@stackmemoryai/stackmemory 1.2.2 → 1.2.4

package/dist/src/cli/commands/storage-tier.js

@@ -13,7 +13,9 @@ import chalk from "chalk";
 import * as os from "os";
 import * as path from "path";
 function createStorageTierCommand() {
-  const cmd = new Command("storage").description("Manage two-tier storage system");
+  const cmd = new Command("storage").description(
+    "Manage two-tier storage system"
+  );
   cmd.command("status").description("Show storage tier status and statistics").option("--json", "Output as JSON").action(async (options) => {
     try {
       const storage = await initializeStorage();
@@ -56,10 +58,18 @@ function createStorageTierCommand() {
       console.log(table.toString());
       console.log(`
 \u{1F4C8} Summary:`);
-      console.log(`  Local Usage: ${chalk.cyan(stats.localUsageMB.toFixed(1))} MB`);
-      console.log(`  Compression Ratio: ${chalk.cyan(stats.compressionRatio.toFixed(2))}x`);
-      console.log(`  Pending Migrations: ${chalk.yellow(stats.migrationsPending)}`);
-      console.log(`  Last Migration: ${stats.lastMigration ? chalk.green(stats.lastMigration.toISOString()) : chalk.gray("Never")}`);
+      console.log(
+        `  Local Usage: ${chalk.cyan(stats.localUsageMB.toFixed(1))} MB`
+      );
+      console.log(
+        `  Compression Ratio: ${chalk.cyan(stats.compressionRatio.toFixed(2))}x`
+      );
+      console.log(
+        `  Pending Migrations: ${chalk.yellow(stats.migrationsPending)}`
+      );
+      console.log(
+        `  Last Migration: ${stats.lastMigration ? chalk.green(stats.lastMigration.toISOString()) : chalk.gray("Never")}`
+      );
       await storage.shutdown();
     } catch (error) {
       logger.error("Failed to get storage status", { error });
@@ -75,7 +85,9 @@ function createStorageTierCommand() {
         console.log("Would migrate based on current triggers");
       } else {
         console.log("\u{1F504} Starting migration process...");
-        console.log("Migration triggered. Use `storage status` to monitor progress.");
+        console.log(
+          "Migration triggered. Use `storage status` to monitor progress."
+        );
       }
       await storage.shutdown();
     } catch (error) {
@@ -87,7 +99,9 @@ function createStorageTierCommand() {
   cmd.command("cleanup").description("Clean up old data and optimize storage").option("--force", "Force cleanup without confirmation").option("--tier <tier>", "Clean specific tier only").action(async (options) => {
     try {
       if (!options.force) {
-        console.log("\u26A0\uFE0F  This will permanently delete old data. Use --force to confirm.");
+        console.log(
+          "\u26A0\uFE0F  This will permanently delete old data. Use --force to confirm."
+        );
         process.exit(1);
       }
       const storage = await initializeStorage();
@@ -172,7 +186,11 @@ function getStorageConfig() {
     },
     migration: {
       ...defaultTwoTierConfig.migration,
-      offlineQueuePath: path.join(homeDir, ".stackmemory", "offline-queue.json")
+      offlineQueuePath: path.join(
+        homeDir,
+        ".stackmemory",
+        "offline-queue.json"
+      )
     }
   };
   return config;

package/dist/src/cli/index.js

@@ -61,8 +61,6 @@ import { filterPending } from "../integrations/mcp/pending-utils.js";
 import { ProjectManager } from "../core/projects/project-manager.js";
 import { join } from "path";
 import { existsSync, mkdirSync } from "fs";
-import inquirer from "inquirer";
-import { enableChromaDB } from "../core/config/storage-config.js";
 import { createRequire } from "module";
 import { fileURLToPath } from "url";
 import * as pathModule from "path";
@@ -104,10 +102,7 @@ program.name("stackmemory").description(
 ).version(VERSION);
 program.command("init").description(
   "Initialize StackMemory in current project (zero-config by default)"
-).option("-i, --interactive", "Interactive mode with configuration prompts").option(
-  "--chromadb",
-  "Enable ChromaDB for semantic search (prompts for API key)"
-).option("--daemon", "Start the background daemon after initialization").action(async (options) => {
+).option("-i, --interactive", "Interactive mode with configuration prompts").option("--daemon", "Start the background daemon after initialization").action(async (options) => {
   try {
     const projectRoot = process.cwd();
     const dbDir = join(projectRoot, ".stackmemory");
@@ -120,28 +115,6 @@ program.command("init").description(
     if (!existsSync(dbDir)) {
       mkdirSync(dbDir, { recursive: true });
     }
-    if (options.chromadb) {
-      await promptAndEnableChromaDB();
-    } else if (options.interactive && process.stdin.isTTY) {
-      console.log(chalk.cyan("\nStorage Configuration"));
-      console.log(
-        chalk.gray("SQLite (default) is fast and requires no setup.")
-      );
-      console.log(
-        chalk.gray("ChromaDB adds semantic search but requires an API key.\n")
-      );
-      const { enableChroma } = await inquirer.prompt([
-        {
-          type: "confirm",
-          name: "enableChroma",
-          message: "Enable ChromaDB for semantic search?",
-          default: false
-        }
-      ]);
-      if (enableChroma) {
-        await promptAndEnableChromaDB();
-      }
-    }
     const dbPath = join(dbDir, "context.db");
     if (!isTestEnv()) {
       const db = await openDatabase(dbPath);
@@ -195,35 +168,6 @@ program.command("init").description(
     process.exit(1);
   }
 });
-async function promptAndEnableChromaDB() {
-  const answers = await inquirer.prompt([
-    {
-      type: "password",
-      name: "apiKey",
-      message: "Enter your ChromaDB API key:",
-      validate: (input) => {
-        if (!input || input.trim().length === 0) {
-          return "API key is required for ChromaDB";
-        }
-        return true;
-      }
-    },
-    {
-      type: "input",
-      name: "apiUrl",
-      message: "ChromaDB API URL (press Enter for default):",
-      default: "https://api.trychroma.com"
-    }
-  ]);
-  enableChromaDB({
-    apiKey: answers.apiKey,
-    apiUrl: answers.apiUrl
-  });
-  console.log(chalk.green("[OK] ChromaDB enabled for semantic search."));
-  console.log(
-    chalk.gray("API key saved to ~/.stackmemory/storage-config.json")
-  );
-}
 program.command("status").description("Show current StackMemory status").option("--all", "Show all active frames across sessions").option("--project", "Show all active frames in current project").option("--session <id>", "Show frames for specific session").action(async (options) => {
   return trace.command("stackmemory-status", options, async () => {
     try {

package/dist/src/core/config/feature-flags.js

@@ -11,8 +11,6 @@ function isFeatureEnabled(feature) {
   switch (feature) {
     case "linear":
       return process.env["STACKMEMORY_LINEAR"] !== "false" && (!!process.env["LINEAR_API_KEY"] || !!process.env["LINEAR_OAUTH_TOKEN"]);
-    case "chromadb":
-      return process.env["STACKMEMORY_CHROMADB"] === "true";
     case "aiSummaries":
       return process.env["STACKMEMORY_AI"] !== "false" && (!!process.env["ANTHROPIC_API_KEY"] || !!process.env["OPENAI_API_KEY"]);
     case "skills":
@@ -29,7 +27,6 @@ function getFeatureFlags() {
   return {
     core: true,
     linear: isFeatureEnabled("linear"),
-    chromadb: isFeatureEnabled("chromadb"),
     aiSummaries: isFeatureEnabled("aiSummaries"),
     skills: isFeatureEnabled("skills"),
     ralph: isFeatureEnabled("ralph"),
@@ -46,7 +43,6 @@ function logFeatureStatus() {
     console.log(
       `  Linear: ${flags.linear ? "enabled" : "disabled (no API key)"}`
     );
-    console.log(`  ChromaDB: ${flags.chromadb ? "enabled" : "disabled"}`);
     console.log(
       `  AI Summaries: ${flags.aiSummaries ? "enabled" : "disabled (no API key)"}`
     );

package/dist/src/core/context/dual-stack-manager.js

@@ -99,9 +99,16 @@ class DualStackManager {
         )
       `;
       if (this.adapter.isConnected()) {
-        await this.adapter.execute?.(createStackContextsTable) || this.executeSchemaQuery(createStackContextsTable);
-        await this.adapter.execute?.(createHandoffRequestsTable) || this.executeSchemaQuery(createHandoffRequestsTable);
-        await this.adapter.execute?.(createStackSyncLogTable) || this.executeSchemaQuery(createStackSyncLogTable);
+        const adapterAny = this.adapter;
+        if (!await adapterAny.execute?.(createStackContextsTable)) {
+          this.executeSchemaQuery(createStackContextsTable);
+        }
+        if (!await adapterAny.execute?.(createHandoffRequestsTable)) {
+          this.executeSchemaQuery(createHandoffRequestsTable);
+        }
+        if (!await adapterAny.execute?.(createStackSyncLogTable)) {
+          this.executeSchemaQuery(createStackSyncLogTable);
+        }
       }
       await this.adapter.commitTransaction();
       logger.info("Dual stack schema initialized successfully");

package/dist/src/core/context/frame-database.js

@@ -56,6 +56,7 @@ class FrameDatabase {
           created_at INTEGER NOT NULL DEFAULT (unixepoch()),
           closed_at INTEGER,
           retention_policy TEXT DEFAULT 'default',
+          importance_score REAL DEFAULT 0.5,
           FOREIGN KEY (parent_frame_id) REFERENCES frames(frame_id)
         );
       `);
@@ -90,6 +91,12 @@ class FrameDatabase {
         );
       } catch {
       }
+      try {
+        this.db.exec(
+          "ALTER TABLE frames ADD COLUMN importance_score REAL DEFAULT 0.5"
+        );
+      } catch {
+      }
       this.db.exec(`
         CREATE INDEX IF NOT EXISTS idx_frames_run ON frames(run_id);
         CREATE INDEX IF NOT EXISTS idx_frames_project ON frames(project_id);
@@ -99,6 +106,7 @@ class FrameDatabase {
         CREATE INDEX IF NOT EXISTS idx_frames_project_state ON frames(project_id, state);
         CREATE INDEX IF NOT EXISTS idx_frames_project_created ON frames(project_id, created_at DESC);
         CREATE INDEX IF NOT EXISTS idx_frames_retention_created ON frames(retention_policy, created_at);
+        CREATE INDEX IF NOT EXISTS idx_frames_gc_score ON frames(state, retention_policy, importance_score ASC, created_at ASC);
         CREATE INDEX IF NOT EXISTS idx_events_frame ON events(frame_id);
         CREATE INDEX IF NOT EXISTS idx_events_seq ON events(frame_id, seq);
         CREATE INDEX IF NOT EXISTS idx_anchors_frame ON anchors(frame_id);
@@ -142,6 +150,30 @@ class FrameDatabase {
         -- Set initial schema version if not exists
         INSERT OR IGNORE INTO schema_version (version) VALUES (1);
       `);
+      this.db.exec(`
+        CREATE TABLE IF NOT EXISTS cord_tasks (
+          task_id TEXT PRIMARY KEY,
+          parent_id TEXT,
+          project_id TEXT NOT NULL,
+          run_id TEXT NOT NULL,
+          goal TEXT NOT NULL,
+          prompt TEXT NOT NULL DEFAULT '',
+          result TEXT,
+          status TEXT NOT NULL DEFAULT 'pending'
+            CHECK (status IN ('pending','active','completed','blocked','asked')),
+          context_mode TEXT NOT NULL DEFAULT 'spawn'
+            CHECK (context_mode IN ('spawn','fork','ask')),
+          blocked_by TEXT NOT NULL DEFAULT '[]',
+          depth INTEGER NOT NULL DEFAULT 0,
+          created_at INTEGER NOT NULL DEFAULT (unixepoch()),
+          completed_at INTEGER,
+          FOREIGN KEY (parent_id) REFERENCES cord_tasks(task_id)
+        );
+        CREATE INDEX IF NOT EXISTS idx_cord_tasks_project ON cord_tasks(project_id);
+        CREATE INDEX IF NOT EXISTS idx_cord_tasks_parent ON cord_tasks(parent_id);
+        CREATE INDEX IF NOT EXISTS idx_cord_tasks_status ON cord_tasks(status);
+        CREATE INDEX IF NOT EXISTS idx_cord_tasks_project_status ON cord_tasks(project_id, status);
+      `);
       logger.info("Frame database schema initialized");
     } catch (error) {
       throw new DatabaseError(

package/dist/src/core/context/frame-handoff-manager.js

@@ -583,12 +583,12 @@ class FrameHandoffManager {
         ErrorCode.RESOURCE_NOT_FOUND
       );
     }
-    const self = this;
+    const activeHandoffs = this.activeHandoffs;
     return {
       async *[Symbol.asyncIterator]() {
         let lastStatus = progress.status;
         while (lastStatus !== "completed" && lastStatus !== "failed" && lastStatus !== "cancelled") {
-          const currentProgress = self.activeHandoffs.get(requestId);
+          const currentProgress = activeHandoffs.get(requestId);
           if (currentProgress && currentProgress.status !== lastStatus) {
             lastStatus = currentProgress.status;
             yield currentProgress;

package/dist/src/core/context/{refactored-frame-manager.js → frame-manager.js}

@@ -18,7 +18,7 @@ import { FrameDatabase } from "./frame-database.js";
 import { FrameStack } from "./frame-stack.js";
 import { FrameDigestGenerator } from "./frame-digest.js";
 import { FrameRecovery } from "./frame-recovery.js";
-class RefactoredFrameManager {
+class FrameManager {
   frameDb;
   frameStack;
   digestGenerator;
@@ -53,7 +53,7 @@ class RefactoredFrameManager {
     this.frameRecovery = new FrameRecovery(db);
     this.frameRecovery.setCurrentRunId(this.currentRunId);
     this.frameDb.initSchema();
-    logger.info("RefactoredFrameManager initialized", {
+    logger.info("FrameManager initialized", {
       projectId: this.projectId,
       runId: this.currentRunId,
       sessionId: this.sessionId
@@ -756,5 +756,5 @@ class RefactoredFrameManager {
   }
 }
 export {
-  RefactoredFrameManager
+  FrameManager
 };

package/dist/src/core/context/index.js

@@ -2,7 +2,7 @@ import { fileURLToPath as __fileURLToPath } from 'url';
 import { dirname as __pathDirname } from 'path';
 const __filename = __fileURLToPath(import.meta.url);
 const __dirname = __pathDirname(__filename);
-import { RefactoredFrameManager } from "./refactored-frame-manager.js";
+import { FrameManager } from "./frame-manager.js";
 import { FrameDatabase } from "./frame-database.js";
 import { FrameStack } from "./frame-stack.js";
 import { FrameDigestGenerator } from "./frame-digest.js";
@@ -16,7 +16,7 @@ import {
 export {
   FrameDatabase,
   FrameDigestGenerator,
-  RefactoredFrameManager as FrameManager,
+  FrameManager,
   FrameRecovery,
   FrameStack,
   frameLifecycleHooks,

package/dist/src/core/database/sqlite-adapter.js

@@ -237,6 +237,10 @@ class SQLiteAdapter extends FeatureAwareDatabaseAdapter {
         "FTS5 index populated from existing frames (migration v1\u2192v2)"
       );
     }
+    if (version < 3) {
+      this.db.prepare("INSERT OR REPLACE INTO schema_version (version) VALUES (?)").run(3);
+      logger.info("Schema migration v2\u2192v3: GC importance_score support");
+    }
   }
   /**
    * Initialize sqlite-vec for vector search
@@ -305,6 +309,7 @@ class SQLiteAdapter extends FeatureAwareDatabaseAdapter {
     const retentionDays = options.retentionDays ?? 90;
     const batchSize = options.batchSize ?? 100;
     const dryRun = options.dryRun ?? false;
+    const protectedRunIds = options.protectedRunIds ?? [];
     const nowSec = Math.floor(Date.now() / 1e3);
     const defaultCutoff = nowSec - retentionDays * 86400;
     const ttl30dCutoff = nowSec - 30 * 86400;
@@ -317,8 +322,17 @@ class SQLiteAdapter extends FeatureAwareDatabaseAdapter {
            OR (retention_policy = 'ttl_7d' AND created_at < ?)
          )
          AND retention_policy != 'keep_forever'
+         AND state = 'closed'
+         AND run_id NOT IN (SELECT value FROM json_each(?))
+         ORDER BY importance_score ASC, created_at ASC
          LIMIT ?`
-    ).all(defaultCutoff, ttl30dCutoff, ttl7dCutoff, batchSize);
+    ).all(
+      defaultCutoff,
+      ttl30dCutoff,
+      ttl7dCutoff,
+      JSON.stringify(protectedRunIds),
+      batchSize
+    );
     const frameIds = candidates.map((r) => r.frame_id);
     if (frameIds.length === 0) {
       return {
@@ -388,6 +402,69 @@ class SQLiteAdapter extends FeatureAwareDatabaseAdapter {
       ftsEntriesDeleted: frameIds.length
     };
   }
+  /**
+   * Compute importance score for a single frame.
+   * Score range: [0.0, 1.0] — higher means more important, less likely to be GC'd.
+   */
+  computeImportanceScore(frameId) {
+    if (!this.db)
+      throw new DatabaseError(
+        "Database not connected",
+        ErrorCode.DB_CONNECTION_FAILED
+      );
+    const frame = this.db.prepare(
+      "SELECT frame_id, digest_text, created_at FROM frames WHERE frame_id = ?"
+    ).get(frameId);
+    if (!frame) return 0.3;
+    let score = 0.3;
+    const decisionCount = this.db.prepare(
+      "SELECT COUNT(*) as count FROM anchors WHERE frame_id = ? AND type = 'DECISION'"
+    ).get(frameId).count;
+    if (decisionCount > 0) score += 0.15;
+    const eventCount = this.db.prepare("SELECT COUNT(*) as count FROM events WHERE frame_id = ?").get(frameId).count;
+    if (eventCount > 3) score += 0.1;
+    if (frame.digest_text) score += 0.15;
+    const childCount = this.db.prepare(
+      "SELECT COUNT(*) as count FROM frames WHERE parent_frame_id = ?"
+    ).get(frameId).count;
+    if (childCount > 0) score += 0.1;
+    const nowSec = Math.floor(Date.now() / 1e3);
+    if (nowSec - frame.created_at < 86400) score += 0.1;
+    return Math.round(Math.min(score, 1) * 100) / 100;
+  }
+  /**
+   * Recompute importance scores for frames still at default score (0.5).
+   * Processes oldest frames first in batches.
+   * Returns count of frames updated.
+   */
+  recomputeImportanceScores(batchSize = 100) {
+    if (!this.db)
+      throw new DatabaseError(
+        "Database not connected",
+        ErrorCode.DB_CONNECTION_FAILED
+      );
+    const frames = this.db.prepare(
+      "SELECT frame_id FROM frames WHERE importance_score = 0.5 ORDER BY created_at ASC LIMIT ?"
+    ).all(batchSize);
+    const updateStmt = this.db.prepare(
+      "UPDATE frames SET importance_score = ? WHERE frame_id = ?"
+    );
+    let updated = 0;
+    for (const { frame_id } of frames) {
+      const score = this.computeImportanceScore(frame_id);
+      if (score !== 0.5) {
+        updateStmt.run(score, frame_id);
+        updated++;
+      }
+    }
+    if (updated > 0) {
+      logger.info("Recomputed importance scores", {
+        checked: frames.length,
+        updated
+      });
+    }
+    return updated;
+  }
   async migrateSchema(targetVersion) {
     if (!this.db)
       throw new DatabaseError(
@@ -1252,6 +1329,89 @@ class SQLiteAdapter extends FeatureAwareDatabaseAdapter {
     }
     return Buffer.from(JSON.stringify(data, null, 2));
   }
+  /**
+   * Get recent frames from other run_ids within the same project.
+   * Used by team tools to read cross-agent context.
+   */
+  async getRecentFramesExcludingRun(projectId, excludeRunId, opts) {
+    if (!this.db)
+      throw new DatabaseError(
+        "Database not connected",
+        ErrorCode.DB_CONNECTION_FAILED
+      );
+    const limit = opts?.limit ?? 10;
+    const params = [projectId, excludeRunId];
+    let whereExtra = "";
+    if (opts?.since) {
+      whereExtra += " AND created_at > ?";
+      params.push(Math.floor(opts.since / 1e3));
+    }
+    if (opts?.types && opts.types.length > 0) {
+      const placeholders = opts.types.map(() => "?").join(",");
+      whereExtra += ` AND type IN (${placeholders})`;
+      params.push(...opts.types);
+    }
+    params.push(limit);
+    const rows = this.db.prepare(
+      `SELECT * FROM frames
+         WHERE project_id = ? AND run_id != ?${whereExtra}
+         ORDER BY created_at DESC
+         LIMIT ?`
+    ).all(...params);
+    const frameIds = rows.map((r) => r.frame_id);
+    const anchorsByFrame = /* @__PURE__ */ new Map();
+    if (frameIds.length > 0) {
+      const placeholders = frameIds.map(() => "?").join(",");
+      const anchorRows = this.db.prepare(
+        `SELECT * FROM anchors WHERE frame_id IN (${placeholders})
+           ORDER BY priority DESC, created_at ASC`
+      ).all(...frameIds);
+      for (const row of anchorRows) {
+        const list = anchorsByFrame.get(row.frame_id) || [];
+        list.push({ ...row, metadata: JSON.parse(row.metadata || "{}") });
+        anchorsByFrame.set(row.frame_id, list);
+      }
+    }
+    return rows.map((row) => ({
+      ...row,
+      inputs: JSON.parse(row.inputs || "{}"),
+      outputs: JSON.parse(row.outputs || "{}"),
+      digest_json: JSON.parse(row.digest_json || "{}"),
+      anchors: anchorsByFrame.get(row.frame_id) || []
+    }));
+  }
+  /**
+   * Get anchors explicitly shared for team visibility.
+   * Finds anchors where metadata contains `"shared":true`.
+   */
+  async getSharedAnchors(projectId, opts) {
+    if (!this.db)
+      throw new DatabaseError(
+        "Database not connected",
+        ErrorCode.DB_CONNECTION_FAILED
+      );
+    const limit = opts?.limit ?? 20;
+    const params = [projectId];
+    let whereExtra = "";
+    if (opts?.since) {
+      whereExtra += " AND a.created_at > ?";
+      params.push(Math.floor(opts.since / 1e3));
+    }
+    params.push(limit);
+    const rows = this.db.prepare(
+      `SELECT a.*, f.name as frame_name, f.run_id
+         FROM anchors a
+         JOIN frames f ON a.frame_id = f.frame_id
+         WHERE f.project_id = ?
+           AND a.metadata LIKE '%"shared":true%'${whereExtra}
+         ORDER BY a.priority DESC, a.created_at DESC
+         LIMIT ?`
+    ).all(...params);
+    return rows.map((row) => ({
+      ...row,
+      metadata: JSON.parse(row.metadata || "{}")
+    }));
+  }
   async importData(data, format, options) {
     if (!this.db)
       throw new DatabaseError(

package/dist/src/core/digest/frame-digest-integration.js

@@ -2,7 +2,7 @@ import { fileURLToPath as __fileURLToPath } from 'url';
 import { dirname as __pathDirname } from 'path';
 const __filename = __fileURLToPath(import.meta.url);
 const __dirname = __pathDirname(__filename);
-import { EnhancedHybridDigestGenerator } from "./enhanced-hybrid-digest.js";
+import { EnhancedHybridDigestGenerator } from "./hybrid-digest.js";
 import { logger } from "../monitoring/logger.js";
 class FrameDigestIntegration {
   frameManager;

package/dist/src/core/digest/index.js

@@ -4,5 +4,5 @@ const __filename = __fileURLToPath(import.meta.url);
 const __dirname = __pathDirname(__filename);
 export * from "./types.js";
 export * from "./hybrid-digest-generator.js";
-export * from "./enhanced-hybrid-digest.js";
+export * from "./hybrid-digest.js";
 export * from "./frame-digest-integration.js";

package/dist/src/core/execution/parallel-executor.js

@@ -106,7 +106,11 @@ class ParallelExecutor extends EventEmitter {
           taskId,
           error: lastError.message
         });
-        this.emit("task-retry", { taskId, attempt: attempts, error: lastError });
+        this.emit("task-retry", {
+          taskId,
+          attempt: attempts,
+          error: lastError
+        });
         if (attempts < maxRetries) {
           await this.delay(Math.pow(2, attempts) * 1e3);
         }

package/dist/src/core/projects/project-isolation.js

@@ -25,9 +25,20 @@ class ProjectIsolationManager {
     try {
       const remoteUrl = this.getGitRemoteUrl(projectRoot);
       const gitInfo = this.parseGitRemote(remoteUrl);
-      const projectId = this.createStableProjectId(gitInfo.organization, gitInfo.repository);
-      const workspaceFilter = this.createWorkspaceFilter(gitInfo.organization, gitInfo.repository, projectRoot);
-      const linearConfig = this.getLinearConfiguration(gitInfo.organization, gitInfo.repository, projectRoot);
+      const projectId = this.createStableProjectId(
+        gitInfo.organization,
+        gitInfo.repository
+      );
+      const workspaceFilter = this.createWorkspaceFilter(
+        gitInfo.organization,
+        gitInfo.repository,
+        projectRoot
+      );
+      const linearConfig = this.getLinearConfiguration(
+        gitInfo.organization,
+        gitInfo.repository,
+        projectRoot
+      );
       const identification = {
         projectId,
         organization: gitInfo.organization,
@@ -45,7 +56,10 @@ class ProjectIsolationManager {
       });
       return identification;
     } catch (error) {
-      logger.warn("Could not determine git remote, using fallback identification", { error });
+      logger.warn(
+        "Could not determine git remote, using fallback identification",
+        { error }
+      );
       const fallback = this.createFallbackIdentification(projectRoot);
       this.projectCache.set(cacheKey, fallback);
       return fallback;

package/dist/src/core/security/index.js

@@ -15,6 +15,7 @@ import {
   validateInput,
   createAggregateSchema,
   validateShellArg,
+  validateShellCommand,
   safeJsonParse
 } from "./input-sanitizer.js";
 export {
@@ -30,5 +31,6 @@ export {
   sanitizeIdentifier,
   validateInput,
   validateShellArg,
+  validateShellCommand,
   validateTableName
 };

package/dist/src/core/security/input-sanitizer.js

@@ -280,6 +280,28 @@ function createAggregateSchema(allowedFields) {
     limit: z.number().int().min(1).max(1e3).optional()
   });
 }
+const DANGEROUS_SHELL_PATTERNS = [
+  /\brm\s+(-[a-zA-Z]*r[a-zA-Z]*f|--recursive)\b/i,
+  // rm -rf, rm -fr, rm --recursive
+  /\brm\s+-[a-zA-Z]*r\b/i,
+  // rm -r (any flag combo with r)
+  /\bmkfs\b/i,
+  /\bdd\s+if=/i,
+  /\b:\(\)\s*\{/i
+  // fork bomb
+];
+function validateShellCommand(command) {
+  for (const pattern of DANGEROUS_SHELL_PATTERNS) {
+    if (pattern.test(command)) {
+      throw new ValidationError(
+        `Blocked dangerous shell command: ${command.substring(0, 80)}`,
+        ErrorCode.VALIDATION_FAILED,
+        { reason: "dangerous_command" }
+      );
+    }
+  }
+  return command;
+}
 function validateShellArg(arg) {
   if (!arg) return "";
   const dangerousChars = /[;&|`$(){}[\]<>!#*?~\n\r]/;
@@ -316,5 +338,6 @@ export {
   sanitizeIdentifier,
   validateInput,
   validateShellArg,
+  validateShellCommand,
   validateTableName
 };

package/dist/src/core/utils/update-checker.js

@@ -63,12 +63,16 @@ class UpdateChecker {
   static async fetchLatestVersion() {
     try {
       const fetchVersion = async () => {
-        const output = execFileSync("npm", ["view", this.PACKAGE_NAME, "version"], {
-          encoding: "utf-8",
-          stdio: ["pipe", "pipe", "ignore"],
-          timeout: 5e3
-          // 5 second timeout
-        }).trim();
+        const output = execFileSync(
+          "npm",
+          ["view", this.PACKAGE_NAME, "version"],
+          {
+            encoding: "utf-8",
+            stdio: ["pipe", "pipe", "ignore"],
+            timeout: 5e3
+            // 5 second timeout
+          }
+        ).trim();
         return output;
       };
       return await gracefulDegrade(

package/dist/src/daemon/daemon-config.js

@@ -30,8 +30,9 @@ const DEFAULT_DAEMON_CONFIG = {
     ftsRebuildInterval: 24,
     // hours
     embeddingBatchSize: 50,
-    vacuumInterval: 168
+    vacuumInterval: 168,
     // weekly
+    gcIntervalSeconds: 60
   },
   memory: {
     enabled: true,