5).map((f) => f.replace(projectPath + "/", "")),
-        // Show first 5
-        watchedExtensions: Array.from(WATCH_EXTENSIONS)
-      });
-      if (filesToCheck.length === 0) {
-        console.debug("[Initial Scan] No recent files found for initial scan");
-        return;
-      }
-      const maxInitialFiles = 10;
-      const filesToScan = filesToCheck.slice(0, maxInitialFiles);
-      if (!isInteractiveMode()) {
-        console.error(`   Scanning ${filesToScan.length} recent file(s) against ${activeGoals.length} goal(s)...`);
-      }
-      const maxCharsPerFile = 3e3;
-      const fileContents = await Promise.all(
-        filesToScan.map(async (file) => {
-          try {
-            const content = await readFile2(file, "utf-8");
-            const relativePath = file.replace(projectPath + "/", "");
-            return { path: relativePath, content: content.slice(0, maxCharsPerFile) };
-          } catch {
-            return null;
-          }
-        })
-      );
-      const valid = fileContents.filter(Boolean);
-      if (valid.length === 0) return;
-      const filesBlock = valid.map(
-        (f) => `### ${f.path}
-\`\`\`
-${f.content}
-\`\`\``
-      ).join("\n\n");
-      const goalsSection = `
-USER-DEFINED GOALS (check EVERY file against ALL goals):
-${activeGoals.map((g, i) => `  ${i + 1}. "${g.description}"`).join("\n")}
-
-This is an INITIAL SCAN at watch startup. Report ALL goal violations you find.
-`;
-      const result = await runAIAnalysis({
-        systemPrompt: `You are checking code for GOAL VIOLATIONS ONLY.
-${goalsSection}
-Reply ONLY with a JSON array. Each element must have:
-- "file": relative file path
-- "severity": "critical" | "major" | "minor"
-- "description": 1-sentence description of the goal violation
-- "confidence": number 0-100, how confident you are this is a violation
-- "suggestedFix": 1-sentence description of what should change
-- "isGoalViolation": true (always true for this scan)
-- "goalIndex": 0-based index of the violated goal
-
-Be thorough. If a goal says "no emojis" and you see ANY emoji in the file, report it. If a goal says "no console.log" and you see console.log, report it.
-
-If no violations found, reply with: []
-Output ONLY the JSON array, no markdown fences, no commentary.`,
-        userPrompt: `Check these files for goal violations:
-
-${filesBlock}`,
-        maxTokens: 2048,
-        temperature: 0.1
-      });
-      if (result.tokensUsed) {
-        this.recordTokenUsage(result.tokensUsed.input + result.tokensUsed.output);
-      }
-      if (!result.success || !result.content.trim()) return;
-      let issues = [];
-      try {
-        const parsed = JSON.parse(result.content.trim());
-        issues = Array.isArray(parsed) ? parsed : [];
-      } catch {
-        return;
-      }
-      const issuesToStore = [];
-      let violationsFound = 0;
-      for (const issue of issues) {
-        if (!issue.isGoalViolation || issue.confidence < 40) continue;
-        violationsFound++;
-        if (issue.goalIndex != null && issue.goalIndex >= 0 && issue.goalIndex < activeGoals.length) {
-          const goal = activeGoals[issue.goalIndex];
-          if (!goal) continue;
-          const fixId = `fix-${Date.now()}-${Math.random().toString(36).slice(2, 8)}`;
-          issuesToStore.push({
-            id: fixId,
-            file: issue.file,
-            agent: "goal-violation",
-            severity: issue.severity === "critical" ? "critical" : issue.severity === "major" ? "serious" : "moderate",
-            issue: `Goal "${goal.description}" violated: ${issue.description}`,
-            fix: issue.suggestedFix || "Review and fix",
-            category: "goal-violation",
-            confidence: issue.confidence,
-            autoFixable: true
-          });
-          await recordGoalViolationCaught(goal, issue.file, projectPath);
-          const confidenceStr = issue.confidence >= 80 ? "high" : issue.confidence >= 60 ? "medium" : "low";
-          const nudgeMsg = `Goal "${goal.description}" violated in ${issue.file}: ${issue.description} [${confidenceStr} confidence]`;
-          getOutputManager().nudge(nudgeMsg, "warning", issue.file);
-          await this.persistNudge({
-            message: nudgeMsg,
-            severity: "warning",
-            file: issue.file,
-            category: "quality",
-            goalId: goal.id,
-            priority: issue.confidence >= 80 ? 8 : issue.confidence >= 60 ? 6 : 4,
-            ...issue.suggestedFix && { suggestedAction: issue.suggestedFix }
-          });
-        }
-      }
-      if (issuesToStore.length > 0) {
-        await storeIssues(issuesToStore, basename2(projectPath), projectPath);
-      }
-      if (!isInteractiveMode()) {
-        if (violationsFound > 0) {
-          console.error(`   [!] Found ${violationsFound} goal violation(s) in recent files`);
-        } else {
-          console.error(`   [\u2713] No goal violations found in recent files`);
-        }
-      }
-    } catch (error) {
-      if (!isInteractiveMode()) {
-        console.error(`   [!] Initial goal scan error: ${error}`);
-      }
-    }
-  }
-  async syncPipelineIntegrations() {
-    const projectPath = this.watchedDirectory || getWorkingDirectory(void 0, true);
-    try {
-      const config = await loadConfig();
-      const hasLinear = !!(config.apiKeys?.linear ?? process.env.LINEAR_API_KEY);
-      const hasGithub = !!(config.apiKeys?.github ?? process.env.GITHUB_TOKEN);
-      if (!hasLinear && !hasGithub) return;
-      const graph = new ContextGraph(projectPath);
-      if (hasLinear) {
-        try {
-          const { LinearIngester: LinearIngester2 } = await import("./linear-ingester-JRDQAIAA.js");
-          const ingester = new LinearIngester2(projectPath, graph);
-          await ingester.syncTickets();
-          if (!isInteractiveMode()) {
-            console.error("[Pipeline] Linear tickets synced");
-          }
-        } catch (error) {
-          if (!isInteractiveMode()) {
-            console.error(`[Pipeline] Linear sync failed: ${error}`);
-          }
-        }
-      }
-      if (hasGithub) {
-        try {
-          const { GitHubIngester: GitHubIngester2 } = await import("./github-ingester-J2ZFYXVE.js");
-          const ingester = new GitHubIngester2(graph);
-          const token = await ingester.getApiToken();
-          const repoInfo = ingester.getRepoInfo(projectPath);
-          if (repoInfo) {
-            await ingester.syncPullRequests(repoInfo.owner, repoInfo.name, token);
-            await ingester.syncIssues(repoInfo.owner, repoInfo.name, token);
-            if (!isInteractiveMode()) {
-              console.error("[Pipeline] GitHub PRs/issues synced");
-            }
-          }
-        } catch (error) {
-          if (!isInteractiveMode()) {
-            console.error(`[Pipeline] GitHub sync failed: ${error}`);
-          }
-        }
-      }
-    } catch {
-    }
-  }
-  async stopWatching() {
-    if (!this.state.isRunning) {
-      return {
-        content: [{
-          type: "text",
-          text: "[!] Watch mode is not running."
-        }]
-      };
-    }
-    for (const watcher of this.watchers.values()) {
-      watcher.close();
-    }
-    this.watchers.clear();
-    if (this.extractionPipeline) {
-      this.extractionPipeline.close();
-      this.extractionPipeline = null;
-    }
-    if (this.pipelineSyncTimer) {
-      clearInterval(this.pipelineSyncTimer);
-      this.pipelineSyncTimer = null;
-    }
-    if (this.codebaseIndex) {
-      await this.codebaseIndex.save();
-      this.codebaseIndex = null;
-    }
-    if (this.state.scanDebounceTimer) {
-      clearTimeout(this.state.scanDebounceTimer);
-    }
-    this.state.isRunning = false;
-    if (!isInteractiveMode()) {
-      console.error("\n[*] Watch mode stopped.\n");
-    }
-    if (this.streamingManager) {
-      this.streamingManager.reportWatchStatus({ watching: false, directories: 0 });
-    }
-    const outputManager = getOutputManager();
-    outputManager.clearTUICallbacks();
-    outputManager.setMode("console");
-    if (this.dashboard) {
-      this.dashboard.stop();
-      this.dashboard = void 0;
-    }
-    const budget = this.state.tokenBudget;
-    const tokensK = (budget.used / 1e3).toFixed(1);
-    return {
-      content: [{
-        type: "text",
-        text: `[*] **TRIE AGENT STOPPED**
-
-### Session Summary:
-- Files scanned: ${this.state.filesScanned}
-- Issues found: ${this.state.totalIssuesFound}
-- Tokens used: ${tokensK}k / ${(budget.hourlyLimit / 1e3).toFixed(0)}k hourly limit
-- Scans skipped (trie-throttled): ${budget.scansSaved}
-- Governance ledger: Updated continuously
-
-Use \`trie_watch start\` to resume.`
-      }]
-    };
-  }
-  async getStatus() {
-    if (!this.state.isRunning) {
-      return {
-        content: [{
-          type: "text",
-          text: `[*] **Watch Mode Status: STOPPED**
-
-Use \`trie_watch start\` to begin autonomous scanning.`
-        }]
-      };
-    }
-    const recentScans = Array.from(this.state.lastScan.entries()).sort((a, b) => b[1] - a[1]).slice(0, 5).map(([file, time]) => {
-      const ago = Math.round((Date.now() - time) / 1e3);
-      return `- \`${basename2(file)}\` (${ago}s ago)`;
-    }).join("\n");
-    const recentNudges = this.state.nudges.slice(-3).map(
-      (n) => `- ${basename2(n.file)} [${n.severity}] @ ${n.timestamp}`
-    ).join("\n");
-    let agencyStatus = "";
-    try {
-      const { getTrieAgent } = await import("./trie-agent-ET3DAP5Y.js");
-      const trieAgent = getTrieAgent(this.watchedDirectory || getWorkingDirectory(void 0, true));
-      await trieAgent.initialize();
-      const status = await trieAgent.getAgencyStatus();
-      agencyStatus = `
-### [AI] Trie Agent:
-- **Goals:** ${status.goals.active} active, ${status.goals.completed} completed${status.goals.topGoal ? ` (${status.goals.topGoal.slice(0, 40)}...)` : ""}
-- **Hypotheses:** ${status.hypotheses.testing} testing, ${status.hypotheses.validated} validated
-- **Risk Level:** ${status.riskLevel.toUpperCase()}
-- **Effectiveness:** ${status.effectiveness}%
-- **Scan Frequency:** ${Math.round(status.scanFrequency / 1e3)}s${status.isQuietHours ? " (quiet hours)" : ""}`;
-    } catch {
-    }
-    const budget = this.state.tokenBudget;
-    const remaining = this.getRemainingBudget();
-    const tokensK = (budget.used / 1e3).toFixed(1);
-    const remainingK = (remaining / 1e3).toFixed(1);
-    return {
-      content: [{
-        type: "text",
-        text: `[*] **WATCH MODE Status: RUNNING**
-
-### Stats:
-- Directories watched: ${this.watchers.size}
-- Files scanned: ${this.state.filesScanned}
-- Issues found: ${this.state.totalIssuesFound}
-- Pending: ${this.state.pendingFiles.size}
-
-### Token Budget:
-- Used: ${tokensK}k / ${(budget.hourlyLimit / 1e3).toFixed(0)}k hourly
-- Remaining: ${remainingK}k
-- Scans skipped (trie-throttled): ${budget.scansSaved}
-${agencyStatus}
-
-### Recently Scanned:
-${recentScans || "(none yet)"}
-
-### Recent Nudges:
-${recentNudges || "(none)"}
-
-### Commands:
-- \`trie_watch issues\` - Get all issues found
-- \`trie_watch stop\` - Stop watching`
-      }]
-    };
-  }
-  /**
-   * Helper to persist a nudge to both in-memory state and SQL storage
-   */
-  async persistNudge(params) {
-    const timestamp = (/* @__PURE__ */ new Date()).toISOString();
-    const nudgeId = createHash("sha256").update(`${params.message}|${params.file || ""}|${timestamp}`).digest("hex").slice(0, 16);
-    const nudge = {
-      id: nudgeId,
-      message: params.message,
-      severity: params.severity,
-      timestamp,
-      resolved: false,
-      dismissed: false,
-      priority: params.priority ?? 5,
-      relatedIssues: params.relatedIssues ?? [],
-      metadata: {},
-      ...params.file && { file: params.file },
-      ...params.category && { category: params.category },
-      ...params.goalId && { goalId: params.goalId },
-      ...params.suggestedAction && { suggestedAction: params.suggestedAction }
-    };
-    this.state.nudges.push({
-      file: params.file || "unknown",
-      // Keep full path for consistency with loaded nudges
-      message: params.message,
-      severity: params.severity === "warning" || params.severity === "info" ? "high" : params.severity,
-      timestamp: (/* @__PURE__ */ new Date()).toLocaleTimeString("en-US", { hour12: false })
-    });
-    try {
-      const storage = getStorage(this.watchedDirectory);
-      await storage.storeNudge(nudge);
-      console.debug(`[Watch] \u2713 Persisted nudge to storage: ${nudge.message.slice(0, 60)}...`);
-    } catch (error) {
-      console.error("[Watch] Failed to persist nudge to storage:", error);
-    }
-  }
-  getNudges() {
-    return {
-      content: [
-        {
-          type: "text",
-          text: `[#] Recent nudges (${this.state.nudges.length} this session)
-` + (this.state.nudges.length ? this.state.nudges.map(
-            (n) => `- ${basename2(n.file)} [${n.severity}] @ ${n.timestamp}
-  ${n.message}`
-          ).join("\n") : "(none)")
-        },
-        {
-          type: "json",
-          json: this.state.nudges
-        }
-      ]
-    };
-  }
-  getCurrentIssues() {
-    return {
-      content: [{
-        type: "text",
-        text: `[L] **Issues Found This Session**
-
-Total issues: ${this.state.totalIssuesFound}
-Files scanned: ${this.state.filesScanned}
-
-To get a full report, run \`trie_scan\` on your codebase.`
-      }]
-    };
-  }
-};
-
-// src/tools/pr-review.ts
-import { readFile as readFile3 } from "fs/promises";
-import { existsSync as existsSync3 } from "fs";
-import { join as join3, basename as basename3, resolve as resolve2, isAbsolute as isAbsolute2 } from "path";
-
-// src/skills/built-in/super-reviewer.ts
-var CRITICAL_REVIEW_CHECKLIST = {
-  stateAndLifecycle: [
-    "Uninitialized state accessed before setup",
-    "Missing cleanup on unmount/dispose",
-    "State mutations in wrong lifecycle phase"
-  ],
-  edgeCasesAndRaces: [
-    "Race conditions in async operations",
-    "Missing error handling for edge cases",
-    "Unhandled promise rejections"
-  ],
-  missingPieces: [
-    "Missing input validation",
-    "Missing error handling",
-    "Missing logging/monitoring"
-  ]
-};
-var SuperReviewerAgent = class {
-  async review(_files) {
-    return { issues: [] };
-  }
-  async buildReviewWorkflow(files, context) {
-    return { files, context };
-  }
-};
-
 // src/tools/pr-review.ts
+import { readFile as readFile2 } from "fs/promises";
+import { existsSync as existsSync2 } from "fs";
+import { join as join2, basename as basename2, resolve as resolve2, isAbsolute as isAbsolute2 } from "path";
 var TriePRReviewTool = class {
-  agent = new SuperReviewerAgent();
+  // Review workflow is now ledger-driven; keep a lightweight built-in checklist.
+  CRITICAL_REVIEW_CHECKLIST = {
+    stateAndLifecycle: [
+      "Uninitialized state accessed before setup",
+      "Missing cleanup on unmount/dispose",
+      "State mutations in wrong lifecycle phase"
+    ],
+    edgeCasesAndRaces: [
+      "Race conditions in async operations",
+      "Missing error handling for edge cases",
+      "Unhandled promise rejections"
+    ],
+    missingPieces: [
+      "Missing input validation",
+      "Missing error handling",
+      "Missing logging/monitoring"
+    ]
+  };
   exec(command, cwd, maxBuffer) {
     const opts = {
       captureOutput: false,
@@ -2272,18 +848,15 @@ Usage:
         };
       }
       const designDocs = await this.findDesignDocs(changes.files, prInfo);
-      const workflow = await this.agent.buildReviewWorkflow(
-        changes.files,
-        {
-          prNumber: prInfo.number,
-          prTitle: prInfo.title,
-          prAuthor: prInfo.author,
-          baseBranch: prInfo.baseBranch,
-          headBranch: prInfo.headBranch,
-          mode: mode || "own",
-          designDocs
-        }
-      );
+      const workflow = this.buildReviewWorkflow(changes.files, {
+        ...prInfo.number ? { prNumber: prInfo.number } : {},
+        ...prInfo.title ? { prTitle: prInfo.title } : {},
+        ...prInfo.author ? { prAuthor: prInfo.author } : {},
+        ...prInfo.baseBranch ? { baseBranch: prInfo.baseBranch } : {},
+        ...prInfo.headBranch ? { headBranch: prInfo.headBranch } : {},
+        mode: mode || "own",
+        designDocs
+      });
       const fileContents = await this.preloadFiles(changes.files.map((f) => f.path));
       const reviewPrompt = this.generateReviewPrompt(workflow, changes, fileContents);
       return {
@@ -2307,14 +880,14 @@ Usage:
   async getPRInfo(pr, worktree) {
     if (worktree) {
       const worktreePath = isAbsolute2(worktree) ? worktree : resolve2(getWorkingDirectory(void 0, true), worktree);
-      if (!existsSync3(worktreePath)) {
+      if (!existsSync2(worktreePath)) {
         return { success: false, error: `Worktree not found: ${worktreePath}` };
       }
       return {
         success: true,
         type: "worktree",
         path: worktreePath,
-        title: `Local changes in ${basename3(worktreePath)}`,
+        title: `Local changes in ${basename2(worktreePath)}`,
         author: this.getGitUser(),
         baseBranch: "HEAD~1",
         headBranch: "HEAD"
@@ -2422,6 +995,36 @@ Usage:
     }
     return files;
   }
+  buildReviewWorkflow(files, context) {
+    const totalAdditions = files.reduce((sum, f) => sum + (f.additions || 0), 0);
+    const totalDeletions = files.reduce((sum, f) => sum + (f.deletions || 0), 0);
+    const reviewMode = context.mode === "others" ? "others" : "own";
+    const reviewInstructions = {
+      mode: reviewMode,
+      description: reviewMode === "own" ? "Your PR \u2014 focus on footguns, missing tests, and production risks." : "Someone else's PR \u2014 focus on correctness, clarity, and maintainability."
+    };
+    const sorted = [...files].sort((a, b) => a.path.localeCompare(b.path));
+    const fileOrder = sorted.map((f, i) => ({
+      index: i + 1,
+      path: f.path,
+      reason: i === 0 ? "Start here to establish baseline context" : "Proceed in filename order"
+    }));
+    return {
+      metadata: {
+        ...context.prNumber ? { prNumber: context.prNumber } : {},
+        prTitle: context.prTitle || "PR Review",
+        prAuthor: context.prAuthor || "unknown",
+        baseBranch: context.baseBranch || "unknown",
+        headBranch: context.headBranch || "unknown",
+        totalFiles: files.length,
+        totalAdditions,
+        totalDeletions,
+        designDocs: context.designDocs
+      },
+      fileOrder,
+      reviewInstructions
+    };
+  }
   /**
    * Find related design docs
    */
@@ -2440,8 +1043,8 @@ Usage:
       "rfcs"
     ];
     for (const docPath of designDocPaths) {
-      const fullPath = join3(cwd, docPath);
-      if (existsSync3(fullPath)) {
+      const fullPath = join2(cwd, docPath);
+      if (existsSync2(fullPath)) {
       }
     }
     return designDocs;
@@ -2454,9 +1057,9 @@ Usage:
     const cwd = getWorkingDirectory(void 0, true);
     await Promise.all(filePaths.map(async (filePath) => {
       try {
-        const fullPath = isAbsolute2(filePath) ? filePath : join3(cwd, filePath);
-        if (existsSync3(fullPath)) {
-          const content = await readFile3(fullPath, "utf-8");
+        const fullPath = isAbsolute2(filePath) ? filePath : join2(cwd, filePath);
+        if (existsSync2(fullPath)) {
+          const content = await readFile2(fullPath, "utf-8");
           contents.set(filePath, content);
         }
       } catch {
@@ -2537,21 +1140,21 @@ Usage:
 `;
     prompt += `**State & Lifecycle:**
 `;
-    for (const check of CRITICAL_REVIEW_CHECKLIST.stateAndLifecycle) {
+    for (const check of this.CRITICAL_REVIEW_CHECKLIST.stateAndLifecycle) {
       prompt += `- ${check}
 `;
     }
     prompt += `
 **Edge Cases & Races:**
 `;
-    for (const check of CRITICAL_REVIEW_CHECKLIST.edgeCasesAndRaces) {
+    for (const check of this.CRITICAL_REVIEW_CHECKLIST.edgeCasesAndRaces) {
       prompt += `- ${check}
 `;
     }
     prompt += `
 **Missing Pieces:**
 `;
-    for (const check of CRITICAL_REVIEW_CHECKLIST.missingPieces) {
+    for (const check of this.CRITICAL_REVIEW_CHECKLIST.missingPieces) {
       prompt += `- ${check}
 `;
     }
@@ -2899,7 +1502,7 @@ var TrieInitTool = class {
       "",
       "1. Edit `.trie/PROJECT.md` with your project description",
       "2. Define coding standards in `.trie/RULES.md`",
-      "3. Run `trie_scan` to analyze your codebase",
+      "3. Run `trie watch` to analyze your codebase",
       '4. Run `trie_init` with action="complete" when setup is done'
     );
     return lines.join("\n");
@@ -3568,11 +2171,7 @@ var ToolRegistry = class {
           properties: {
             action: {
               type: "string",
-              description: "Optional quick action: security, legal, bugs, types, devops, architecture, ux, clean, soc2, performance, e2e, visual_qa, data_flow, agent_smith, pr_review, watch, fix, explain"
-            },
-            agent: {
-              type: "string",
-              description: "Agent key when action=agent or when using a custom skill name"
+              description: "Optional quick action: pr_review, watch, fix, explain, test, visual_qa_browser"
             },
             files: {
               type: "array",
@@ -3623,7 +2222,7 @@ var ToolRegistry = class {
             issueIds: {
               type: "array",
               items: { type: "string" },
-              description: "Issue IDs to dispatch (from trie_scan). If omitted, dispatches all cloud-eligible pending issues. IGNORED if file+issue+fix are provided (ad-hoc mode)."
+              description: "Issue IDs to dispatch (from trie_fix/watch). If omitted, dispatches all cloud-eligible pending issues. IGNORED if file+issue+fix are provided (ad-hoc mode)."
             },
             forceCloud: {
               type: "boolean",
@@ -3817,7 +2416,7 @@ var ToolRegistry = class {
       },
       {
         name: "trie_init",
-        description: "Initialize bootstrap files (.trie/RULES.md, .trie/TEAM.md, .trie/BOOTSTRAP.md). Detects stack and suggests skills.",
+        description: "Initialize bootstrap files (.trie/RULES.md, .trie/TEAM.md, .trie/BOOTSTRAP.md). Detects stack.",
         inputSchema: {
           type: "object",
           properties: {
@@ -4149,17 +2748,10 @@ var ToolRegistry = class {
 };
 
 // src/server/resource-manager.ts
-import { readdir, readFile as readFile4 } from "fs/promises";
-import { existsSync as existsSync4 } from "fs";
-import { join as join4, dirname as dirname2 } from "path";
+import { readdir, readFile as readFile3 } from "fs/promises";
+import { existsSync as existsSync3 } from "fs";
+import { join as join3, dirname as dirname2 } from "path";
 import { fileURLToPath } from "url";
-
-// src/skills/installer.ts
-async function listInstalledSkills() {
-  return [];
-}
-
-// src/server/resource-manager.ts
 var UI_APPS = {
   "ledger": {
     name: "Decision Ledger",
@@ -4183,7 +2775,6 @@ var UI_APPS = {
   }
 };
 var ResourceManager = class {
-  skillRegistry = getSkillRegistry();
   /**
    * Get all available resources dynamically
    */
@@ -4208,12 +2799,6 @@ var ResourceManager = class {
         description: "Detailed context state with scan history and priorities",
         mimeType: "application/json"
       },
-      {
-        uri: "trie://skills",
-        name: "Available Skills",
-        description: "List of all available Trie skills (built-in and custom)",
-        mimeType: "application/json"
-      },
       {
         uri: "trie://config",
         name: "Trie Configuration",
@@ -4232,12 +2817,6 @@ var ResourceManager = class {
         description: "Summary of loaded vulnerability detection signatures",
         mimeType: "application/json"
       },
-      {
-        uri: "trie://skills/installed",
-        name: "Installed Skills",
-        description: "External skills installed from skills.sh that Trie can apply",
-        mimeType: "application/json"
-      },
       {
         uri: "trie://bootstrap",
         name: "Bootstrap Status",
@@ -4270,13 +2849,12 @@ var ResourceManager = class {
       }
     );
     resources.push(...await this.getScanReportResources());
-    resources.push(...await this.getCustomSkillResources());
     resources.push(...this.getUIAppResources());
     return resources;
   }
   async getScanReportResources() {
     try {
-      const reportsDir = join4(getWorkingDirectory(void 0, true), "trie-reports");
+      const reportsDir = join3(getWorkingDirectory(void 0, true), "trie-reports");
       const files = await readdir(reportsDir);
       const reportFiles = files.filter((f) => f.endsWith(".txt") || f.endsWith(".json"));
       return reportFiles.slice(0, 10).map((file) => ({
@@ -4289,20 +2867,6 @@ var ResourceManager = class {
       return [];
     }
   }
-  async getCustomSkillResources() {
-    try {
-      await this.skillRegistry.loadCustomSkills();
-      const customSkills = this.skillRegistry.getCustomSkills();
-      return customSkills.map((skill) => ({
-        uri: `trie://skills/custom/${skill.name}`,
-        name: `Custom Skill: ${skill.name}`,
-        description: skill.description,
-        mimeType: "application/json"
-      }));
-    } catch {
-      return [];
-    }
-  }
   /**
    * Read content for a specific resource
    */
@@ -4321,12 +2885,6 @@ var ResourceManager = class {
     if (parsedUri === "context/state") {
       return await this.getContextStateResource(uri);
     }
-    if (parsedUri === "skills") {
-      return await this.getBuiltInSkillsResource(uri);
-    }
-    if (parsedUri.startsWith("skills/custom/")) {
-      return await this.getCustomSkillResource(uri, parsedUri);
-    }
     if (parsedUri === "config") {
       return await this.getConfigResource(uri);
     }
@@ -4336,9 +2894,6 @@ var ResourceManager = class {
     if (parsedUri === "signatures") {
       return await this.getSignaturesResource(uri);
     }
-    if (parsedUri === "skills/installed") {
-      return await this.getInstalledSkillsResource(uri);
-    }
     if (parsedUri === "bootstrap") {
       return await this.getBootstrapResource(uri);
     }
@@ -4376,10 +2931,10 @@ var ResourceManager = class {
   async getUIAppResource(uri, appId) {
     const currentFile = fileURLToPath(import.meta.url);
     const distDir = dirname2(dirname2(currentFile));
-    const uiDir = join4(distDir, "ui");
-    const htmlPath = join4(uiDir, `${appId}.html`);
+    const uiDir = join3(distDir, "ui");
+    const htmlPath = join3(uiDir, `${appId}.html`);
     try {
-      if (!existsSync4(htmlPath)) {
+      if (!existsSync3(htmlPath)) {
         return {
           contents: [{
             uri,
@@ -4388,7 +2943,7 @@ var ResourceManager = class {
           }]
         };
       }
-      const content = await readFile4(htmlPath, "utf-8");
+      const content = await readFile3(htmlPath, "utf-8");
       return {
         contents: [{
           uri,
@@ -4554,24 +3109,16 @@ var ResourceManager = class {
     summary.push("## Available Tools", "");
     summary.push("| Tool | Purpose |");
     summary.push("|------|---------|");
-    summary.push("| `trie_scan` | Scan code with intelligent agent selection |");
+    summary.push("| `trie_fix` | Apply high-confidence fixes |");
     summary.push("| `trie_fix` | Generate fix recommendations |");
     summary.push("| `trie_memory` | Search issue history |");
     summary.push("| `trie_init` | Initialize bootstrap files |");
     summary.push("");
-    try {
-      const skills = await listInstalledSkills();
-      if (skills.length > 0) {
-        summary.push(`**Skills:** ${skills.length} installed (${skills.slice(0, 3).map((s) => s.name).join(", ")}${skills.length > 3 ? "..." : ""})`);
-        summary.push("");
-      }
-    } catch {
-    }
     summary.push("---", "", "# Detailed Context", "");
-    const agentsMdPath = join4(getTrieDirectory(workDir), "AGENTS.md");
+    const agentsMdPath = join3(getTrieDirectory(workDir), "AGENTS.md");
     try {
-      if (existsSync4(agentsMdPath)) {
-        const agentsContent = await readFile4(agentsMdPath, "utf-8");
+      if (existsSync3(agentsMdPath)) {
+        const agentsContent = await readFile3(agentsMdPath, "utf-8");
         summary.push(agentsContent);
       } else {
         const contextSummary = await getContextForAI();
@@ -4649,41 +3196,6 @@ This information is automatically available to Claude Code, Cursor, and other AI
       }]
     };
   }
-  async getBuiltInSkillsResource(uri) {
-    await this.skillRegistry.loadCustomSkills();
-    const skills = this.skillRegistry.getSkillDescriptions();
-    return {
-      contents: [{
-        uri,
-        mimeType: "application/json",
-        text: JSON.stringify({
-          totalSkills: skills.length,
-          builtinCount: skills.filter((a) => !a.isCustom).length,
-          customCount: skills.filter((a) => a.isCustom).length,
-          skills: skills.map((a) => ({
-            name: a.name,
-            description: a.description,
-            type: a.isCustom ? "custom" : "builtin"
-          }))
-        }, null, 2)
-      }]
-    };
-  }
-  async getCustomSkillResource(uri, parsedUri) {
-    const skillName = parsedUri.replace("skills/custom/", "");
-    await this.skillRegistry.loadCustomSkills();
-    const metadata = this.skillRegistry.getCustomSkillMetadata(skillName);
-    if (!metadata) {
-      throw new Error(`Custom skill not found: ${skillName}`);
-    }
-    return {
-      contents: [{
-        uri,
-        mimeType: "application/json",
-        text: JSON.stringify(metadata, null, 2)
-      }]
-    };
-  }
   async getConfigResource(uri) {
     const config = await loadConfig();
     return {
@@ -4696,8 +3208,8 @@ This information is automatically available to Claude Code, Cursor, and other AI
   }
   async getCacheStatsResource(uri) {
     try {
-      const cachePath = join4(getTrieDirectory(getWorkingDirectory(void 0, true)), ".trie-cache.json");
-      const cacheContent = await readFile4(cachePath, "utf-8");
+      const cachePath = join3(getTrieDirectory(getWorkingDirectory(void 0, true)), ".trie-cache.json");
+      const cacheContent = await readFile3(cachePath, "utf-8");
       const cache = JSON.parse(cacheContent);
       const fileCount = Object.keys(cache.files || {}).length;
       const totalVulns = Object.values(cache.files || {}).reduce((acc, file) => {
@@ -4724,15 +3236,15 @@ This information is automatically available to Claude Code, Cursor, and other AI
           mimeType: "application/json",
           text: JSON.stringify({
             error: "No cache found. Run a scan first to build the cache.",
-            hint: "Use trie_scan to scan your codebase"
+            hint: "Run trie watch to analyze your codebase"
           }, null, 2)
         }]
       };
     }
   }
   async getSignaturesResource(uri) {
-    const { getVulnerabilityStats } = await import("./vulnerability-signatures-EIJQX2TS.js");
-    const { getVibeCodeStats } = await import("./vibe-code-signatures-ELEWJFGZ.js");
+    const { getVulnerabilityStats } = await import("./vulnerability-signatures-EIKOHFPK.js");
+    const { getVibeCodeStats } = await import("./vibe-code-signatures-J4GD4JOV.js");
     const vulnStats = getVulnerabilityStats();
     const vibeStats = getVibeCodeStats();
     return {
@@ -4747,38 +3259,11 @@ This information is automatically available to Claude Code, Cursor, and other AI
       }]
     };
   }
-  async getInstalledSkillsResource(uri) {
-    const skills = await listInstalledSkills();
-    const state = await loadContextState();
-    const skillsWithUsage = skills.map((skill) => {
-      const record = state.skills?.[skill.name];
-      return {
-        name: skill.name,
-        description: skill.description,
-        source: skill.installedFrom,
-        installedAt: skill.installedAt,
-        timesApplied: record?.timesApplied || 0,
-        appliedBy: record?.appliedBy || [],
-        lastApplied: record?.lastApplied
-      };
-    });
-    return {
-      contents: [{
-        uri,
-        mimeType: "application/json",
-        text: JSON.stringify({
-          totalSkills: skills.length,
-          skills: skillsWithUsage,
-          note: "Skills are capabilities applied by agents, not autonomous agents themselves."
-        }, null, 2)
-      }]
-    };
-  }
   async getScanReportResource(uri, parsedUri) {
     const fileName = parsedUri.replace("reports/", "");
-    const reportPath = join4(getWorkingDirectory(void 0, true), "trie-reports", fileName);
+    const reportPath = join3(getWorkingDirectory(void 0, true), "trie-reports", fileName);
     try {
-      const content = await readFile4(reportPath, "utf-8");
+      const content = await readFile3(reportPath, "utf-8");
       return {
         contents: [{
           uri,
@@ -5254,38 +3739,6 @@ var RequestHandlers = class {
           return await this.toolRegistry.getTool("register_agent").execute(args);
         case "watch":
           return await this.toolRegistry.getTool("watch").execute(args);
-        // Individual agent commands
-        case "security":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "security" });
-        case "legal":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "legal" });
-        case "accessibility":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "accessibility" });
-        case "design":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "design-engineer" });
-        case "architecture":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "software-architect" });
-        case "bugs":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "bug-finding" });
-        case "ux":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "user-testing" });
-        case "types":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "typecheck" });
-        case "devops":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "devops" });
-        case "clean":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "trie_clean" });
-        case "soc2":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "soc2" });
-        // New agents
-        case "performance":
-        case "perf":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "performance" });
-        case "e2e":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "e2e" });
-        case "visual_qa":
-        case "visual":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "visual-qa" });
         case "visual_qa_browser": {
           try {
             const result = await runVisualQA(args);
@@ -5328,31 +3781,6 @@ npx playwright install chromium
             };
           }
         }
-        case "data_flow":
-        case "dataflow":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "data-flow" });
-        // Special agents
-        case "agent_smith":
-        case "agentsmith":
-        case "smith":
-          if (args?.clear_memory || args?.show_stats) {
-            return await this.handleAgentSmith(args);
-          }
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "agent-smith" });
-        case "super_reviewer":
-        case "superreviewer":
-        case "reviewer":
-          return await this.toolRegistry.getTool("agent").execute({ ...args, agent: "super-reviewer" });
-        // Custom skill tools (with backward-compatible agent aliases)
-        case "create_skill":
-        case "create_agent":
-          return await this.toolRegistry.getTool("create_skill").execute(args);
-        case "save_skill":
-        case "save_agent":
-          return await this.toolRegistry.getTool("save_skill").execute(args);
-        case "list_skills":
-        case "list_agents":
-          return await this.toolRegistry.getTool("list_skills").execute(args);
         case "pr_review":
           return await this.toolRegistry.getTool("pr_review").execute(args);
         case "project":
@@ -5454,45 +3882,16 @@ npx playwright install chromium
           "",
           "**Most common:**",
           "- `trie` (no args) \u2014 show this menu",
-          '- `trie` with `{ action: "scan", files?: [], directory?: "" }` \u2014 auto triage & scan',
-          '- `trie` with `{ action: "security", files?: [] }` \u2014 single-skill run (any skill name works)',
-          '- `trie` with `{ action: "agent_smith" }` \u2014 aggressive AI-pattern hunter',
-          "",
-          "**Other actions:**",
-          '- `action: "pr_review"` \u2014 interactive PR review',
           '- `action: "fix"` \u2014 high-confidence fixes',
           '- `action: "watch"` \u2014 start/stop/status autonomous watch',
+          '- `action: "pr_review"` \u2014 interactive PR review',
+          "",
+          "**Other actions:**",
           '- `action: "test"` \u2014 generate/coverage/suggest/run tests (requires `files` + `action`)',
           '- `action: "explain"` \u2014 explain code/issues/risks',
-          '- `action: "list_skills"` \u2014 list all skills (external + custom)',
           '- `action: "visual_qa_browser"` \u2014 screenshots for visual QA',
           "",
-          "**Built-in skills:**",
-          "`security`, `legal`, `accessibility`, `design`, `architecture`, `bugs`, `ux`, `types`, `devops`, `clean`, `soc2`, `performance`, `e2e`, `visual_qa`, `data_flow`",
-          "",
-          "**Special skills:**",
-          "`agent_smith` \u2014 35 vibe code hunters with cross-file detection",
-          "`super_reviewer` \u2014 Interactive PR review with cross-examination",
-          "",
-          "All commands accept `trie_` prefix (e.g., `trie_scan`, `trie_security`). Short names still work for compatibility."
-        ].join("\n")
-      }]
-    };
-  }
-  async handleAgentSmith(_smithArgs) {
-    return {
-      content: [{
-        type: "text",
-        text: [
-          "\u{1F916} Agent Smith functionality has been integrated into the decision ledger.",
-          "",
-          "The autonomous agent now:",
-          "- Extracts patterns automatically via `trie watch`",
-          "- Builds decision ledger from every change",
-          "- Predicts problems via `trie gotcha`",
-          "",
-          "Start the agent: `trie_watch start`",
-          "Query the ledger: `trie_gotcha`"
+          "All commands accept `trie_` prefix (e.g., `trie_fix`, `trie_watch`)."
         ].join("\n")
       }]
     };
@@ -5550,7 +3949,7 @@ var MCPServer = class {
   /**
    * Show startup banner
    */
-  showStartupBanner(skillCount, aiTool) {
+  showStartupBanner(toolCount, aiTool) {
     console.error(`
  \u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2557\u2588\u2588\u2588\u2588\u2588\u2588\u2557 \u2588\u2588\u2557\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2557
  \u255A\u2550\u2550\u2588\u2588\u2554\u2550\u2550\u255D\u2588\u2588\u2554\u2550\u2550\u2588\u2588\u2557\u2588\u2588\u2551\u2588\u2588\u2554\u2550\u2550\u2550\u2550\u255D
@@ -5558,21 +3957,19 @@ var MCPServer = class {
     \u2588\u2588\u2551   \u2588\u2588\u2554\u2550\u2550\u2588\u2588\u2557\u2588\u2588\u2551\u2588\u2588\u2554\u2550\u2550\u255D
     \u2588\u2588\u2551   \u2588\u2588\u2551  \u2588\u2588\u2551\u2588\u2588\u2551\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2557
     \u255A\u2550\u255D   \u255A\u2550\u255D  \u255A\u2550\u255D\u255A\u2550\u255D\u255A\u2550\u2550\u2550\u2550\u2550\u2550\u255D
-  Your central registry for Trie and its skills
+  Your central registry for Trie tools
 
   by Louis Kishfy
 
   Download the Trie workspace: https://www.trie.dev
   Follow me on X: https://x.com/louiskishfy
 
-  ${skillCount} skills ready | ${aiTool}
+  ${toolCount} tools ready | ${aiTool}
 
   Quick Start:
-    \u2022 "Scan this code" - Run all relevant skills
-    \u2022 "Run trie_security" - Security scan only
-    \u2022 "Run trie_soc2" - SOC 2 compliance check
-    \u2022 "Use trie_list_skills" - See all skills
-    \u2022 "Use trie_create_skill" - Make custom skill
+    \u2022 "Scan this code" - Run Trie analysis
+    \u2022 "Use trie" - Open the Trie menu
+    \u2022 "Use trie_fix" - Apply high-confidence fixes
 
   Ready.
 `);
@@ -5584,9 +3981,8 @@ var MCPServer = class {
     try {
       const aiTool = detectAITool();
       await loadConfig();
-      const registry = getSkillRegistry();
-      const skillCount = registry.getAllSkills().length;
-      this.showStartupBanner(skillCount, aiTool.name);
+      const toolCount = this.toolRegistry.getAllTools().length;
+      this.showStartupBanner(toolCount, aiTool.name);
       const transport = new StdioServerTransport();
       await this.server.connect(transport);
     } catch (error) {