@mnemonik/scanner 5.6.2 → 5.74.16

package/README.md

@@ -75,7 +75,6 @@ It respects `.gitignore` and skips common directories (`node_modules`, `.git`, `
 
 The daemon is designed to run continuously with minimal impact:
 
-- **Memory**: Capped at 256MB
 - **CPU**: Event-driven (idle when no files change)
 - **Disk**: Log rotation at 5MB
 - **Network**: Only changed files are pushed (hash-based diffing)

package/dist/client.d.ts

@@ -14,6 +14,14 @@ export interface ScanPushFile {
             size: number;
         };
     }>;
+    /**
+     * Optional raw file content. Sent by the scanner daemon for ALL files
+     * (code and authority/manifest alike) so the doc-truth worker can run
+     * claim extraction against whole documents without filesystem access.
+     * Omitted when the file exceeds the server's 5 MB schema cap or when
+     * the raw content could not be read (chunk-based fallback path).
+     */
+    content?: string;
 }
 export interface ScanPushCommit {
     sha: string;
@@ -68,5 +76,21 @@ export declare class MnemonikClient {
         success: boolean;
     }>;
     sendHeartbeat(projectId: string): Promise<void>;
+    /**
+     * Notify the server of files that have been removed since the daemon's
+     * previous scan of this project. Server deprecates exactly those code
+     * memories. Empty arrays are accepted as no-ops so the daemon can call
+     * this every tick regardless of whether anything was removed.
+     *
+     * The caller is responsible for computing the removal set locally — the
+     * old inventory-diff shape that asked the server to derive removals from
+     * a "known files" list has been removed because a small/malformed list
+     * would mass-deprecate. The narrow `removedFiles` shape cannot exhibit
+     * that failure mode by construction.
+     */
+    reportRemovedFiles(projectId: string, removedFiles: string[]): Promise<{
+        deprecated: number;
+        couplingsRemoved: number;
+    }>;
     healthCheck(): Promise<boolean>;
 }

package/dist/client.js

@@ -90,6 +90,25 @@ export class MnemonikClient {
     async sendHeartbeat(projectId) {
         await this.request('/api/v1/scan/heartbeat', { projectId });
     }
+    /**
+     * Notify the server of files that have been removed since the daemon's
+     * previous scan of this project. Server deprecates exactly those code
+     * memories. Empty arrays are accepted as no-ops so the daemon can call
+     * this every tick regardless of whether anything was removed.
+     *
+     * The caller is responsible for computing the removal set locally — the
+     * old inventory-diff shape that asked the server to derive removals from
+     * a "known files" list has been removed because a small/malformed list
+     * would mass-deprecate. The narrow `removedFiles` shape cannot exhibit
+     * that failure mode by construction.
+     */
+    async reportRemovedFiles(projectId, removedFiles) {
+        const result = await this.request('/api/v1/scan/reconcile', { projectId, removedFiles });
+        return {
+            deprecated: result.deprecated ?? 0,
+            couplingsRemoved: result.couplingsRemoved ?? 0,
+        };
+    }
     async healthCheck() {
         try {
             const res = await fetch(`${this.serverUrl}/api/v1/health`, {

package/dist/client.js.map

@@ -1 +1 @@
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+{"version":3,"file":"client.js","sourceRoot":"","sources":["../src/client.ts"],"names":[],"mappings":"AAqDA,MAAM,OAAO,cAAc;IAEf;IACA;IAFV,YACU,SAAiB,EACjB,MAAc;QADd,cAAS,GAAT,SAAS,CAAQ;QACjB,WAAM,GAAN,MAAM,CAAQ;IACrB,CAAC;IAEI,KAAK,CAAC,OAAO,CAAI,IAAY,EAAE,IAAa,EAAE,OAAO,GAAG,CAAC;QAC/D,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,SAAS,GAAG,IAAI,EAAE,CAAC;QACvC,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,IAAI,OAAO,EAAE,OAAO,EAAE,EAAE,CAAC;YACpD,IAAI,CAAC;gBACH,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;oBAC3B,MAAM,EAAE,MAAM;oBACd,OAAO,EAAE;wBACP,cAAc,EAAE,kBAAkB;wBAClC,aAAa,EAAE,UAAU,IAAI,CAAC,MAAM,EAAE;qBACvC;oBACD,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC;iBAC3B,CAAC,CAAC;gBAEH,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;oBACZ,MAAM,IAAI,GAAG,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,eAAe,CAAC,CAAC;oBAC3D,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,EAAE,CAAC;wBAC7C,MAAM,IAAI,KAAK,CAAC,gBAAgB,GAAG,CAAC,MAAM,wBAAwB,CAAC,CAAC;oBACtE,CAAC;oBACD,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,IAAI,OAAO,GAAG,OAAO,EAAE,CAAC;wBAC5C,MAAM,UAAU,GAAG,QAAQ,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,IAAI,GAAG,EAAE,EAAE,CAAC,CAAC;wBACvE,MAAM,IAAI,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,UAAU,GAAG,IAAI,CAAC,CAAC,CAAC;wBAC3D,SAAS;oBACX,CAAC;oBACD,IAAI,GAAG,CAAC,MAAM,IAAI,GAAG,IAAI,OAAO,GAAG,OAAO,EAAE,CAAC;wBAC3C,MAAM,IAAI,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,IAAI,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;wBAC9D,SAAS;oBACX,CAAC;oBACD,MAAM,IAAI,KAAK,CAAC,GAAG,GAAG,CAAC,MAAM,IAAI,GAAG,CAAC,UAAU,KAAK,IAAI,EAAE,CAAC,CAAC;gBAC9D,CAAC;gBAED,OAAO,GAAG,CAAC,IAAI,EAAgB,CAAC;YAClC,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACb,IAAI,OAAO,GAAG,OAAO,IAAK,GAAa,CAAC,OAAO,EAAE,QAAQ,CAAC,cAAc,CAAC,EAAE,CAAC;oBAC1E,MAAM,IAAI,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,IAAI,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;oBAC9D,SAAS;gBACX,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC;QACH,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,cAAc,IAAI,iBAAiB,OAAO,UAAU,CAAC,CAAC;IACxE,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,SAAS,CACb,SAAiB;QAEjB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,OAAO,CAAqB,qBAAqB,EAAE,EAAE,SAAS,EAAE,CAAC,CAAC;QAC5F,OAAO;YACL,UAAU,EAAE,IAAI,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;YAC9D,SAAS,EAAE,MAAM,CAAC,SAAS,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,eAAe,EAAE,IAAI,EAAE;SACzE,CAAC;IACJ,CAAC;IAED;;;;;;;;OAQG;IACH,KAAK,CAAC,SAAS,CACb,SAAiB,EACjB,KAAqB,EACrB,OAA0B;QAE1B,MAAM,UAAU,GAAG,CAAC,CAAC,OAAO,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC;QACnD,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACvB,IAAI,UAAU,EAAE,CAAC;gBACf,MAAM,IAAI,CAAC,OAAO,CAAC,mBAAmB,EAAE,EAAE,SAAS,EAAE,KAAK,EAAE,EAAE,EAAE,OAAO,EAAE,CAAC,CAAC;YAC7E,CAAC;YACD,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC;QAC3B,CAAC;QAED,MAAM,SAAS,GAAG,EAAE,CAAC;QACrB,IAAI,eAAe,GAAG,KAAK,CAAC;QAC5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,IAAI,SAAS,EAAE,CAAC;YACjD,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,CAAC;YAC5C,MAAM,IAAI,GAAoB,EAAE,SAAS,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC;YAC1D,IAAI,CAAC,eAAe,IAAI,UAAU,EAAE,CAAC;gBACnC,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC;gBACvB,eAAe,GAAG,IAAI,CAAC;YACzB,CAAC;YACD,MAAM,IAAI,CAAC,OAAO,CAAC,mBAAmB,EAAE,IAAI,CAAC,CAAC;QAChD,CAAC;QACD,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC;IAC3B,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,SAAiB;QACnC,MAAM,IAAI,CAAC,OAAO,CAAC,wBAAwB,EAAE,EAAE,SAAS,EAAE,CAAC,CAAC;IAC9D,CAAC;IAED;;;;;;;;;;;OAWG;IACH,KAAK,CAAC,kBAAkB,CACtB,SAAiB,EACjB,YAAsB;QAEtB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,OAAO,CAI9B,wBAAwB,EAAE,EAAE,SAAS,EAAE,YAAY,EAAE,CAAC,CAAC;QAC1D,OAAO;YACL,UAAU,EAAE,MAAM,CAAC,UAAU,IAAI,CAAC;YAClC,gBAAgB,EAAE,MAAM,CAAC,gBAAgB,IAAI,CAAC;SAC/C,CAAC;IACJ,CAAC;IAED,KAAK,CAAC,WAAW;QACf,IAAI,CAAC;YACH,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,IAAI,CAAC,SAAS,gBAAgB,EAAE;gBACzD,OAAO,EAAE,EAAE,aAAa,EAAE,UAAU,IAAI,CAAC,MAAM,EAAE,EAAE;aACpD,CAAC,CAAC;YACH,OAAO,GAAG,CAAC,EAAE,CAAC;QAChB,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,KAAK,CAAC;QACf,CAAC;IACH,CAAC;CACF"}

package/dist/daemon.d.ts

@@ -31,6 +31,12 @@ export declare class ScannerDaemon {
     private addProject;
     private waitForServer;
     private initialScan;
+    /**
+     * Send the explicit list of paths that vanished since the previous scan.
+     * Empty lists short-circuit so we don't pay an HTTP round-trip when
+     * nothing was removed this tick.
+     */
+    private sendRemovedFiles;
     /**
      * Fetch commits since the last mine. Swallows errors — a git failure must
      * not block the file scan push.
@@ -38,5 +44,6 @@ export declare class ScannerDaemon {
     private collectCommits;
     private handleChanges;
     private startRetryLoop;
+    private collectAuthorityPushFiles;
     private groupChunksByFile;
 }

package/dist/daemon.js

@@ -2,6 +2,8 @@ import { createHash } from 'crypto';
 import { readFile } from 'fs/promises';
 import { join } from 'path';
 import { CodeScanner } from '@mnemonik/shared';
+/** Maximum raw content bytes accepted by the server's scanFileSchema. */
+const MAX_PUSH_CONTENT_BYTES = 5_000_000;
 import { MnemonikClient } from './client.js';
 import { FileWatcher } from './watcher.js';
 import { ProjectDiscovery } from './discovery.js';
@@ -112,18 +114,39 @@ export class ScannerDaemon {
                 await this.addProject(discovered_project);
             }
         }
+        // Periodic removed-files diff for already-watched projects. Cheap
+        // path-only walk (no chunking, no file reads), compare against the
+        // in-memory snapshot from last tick, send only the disappeared paths.
+        // Picks up deletions that fs.watch delivered as unlink events but
+        // that handleChanges couldn't push (it only knows how to push
+        // chunked content, not "this file no longer exists").
+        for (const project of this.projects.values()) {
+            try {
+                const scanned = await this.scanner.listFiles(project.path);
+                // I1: include authority file paths so they are never treated as removed
+                const authority = await this.scanner.collectAuthorityFiles(project.path);
+                const currentSet = new Set([...scanned, ...authority.map((a) => a.path)]);
+                const removedFiles = [...project.lastInventory].filter((p) => !currentSet.has(p));
+                await this.sendRemovedFiles(project.projectId, removedFiles);
+                project.lastInventory = currentSet;
+            }
+            catch (err) {
+                console.warn(`[scanner] [${project.projectId.slice(0, 8)}] periodic removed-files report failed: ${err.message}`);
+            }
+        }
         console.log(`[scanner] Watching ${this.projects.size} project(s)`);
     }
     async addProject(discovered) {
         const label = discovered.projectName ?? discovered.projectId.slice(0, 8);
         console.log(`[scanner] Adding project: ${label} (${discovered.path})`);
-        let gitState = {
+        let scanResult = {
             isGitRepo: false,
             gitMiningEnabled: false,
             lastMinedCommit: null,
+            currentPaths: [],
         };
         try {
-            gitState = await this.initialScan(discovered.projectId, discovered.path);
+            scanResult = await this.initialScan(discovered.projectId, discovered.path);
         }
         catch (err) {
             console.warn(`[scanner] Initial scan failed for ${label}:`, err.message);
@@ -152,9 +175,10 @@ export class ScannerDaemon {
             watcher,
             pendingRetries: new Set(),
             retryTimer: null,
-            isGitRepo: gitState.isGitRepo,
-            gitMiningEnabled: gitState.gitMiningEnabled,
-            lastMinedCommit: gitState.lastMinedCommit,
+            isGitRepo: scanResult.isGitRepo,
+            gitMiningEnabled: scanResult.gitMiningEnabled,
+            lastMinedCommit: scanResult.lastMinedCommit,
+            lastInventory: new Set(scanResult.currentPaths),
         });
     }
     async waitForServer() {
@@ -185,7 +209,12 @@ export class ScannerDaemon {
         const chunks = await this.scanner.scanDirectory(projectRoot);
         const status = await this.client.getStatus(projectId);
         const files = await this.groupChunksByFile(chunks, projectRoot);
-        const filesToPush = files.filter((f) => {
+        const authorityFiles = await this.collectAuthorityPushFiles(projectRoot);
+        // C1: dedupe — chunk-scanned entries win over authority duplicates
+        // (e.g. setup.py matches both .py includeExtensions and AUTHORITY_FILE_MATCHERS)
+        const seen = new Set(files.map((f) => f.path));
+        const allFiles = [...files, ...authorityFiles.filter((a) => !seen.has(a.path))];
+        const filesToPush = allFiles.filter((f) => {
             const serverHash = status.fileHashes.get(f.path);
             return !serverHash || serverHash !== f.hash;
         });
@@ -213,6 +242,17 @@ export class ScannerDaemon {
                 console.warn(`[scanner] Initial push failed for ${projectId.slice(0, 8)}: ${err.message}`);
             }
         }
+        // Initial-scan removed-files diff: bootstrap "before" from the
+        // server's known-paths set (status.fileHashes is what the server
+        // currently has for this project). Anything the server knows that
+        // the daemon doesn't see on disk now = removed. Closes the
+        // daemon-was-offline case and the newly-added-ignore-pattern case.
+        const currentPaths = allFiles.map((f) => f.path);
+        const currentPathSet = new Set(currentPaths);
+        const removedFiles = [...status.fileHashes.keys()].filter((p) => !currentPathSet.has(p));
+        await this.sendRemovedFiles(projectId, removedFiles).catch((err) => {
+            console.warn(`[scanner] [${projectId.slice(0, 8)}] removedFiles report failed (non-blocking): ${err.message}`);
+        });
         const duration = ((Date.now() - startTime) / 1000).toFixed(1);
         console.log(`[scanner] Scan complete for ${projectId.slice(0, 8)}: ` +
             `${chunks.length} chunks, ${filesToPush.length} pushed, ${commits.length} commits (${duration}s)`);
@@ -220,8 +260,24 @@ export class ScannerDaemon {
             isGitRepo,
             gitMiningEnabled: status.gitMining.enabled,
             lastMinedCommit: watermark,
+            currentPaths,
         };
     }
+    /**
+     * Send the explicit list of paths that vanished since the previous scan.
+     * Empty lists short-circuit so we don't pay an HTTP round-trip when
+     * nothing was removed this tick.
+     */
+    async sendRemovedFiles(projectId, removedFiles) {
+        if (removedFiles.length === 0)
+            return;
+        const result = await this.client.reportRemovedFiles(projectId, removedFiles);
+        if (result.deprecated > 0 || result.couplingsRemoved > 0) {
+            console.log(`[scanner] [${projectId.slice(0, 8)}] Removed: ` +
+                `${removedFiles.length} paths sent, ${result.deprecated} memories deprecated, ` +
+                `${result.couplingsRemoved} couplings removed`);
+        }
+    }
     /**
      * Fetch commits since the last mine. Swallows errors — a git failure must
      * not block the file scan push.
@@ -246,6 +302,10 @@ export class ScannerDaemon {
             if (chunks.length === 0)
                 return;
             const files = await this.groupChunksByFile(chunks, projectRoot);
+            const authorityFiles = await this.collectAuthorityPushFiles(projectRoot);
+            // C1: dedupe — chunk-scanned entries win over authority duplicates
+            const seen = new Set(files.map((f) => f.path));
+            const allFiles = [...files, ...authorityFiles.filter((a) => !seen.has(a.path))];
             // attach any new commits since our cached watermark. Only the
             // first push carries them (idempotent jobId on the server collapses
             // duplicates anyway, but one payload saves bandwidth).
@@ -256,9 +316,9 @@ export class ScannerDaemon {
             const succeededPaths = new Set();
             let hadFailure = false;
             let firstBatchSucceeded = false;
-            if (files.length > 0) {
-                for (let i = 0; i < files.length; i += batchSize) {
-                    const batch = files.slice(i, i + batchSize);
+            if (allFiles.length > 0) {
+                for (let i = 0; i < allFiles.length; i += batchSize) {
+                    const batch = allFiles.slice(i, i + batchSize);
                     try {
                         // Only attach commits to the first batch.
                         await this.client.pushFiles(projectId, batch, i === 0 ? commits : undefined);
@@ -318,6 +378,10 @@ export class ScannerDaemon {
         }, 10_000);
         project.retryTimer.unref();
     }
+    async collectAuthorityPushFiles(projectRoot) {
+        const authority = await this.scanner.collectAuthorityFiles(projectRoot);
+        return authority.map((f) => ({ path: f.path, hash: f.hash, chunks: [], content: f.content }));
+    }
     async groupChunksByFile(chunks, projectRoot) {
         const fileMap = new Map();
         for (const chunk of chunks) {
@@ -341,6 +405,8 @@ export class ScannerDaemon {
                 const absPath = join(projectRoot, file.path);
                 const raw = await readFile(absPath, 'utf-8');
                 file.hash = createHash('sha256').update(raw).digest('hex');
+                // C2: drop content if it would exceed the server schema cap (5MB)
+                file.content = raw.length <= MAX_PUSH_CONTENT_BYTES ? raw : undefined;
             }
             catch (err) {
                 console.warn(`[scanner] Cannot read ${file.path} for hashing, using chunk-based fallback`, {
@@ -348,6 +414,8 @@ export class ScannerDaemon {
                 });
                 const allContent = file.chunks.map((c) => c.content).join('\n');
                 file.hash = createHash('sha256').update(allContent).digest('hex');
+                // C2: drop content if it would exceed the server schema cap (5MB)
+                file.content = allContent.length <= MAX_PUSH_CONTENT_BYTES ? allContent : undefined;
             }
         }
         return Array.from(fileMap.values());

package/dist/daemon.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mnemonik/scanner",
-  "version": "5.6.2",
+  "version": "5.74.16",
   "description": "Automatic codebase indexing daemon for Mnemonik",
   "type": "module",
   "bin": {

package/src/client.ts

@@ -14,6 +14,14 @@ export interface ScanPushFile {
       size: number;
     };
   }>;
+  /**
+   * Optional raw file content. Sent by the scanner daemon for ALL files
+   * (code and authority/manifest alike) so the doc-truth worker can run
+   * claim extraction against whole documents without filesystem access.
+   * Omitted when the file exceeds the server's 5 MB schema cap or when
+   * the raw content could not be read (chunk-based fallback path).
+   */
+  content?: string;
 }
 
 export interface ScanPushCommit {
@@ -146,6 +154,33 @@ export class MnemonikClient {
     await this.request('/api/v1/scan/heartbeat', { projectId });
   }
 
+  /**
+   * Notify the server of files that have been removed since the daemon's
+   * previous scan of this project. Server deprecates exactly those code
+   * memories. Empty arrays are accepted as no-ops so the daemon can call
+   * this every tick regardless of whether anything was removed.
+   *
+   * The caller is responsible for computing the removal set locally — the
+   * old inventory-diff shape that asked the server to derive removals from
+   * a "known files" list has been removed because a small/malformed list
+   * would mass-deprecate. The narrow `removedFiles` shape cannot exhibit
+   * that failure mode by construction.
+   */
+  async reportRemovedFiles(
+    projectId: string,
+    removedFiles: string[]
+  ): Promise<{ deprecated: number; couplingsRemoved: number }> {
+    const result = await this.request<{
+      success: boolean;
+      deprecated: number;
+      couplingsRemoved: number;
+    }>('/api/v1/scan/reconcile', { projectId, removedFiles });
+    return {
+      deprecated: result.deprecated ?? 0,
+      couplingsRemoved: result.couplingsRemoved ?? 0,
+    };
+  }
+
   async healthCheck(): Promise<boolean> {
     try {
       const res = await fetch(`${this.serverUrl}/api/v1/health`, {

package/src/daemon.ts

@@ -2,6 +2,9 @@ import { createHash } from 'crypto';
 import { readFile } from 'fs/promises';
 import { join } from 'path';
 import { CodeScanner, type CodeChunk } from '@mnemonik/shared';
+
+/** Maximum raw content bytes accepted by the server's scanFileSchema. */
+const MAX_PUSH_CONTENT_BYTES = 5_000_000;
 import { MnemonikClient, type ScanPushCommit, type ScanPushFile } from './client.js';
 import { FileWatcher } from './watcher.js';
 import { ProjectDiscovery, type DiscoveredProject } from './discovery.js';
@@ -29,6 +32,13 @@ interface WatchedProject {
   isGitRepo: boolean;
   gitMiningEnabled: boolean;
   lastMinedCommit: string | null;
+  // Snapshot of file paths observed during the most recent full scan
+  // (initial + periodic refresh). Used as the "before" side of the local
+  // diff that computes removedFiles each scan tick. Empty on first call
+  // for a project; the daemon-restart bootstrap is handled by seeding
+  // from `client.getStatus()` (the server's known-paths set) before the
+  // first scan completes.
+  lastInventory: Set<string>;
 }
 
 export class ScannerDaemon {
@@ -148,6 +158,28 @@ export class ScannerDaemon {
       }
     }
 
+    // Periodic removed-files diff for already-watched projects. Cheap
+    // path-only walk (no chunking, no file reads), compare against the
+    // in-memory snapshot from last tick, send only the disappeared paths.
+    // Picks up deletions that fs.watch delivered as unlink events but
+    // that handleChanges couldn't push (it only knows how to push
+    // chunked content, not "this file no longer exists").
+    for (const project of this.projects.values()) {
+      try {
+        const scanned = await this.scanner.listFiles(project.path);
+        // I1: include authority file paths so they are never treated as removed
+        const authority = await this.scanner.collectAuthorityFiles(project.path);
+        const currentSet = new Set([...scanned, ...authority.map((a) => a.path)]);
+        const removedFiles = [...project.lastInventory].filter((p) => !currentSet.has(p));
+        await this.sendRemovedFiles(project.projectId, removedFiles);
+        project.lastInventory = currentSet;
+      } catch (err) {
+        console.warn(
+          `[scanner] [${project.projectId.slice(0, 8)}] periodic removed-files report failed: ${(err as Error).message}`
+        );
+      }
+    }
+
     console.log(`[scanner] Watching ${this.projects.size} project(s)`);
   }
 
@@ -155,13 +187,19 @@ export class ScannerDaemon {
     const label = discovered.projectName ?? discovered.projectId.slice(0, 8);
     console.log(`[scanner] Adding project: ${label} (${discovered.path})`);
 
-    let gitState = {
+    let scanResult: {
+      isGitRepo: boolean;
+      gitMiningEnabled: boolean;
+      lastMinedCommit: string | null;
+      currentPaths: string[];
+    } = {
       isGitRepo: false,
       gitMiningEnabled: false,
-      lastMinedCommit: null as string | null,
+      lastMinedCommit: null,
+      currentPaths: [],
     };
     try {
-      gitState = await this.initialScan(discovered.projectId, discovered.path);
+      scanResult = await this.initialScan(discovered.projectId, discovered.path);
     } catch (err) {
       console.warn(`[scanner] Initial scan failed for ${label}:`, (err as Error).message);
     }
@@ -197,9 +235,10 @@ export class ScannerDaemon {
       watcher,
       pendingRetries: new Set(),
       retryTimer: null,
-      isGitRepo: gitState.isGitRepo,
-      gitMiningEnabled: gitState.gitMiningEnabled,
-      lastMinedCommit: gitState.lastMinedCommit,
+      isGitRepo: scanResult.isGitRepo,
+      gitMiningEnabled: scanResult.gitMiningEnabled,
+      lastMinedCommit: scanResult.lastMinedCommit,
+      lastInventory: new Set(scanResult.currentPaths),
     });
   }
 
@@ -230,14 +269,24 @@ export class ScannerDaemon {
   private async initialScan(
     projectId: string,
     projectRoot: string
-  ): Promise<{ isGitRepo: boolean; gitMiningEnabled: boolean; lastMinedCommit: string | null }> {
+  ): Promise<{
+    isGitRepo: boolean;
+    gitMiningEnabled: boolean;
+    lastMinedCommit: string | null;
+    currentPaths: string[];
+  }> {
     const startTime = Date.now();
 
     const chunks = await this.scanner.scanDirectory(projectRoot);
     const status = await this.client.getStatus(projectId);
 
     const files = await this.groupChunksByFile(chunks, projectRoot);
-    const filesToPush = files.filter((f) => {
+    const authorityFiles = await this.collectAuthorityPushFiles(projectRoot);
+    // C1: dedupe — chunk-scanned entries win over authority duplicates
+    // (e.g. setup.py matches both .py includeExtensions and AUTHORITY_FILE_MATCHERS)
+    const seen = new Set(files.map((f) => f.path));
+    const allFiles = [...files, ...authorityFiles.filter((a) => !seen.has(a.path))];
+    const filesToPush = allFiles.filter((f) => {
       const serverHash = status.fileHashes.get(f.path);
       return !serverHash || serverHash !== f.hash;
     });
@@ -272,6 +321,20 @@ export class ScannerDaemon {
       }
     }
 
+    // Initial-scan removed-files diff: bootstrap "before" from the
+    // server's known-paths set (status.fileHashes is what the server
+    // currently has for this project). Anything the server knows that
+    // the daemon doesn't see on disk now = removed. Closes the
+    // daemon-was-offline case and the newly-added-ignore-pattern case.
+    const currentPaths = allFiles.map((f) => f.path);
+    const currentPathSet = new Set(currentPaths);
+    const removedFiles = [...status.fileHashes.keys()].filter((p) => !currentPathSet.has(p));
+    await this.sendRemovedFiles(projectId, removedFiles).catch((err) => {
+      console.warn(
+        `[scanner] [${projectId.slice(0, 8)}] removedFiles report failed (non-blocking): ${(err as Error).message}`
+      );
+    });
+
     const duration = ((Date.now() - startTime) / 1000).toFixed(1);
     console.log(
       `[scanner] Scan complete for ${projectId.slice(0, 8)}: ` +
@@ -282,9 +345,27 @@ export class ScannerDaemon {
       isGitRepo,
       gitMiningEnabled: status.gitMining.enabled,
       lastMinedCommit: watermark,
+      currentPaths,
     };
   }
 
+  /**
+   * Send the explicit list of paths that vanished since the previous scan.
+   * Empty lists short-circuit so we don't pay an HTTP round-trip when
+   * nothing was removed this tick.
+   */
+  private async sendRemovedFiles(projectId: string, removedFiles: string[]): Promise<void> {
+    if (removedFiles.length === 0) return;
+    const result = await this.client.reportRemovedFiles(projectId, removedFiles);
+    if (result.deprecated > 0 || result.couplingsRemoved > 0) {
+      console.log(
+        `[scanner] [${projectId.slice(0, 8)}] Removed: ` +
+          `${removedFiles.length} paths sent, ${result.deprecated} memories deprecated, ` +
+          `${result.couplingsRemoved} couplings removed`
+      );
+    }
+  }
+
   /**
    * Fetch commits since the last mine. Swallows errors — a git failure must
    * not block the file scan push.
@@ -317,6 +398,10 @@ export class ScannerDaemon {
       if (chunks.length === 0) return;
 
       const files = await this.groupChunksByFile(chunks, projectRoot);
+      const authorityFiles = await this.collectAuthorityPushFiles(projectRoot);
+      // C1: dedupe — chunk-scanned entries win over authority duplicates
+      const seen = new Set(files.map((f) => f.path));
+      const allFiles = [...files, ...authorityFiles.filter((a) => !seen.has(a.path))];
 
       // attach any new commits since our cached watermark. Only the
       // first push carries them (idempotent jobId on the server collapses
@@ -331,9 +416,9 @@ export class ScannerDaemon {
       let hadFailure = false;
       let firstBatchSucceeded = false;
 
-      if (files.length > 0) {
-        for (let i = 0; i < files.length; i += batchSize) {
-          const batch = files.slice(i, i + batchSize);
+      if (allFiles.length > 0) {
+        for (let i = 0; i < allFiles.length; i += batchSize) {
+          const batch = allFiles.slice(i, i + batchSize);
           try {
             // Only attach commits to the first batch.
             await this.client.pushFiles(projectId, batch, i === 0 ? commits : undefined);
@@ -394,6 +479,11 @@ export class ScannerDaemon {
     project.retryTimer.unref();
   }
 
+  private async collectAuthorityPushFiles(projectRoot: string): Promise<ScanPushFile[]> {
+    const authority = await this.scanner.collectAuthorityFiles(projectRoot);
+    return authority.map((f) => ({ path: f.path, hash: f.hash, chunks: [], content: f.content }));
+  }
+
   private async groupChunksByFile(
     chunks: CodeChunk[],
     projectRoot: string
@@ -422,12 +512,16 @@ export class ScannerDaemon {
         const absPath = join(projectRoot, file.path);
         const raw = await readFile(absPath, 'utf-8');
         file.hash = createHash('sha256').update(raw).digest('hex');
+        // C2: drop content if it would exceed the server schema cap (5MB)
+        file.content = raw.length <= MAX_PUSH_CONTENT_BYTES ? raw : undefined;
       } catch (err) {
         console.warn(`[scanner] Cannot read ${file.path} for hashing, using chunk-based fallback`, {
           error: err instanceof Error ? err.message : String(err),
         });
         const allContent = file.chunks.map((c) => c.content).join('\n');
         file.hash = createHash('sha256').update(allContent).digest('hex');
+        // C2: drop content if it would exceed the server schema cap (5MB)
+        file.content = allContent.length <= MAX_PUSH_CONTENT_BYTES ? allContent : undefined;
       }
     }