pmem-ai 0.7.1 → 0.7.2

package/CHANGELOG.md

@@ -2,6 +2,27 @@
 
 All notable changes to pmem are documented here.
 
+## v0.7.2 — pmem-rt v1 MCP Adapter + Dogfooding Usability Fixes
+
+### Added
+
+- **pmem-rt v1 MCP Server**: New `pmem mcp` command starts a read-only stdio MCP server (`src/mcp/server.ts`) with 4 tools: `pmem_recall`, `pmem_ask`, `pmem_related`, `pmem_status`. All card content carries `content_trust: "untrusted_project_data"`. Uses `@modelcontextprotocol/sdk` (pure ESM, loaded via dynamic import).
+- **Query layer** (`src/core/query/`): Extracted pure query functions (`recallQuery`, `askQuery`, `relatedQuery`, `statusQuery`) shared by CLI and MCP server. No console.log, no process.exit(), no Commander.js dependency.
+- **MCP security** (`src/mcp/security.ts`): `validatePathScope` (realpath + path.sep comparison to prevent symlink escape and prefix confusion), `enforceBudget` (token budget truncation), `addContentTrust` (marks all card objects).
+- **`pmem milestone <version>`**: Records release milestones as memory cards with auto git-tag detection and manifest type registration.
+- **`pmem update --confirm --refresh-verified <ids>`**: Bumps `last_verified` on specified cards during confirm, before rebuild.
+- **`pmem mark-dirty --card <id...>`**: Explicit per-card dirty marking, bypassing git diff.
+
+### Fixed
+
+- **Exclude `.pmem/**` from stale_memory check**: Prevent false-positive warnings from `pmem update --confirm` rewriting manifest.yml / next.md / state.md / index.md.
+- **Separate `--fix` and `--fix-stale` semantics**: `--fix` handles structural index issues only; `--fix-stale` additionally refreshes stale_memory `last_verified` timestamps.
+- **`docs/dogfooding.md`**: Documents self-referential stale patterns, cleanup cadence, and new command workflows.
+
+### Version
+
+Bumped from 0.7.1 → 0.7.2.
+
 ## 0.7.0 - Universal Agent Memory (presets, custom card types, and domain neutrality)
 
 ### Added

package/README.md

@@ -346,14 +346,18 @@ pmem related <id> [--depth N] [--type <edge-type>] [--format compact|json] [--so
 pmem trace <id>
 
 pmem status [--since <timestamp>] [--format compact|json]
-pmem mark-dirty [-r <reason>] [--auto]
+pmem mark-dirty [-r <reason>] [--auto] [--card <id...>]
 pmem update [--auto] [--suggest] [--apply-suggestion <id>] [--confirm] [--force]
             [-s <summary>] [-n <next>] [--format compact|json] [--include-history]
             [--accept-edges <ids>] [--reject-edges <ids>]
+            [--refresh-verified <ids>]
+pmem sync -s "<summary>" [-n "<next>"]
+
+pmem milestone <version> [-m <message>] [--tag <name>]
 
 pmem distill [--suggest] [--confirm] [--apply-suggestion <id>] [--suggest-splits]
 pmem rebuild [--changed] [--full] [--card <id>]
-pmem verify [--fix] [--fix-locks] [--relaxed]
+pmem verify [--fix] [--fix-stale] [--fix-locks] [--relaxed]
 pmem doctor [--format compact|json]
 pmem new <type> <title>
 pmem rename --find <pattern> --replace <replacement> [--write]
@@ -362,6 +366,7 @@ pmem session start [-a <agent-name>]
 pmem session end [-s <summary>]
 pmem integration list|install <framework>|verify
 pmem install [--skills] [--claude] [--codex] [--gemini] [--all]
+pmem mcp
 ```
 
 ## Exit Codes
@@ -379,6 +384,39 @@ Agents should parse structured JSON output (`--format json`) to decide next step
 
 > **Breaking change from v0.6.1:** `pmem update --suggest` and `pmem distill --suggest` previously exited with code `1` when suggestions existed. Scripts that checked `$? -eq 1` must now parse JSON output instead.
 
+## pmem-rt — MCP Runtime for AI Agents (v0.7.2)
+
+pmem-rt is a read-only stdio MCP adapter that lets AI coding agents use pmem as a low-latency memory backend directly in their tool loop.
+
+### Quick Start
+
+```bash
+# In your project
+npm install pmem-ai
+npx pmem init --guided
+npx pmem rebuild
+
+# Configure your agent (e.g. Claude Code settings.json):
+# {
+#   "mcpServers": {
+#     "pmem": { "command": "npx", "args": ["pmem", "mcp"], "cwd": "/absolute/path/to/your-project" }
+#   }
+# }
+```
+
+### MCP Tools
+
+| Tool | Description |
+|------|-------------|
+| `pmem_recall` | Restore project context: name, stage, focus, next, active cards, recent updates |
+| `pmem_ask` | 6-step search: ID → alias → tag → graph expansion → FTS5 → LIKE |
+| `pmem_related` | Graph neighbors of a card, grouped by edge type with direction/confidence |
+| `pmem_status` | Changed files → affected memory cards |
+
+All tools are read-only. Writes continue through the CLI (`pmem update --confirm`, `pmem sync`). Every card carries `content_trust: "untrusted_project_data"`.
+
+[Full integration guide →](docs/pmem-rt.md)
+
 ## Project Layout
 
 ```txt

package/dist/commands/integration.js

@@ -375,7 +375,7 @@ function installIntegration(pmemPath, manifest, framework) {
     console.log(`✓ Integration "${framework}" installed.`);
     console.log(`  Template: .pmem/integrations/${framework}/`);
 }
-const CURRENT_TEMPLATE_VERSION = '0.7.1';
+const CURRENT_TEMPLATE_VERSION = '0.7.2';
 function verifyIntegrations(pmemPath, manifest) {
     if (!manifest)
         return;

package/dist/commands/mcp.d.ts

@@ -0,0 +1,9 @@
+/**
+ * Start a read-only stdio MCP server for agent tool integration.
+ *
+ * IMPORTANT: This command MUST NOT output any console.log — stdout is the
+ * MCP protocol transport channel. Any non-JSON output will cause protocol
+ * errors. Use stderr for diagnostics if absolutely necessary.
+ */
+export declare function mcpCommand(): Promise<void>;
+//# sourceMappingURL=mcp.d.ts.map

package/dist/commands/mcp.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"mcp.d.ts","sourceRoot":"","sources":["../../src/commands/mcp.ts"],"names":[],"mappings":"AAKA;;;;;;GAMG;AACH,wBAAsB,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC,CAmBhD"}

package/dist/commands/mcp.js

@@ -0,0 +1,64 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.mcpCommand = mcpCommand;
+const path = __importStar(require("path"));
+const fs_1 = require("../core/fs");
+const security_1 = require("../mcp/security");
+const server_1 = require("../mcp/server");
+/**
+ * Start a read-only stdio MCP server for agent tool integration.
+ *
+ * IMPORTANT: This command MUST NOT output any console.log — stdout is the
+ * MCP protocol transport channel. Any non-JSON output will cause protocol
+ * errors. Use stderr for diagnostics if absolutely necessary.
+ */
+async function mcpCommand() {
+    const cwd = process.cwd();
+    const pmemPath = path.join(cwd, '.pmem');
+    if (!(0, fs_1.fileExists)(pmemPath)) {
+        process.stderr.write('Error: No .pmem directory found. Run `pmem init` first.\n');
+        process.exit(2);
+    }
+    const dbPath = path.join(pmemPath, 'pmem.db');
+    if (!(0, fs_1.fileExists)(dbPath)) {
+        process.stderr.write('Error: No .pmem/pmem.db found. Run `pmem rebuild` first.\n');
+        process.exit(2);
+    }
+    // Security: validate path scope before starting
+    (0, security_1.validatePathScope)(pmemPath);
+    await (0, server_1.startMcpServer)(pmemPath);
+}
+//# sourceMappingURL=mcp.js.map

package/dist/commands/mcp.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"mcp.js","sourceRoot":"","sources":["../../src/commands/mcp.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAYA,gCAmBC;AA/BD,2CAA6B;AAC7B,mCAAwC;AACxC,8CAAoD;AACpD,0CAA+C;AAE/C;;;;;;GAMG;AACI,KAAK,UAAU,UAAU;IAC9B,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;IAC1B,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;IAEzC,IAAI,CAAC,IAAA,eAAU,EAAC,QAAQ,CAAC,EAAE,CAAC;QAC1B,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,2DAA2D,CAAC,CAAC;QAClF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SAAS,CAAC,CAAC;IAC9C,IAAI,CAAC,IAAA,eAAU,EAAC,MAAM,CAAC,EAAE,CAAC;QACxB,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,4DAA4D,CAAC,CAAC;QACnF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,gDAAgD;IAChD,IAAA,4BAAiB,EAAC,QAAQ,CAAC,CAAC;IAE5B,MAAM,IAAA,uBAAc,EAAC,QAAQ,CAAC,CAAC;AACjC,CAAC"}

package/dist/commands/milestone.d.ts

@@ -0,0 +1,5 @@
+export declare function milestoneCommand(version: string, options?: {
+    message?: string;
+    tag?: string;
+}): void;
+//# sourceMappingURL=milestone.d.ts.map

package/dist/commands/milestone.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"milestone.d.ts","sourceRoot":"","sources":["../../src/commands/milestone.ts"],"names":[],"mappings":"AAQA,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,GAAE;IAAE,OAAO,CAAC,EAAE,MAAM,CAAC;IAAC,GAAG,CAAC,EAAE,MAAM,CAAA;CAAO,GAAG,IAAI,CAyIxG"}

package/dist/commands/milestone.js

@@ -0,0 +1,197 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.milestoneCommand = milestoneCommand;
+const path = __importStar(require("path"));
+const child_process_1 = require("child_process");
+const fs_1 = require("../core/fs");
+const manifest_1 = require("../core/manifest");
+const db_1 = require("../core/db");
+const PMEM_DIR = '.pmem';
+function milestoneCommand(version, options = {}) {
+    const cwd = process.cwd();
+    const pmemPath = path.join(cwd, PMEM_DIR);
+    if (!(0, fs_1.fileExists)(pmemPath)) {
+        console.log('No .pmem directory found. Run `pmem init` first.');
+        process.exit(2);
+    }
+    const manifest = (0, manifest_1.loadManifest)(pmemPath);
+    if (!manifest) {
+        console.log('No manifest found. Run `pmem init` first.');
+        process.exit(2);
+    }
+    const config = (0, manifest_1.resolveConfig)(manifest);
+    // Determine the directory for milestone/trace cards
+    const traceDirName = config.type_dirs['trace'] || config.type_dirs['milestone'] || 'traces';
+    const traceDir = path.join(pmemPath, traceDirName);
+    (0, fs_1.ensureDir)(traceDir);
+    const versionClean = version.replace(/^v/, '');
+    const milestoneId = `milestone.v${versionClean}`;
+    const message = options.message || `Released version ${version}`;
+    const tag = options.tag || `v${versionClean}`;
+    // Check if git tag exists
+    let gitInfo = '';
+    try {
+        const gitDir = (0, child_process_1.execSync)('git rev-parse --git-dir', { cwd, stdio: 'ignore', encoding: 'utf8' }).trim();
+        if (gitDir) {
+            try {
+                const tagSha = (0, child_process_1.execSync)(`git rev-parse refs/tags/${tag}`, { cwd, stdio: 'pipe', encoding: 'utf8' }).trim();
+                gitInfo = `\n## Git Tag\n- Tag: \`${tag}\`\n- Commit: \`${tagSha.slice(0, 8)}\``;
+            }
+            catch {
+                try {
+                    const headSha = (0, child_process_1.execSync)('git rev-parse HEAD', { cwd, encoding: 'utf8' }).trim();
+                    gitInfo = `\n## Git\n- HEAD: \`${headSha.slice(0, 8)}\`\n- Tag \`${tag}\` not yet created (use \`git tag ${tag}\` to create it)`;
+                }
+                catch {
+                    // no git info available
+                }
+            }
+        }
+    }
+    catch {
+        // not a git repo
+    }
+    const milestoneFile = path.join(traceDir, `milestone.${milestoneId}.md`);
+    if ((0, fs_1.fileExists)(milestoneFile)) {
+        console.log(`Milestone card already exists: ${path.relative(cwd, milestoneFile)}`);
+        console.log(`  Edit it directly or use a different version.`);
+        process.exit(2);
+    }
+    (0, fs_1.atomicWrite)(milestoneFile, `---
+id: ${milestoneId}
+type: milestone
+status: shipped
+created: ${new Date().toISOString().split('T')[0]}
+tags: [release, ${tag}]
+---
+
+# Milestone: ${version}
+
+## What
+${message}
+
+## When
+Released ${new Date().toISOString().split('T')[0]}.
+${gitInfo}
+## Next
+Continue development toward the next milestone.
+`);
+    console.log(`Milestone recorded: ${path.relative(cwd, milestoneFile)}`);
+    console.log(`  Version: ${version}`);
+    console.log(`  ID: ${milestoneId}`);
+    // Register 'milestone' in manifest if not already present (review item #3)
+    registerMilestoneType(manifest, config, pmemPath);
+    // Index the card and link to related feature cards
+    let didRebuild = false;
+    const dbPath = path.join(pmemPath, 'pmem.db');
+    if ((0, fs_1.fileExists)(dbPath)) {
+        try {
+            const db = (0, db_1.openDatabase)(pmemPath);
+            (0, db_1.createSchema)(db);
+            // Rebuild to index the new card
+            const { rebuildCommand } = require('./rebuild');
+            rebuildCommand({ card: milestoneId });
+            didRebuild = true;
+            // Link to feature cards whose ID contains the version (tightened: match
+            // `feature.v<version>` prefix or `v<version_underscored>` segment).
+            const versionUnderscored = versionClean.replace(/\./g, '_');
+            const featureCards = db.prepare(`SELECT id FROM cards
+         WHERE type = 'feature'
+           AND (id LIKE ? OR id LIKE ?)
+           AND is_deleted = 0`).all(`feature.v${versionClean}%`, `%v${versionUnderscored}%`);
+            const now = new Date().toISOString();
+            for (const fc of featureCards) {
+                (0, db_1.insertEdge)(db, {
+                    from_id: milestoneId,
+                    to_id: fc.id,
+                    type: 'implements',
+                    source: 'inferred',
+                    confidence: 0.9,
+                    created_at: now,
+                    updated_at: now,
+                });
+            }
+            if (featureCards.length > 0) {
+                console.log(`  Linked to ${featureCards.length} feature card(s): ${featureCards.map(f => f.id).join(', ')}`);
+            }
+            (0, db_1.closeDatabase)();
+        }
+        catch {
+            // DB operations are best-effort
+        }
+    }
+    // Only suggest a manual rebuild when the DB path didn't already do one (review item #4)
+    if (!didRebuild) {
+        console.log(`\nRun \`pmem rebuild\` to index the new milestone card.`);
+    }
+    process.exit(0);
+}
+/**
+ * Ensure 'milestone' is registered in the manifest's card type whitelist
+ * so that verify / rebuild don't produce card_id_violation warnings.
+ */
+function registerMilestoneType(manifest, config, pmemPath) {
+    let changed = false;
+    // v0.7.0+ projects: add to schema.card_types
+    if (manifest.schema && Array.isArray(manifest.schema.card_types)) {
+        if (!manifest.schema.card_types.includes('milestone')) {
+            manifest.schema.card_types.push('milestone');
+            changed = true;
+        }
+        // Also add type_dirs entry if missing
+        if (!manifest.schema.type_dirs) {
+            manifest.schema.type_dirs = {};
+        }
+        if (!manifest.schema.type_dirs['milestone']) {
+            manifest.schema.type_dirs['milestone'] = 'traces';
+            changed = true;
+        }
+    }
+    // v0.6.x projects: add milestone to id_pattern alternation
+    if (manifest.card_policy?.id_pattern) {
+        const pattern = manifest.card_policy.id_pattern;
+        if (!pattern.includes('milestone')) {
+            // Insert milestone before the closing parenthesis of the type alternation
+            manifest.card_policy.id_pattern = pattern.replace(/(\([^)]+)\)/, '$1|milestone)');
+            changed = true;
+        }
+    }
+    if (changed) {
+        (0, manifest_1.saveManifest)(pmemPath, manifest);
+        console.log('  Registered "milestone" type in manifest.');
+    }
+}
+//# sourceMappingURL=milestone.js.map

package/dist/commands/milestone.js.map

@@ -0,0 +1 @@
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package/dist/commands/update.d.ts

@@ -10,8 +10,10 @@ export declare function updateCommand(options: {
     includeHistory?: boolean;
     acceptEdges?: string;
     rejectEdges?: string;
+    refreshVerified?: string;
 }): void;
 export declare function markDirtyCommand(reason: string, options?: {
     auto?: boolean;
+    cardIds?: string[];
 }): void;
 //# sourceMappingURL=update.d.ts.map

package/dist/commands/update.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"update.d.ts","sourceRoot":"","sources":["../../src/commands/update.ts"],"names":[],"mappings":"AAaA,wBAAgB,aAAa,CAAC,OAAO,EAAE;IACrC,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB,GAAG,IAAI,CA+CP;AAED,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,GAAE;IAAE,IAAI,CAAC,EAAE,OAAO,CAAA;CAAO,GAAG,IAAI,CAiGvF"}
+{"version":3,"file":"update.d.ts","sourceRoot":"","sources":["../../src/commands/update.ts"],"names":[],"mappings":"AAaA,wBAAgB,aAAa,CAAC,OAAO,EAAE;IACrC,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,eAAe,CAAC,EAAE,MAAM,CAAC;CAC1B,GAAG,IAAI,CA+CP;AAED,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,GAAE;IAAE,IAAI,CAAC,EAAE,OAAO,CAAC;IAAC,OAAO,CAAC,EAAE,MAAM,EAAE,CAAA;CAAO,GAAG,IAAI,CA0I3G"}

package/dist/commands/update.js

@@ -78,7 +78,7 @@ function updateCommand(options) {
     }
     // --confirm or --force: write changes
     if (options.confirm || options.force) {
-        confirmUpdate(pmemPath, options.summary, options.next);
+        confirmUpdate(pmemPath, options.summary, options.next, options.refreshVerified);
         return;
     }
     // no flag: show current dirty state
@@ -91,6 +91,44 @@ function markDirtyCommand(reason, options = {}) {
         console.log('No .pmem directory found. Run `pmem init` first.');
         return;
     }
+    // --card <id>: explicitly mark specific cards as dirty
+    if (options.cardIds && options.cardIds.length > 0) {
+        const dbPath = path.join(pmemPath, 'pmem.db');
+        if (!(0, fs_1.fileExists)(dbPath)) {
+            console.log('No SQLite database found. Run `pmem rebuild` first.');
+            process.exit(2);
+        }
+        try {
+            const db = (0, db_1.openDatabase)(pmemPath);
+            const activeSession = (0, db_1.getActiveSession)(db);
+            for (const cardId of options.cardIds) {
+                const card = db.prepare('SELECT id FROM cards WHERE id = ? AND is_deleted = 0').get(cardId);
+                if (card) {
+                    (0, db_1.insertDirtyFlag)(db, 'card', cardId, reason, activeSession?.id);
+                    console.log(`Marked card dirty: ${cardId}`);
+                }
+                else {
+                    console.log(`Card not found or deleted: ${cardId}`);
+                }
+            }
+            // Also mark project-level dirty
+            const manifest = (0, manifest_1.loadManifest)(pmemPath);
+            if (manifest) {
+                const timestamp = new Date().toISOString();
+                manifest.memory_status.dirty = true;
+                manifest.memory_status.dirty_reason = reason;
+                manifest.memory_status.dirty_since = timestamp;
+                (0, manifest_1.saveManifest)(pmemPath, manifest);
+                (0, db_1.insertDirtyFlag)(db, 'project', '.pmem', reason, activeSession?.id);
+            }
+            (0, db_1.closeDatabase)();
+            return;
+        }
+        catch (err) {
+            console.error('Could not mark cards as dirty:', err);
+            process.exit(2);
+        }
+    }
     // --auto: detect changed files via git and mark related cards as dirty
     if (options.auto) {
         const dbPath = path.join(pmemPath, 'pmem.db');
@@ -251,7 +289,7 @@ function autoUpdate(pmemPath, manifest) {
         }
     }
 }
-function confirmUpdate(pmemPath, summary, next) {
+function confirmUpdate(pmemPath, summary, next, refreshVerified) {
     const lockPath = path.join(pmemPath, '.lock');
     if (!(0, fs_1.acquireLock)(lockPath)) {
         console.log('Failed to acquire pmem lock after 3s.');
@@ -335,7 +373,53 @@ ${next || 'Continue as planned.'}
             manifest.memory_status.dirty_since = null;
             (0, manifest_1.saveManifest)(pmemPath, manifest);
         }
-        // Rebuild indexes
+        // --refresh-verified: bump last_verified on specified cards.
+        // MUST run BEFORE rebuildCommand() so the updated frontmatter
+        // is picked up by the rebuild and SQLite hashes stay in sync.
+        if (refreshVerified) {
+            const cardIds = refreshVerified.split(',').map(s => s.trim()).filter(Boolean);
+            const refreshDbPath = path.join(pmemPath, 'pmem.db');
+            if ((0, fs_1.fileExists)(refreshDbPath) && cardIds.length > 0) {
+                try {
+                    const refreshDb = (0, db_1.openDatabase)(pmemPath); // open once
+                    const refreshed = [];
+                    for (const cardId of cardIds) {
+                        const card = refreshDb.prepare('SELECT file_path FROM cards WHERE id = ?').get(cardId);
+                        if (card) {
+                            const cardFilePath = path.join(process.cwd(), card.file_path);
+                            if ((0, fs_1.fileExists)(cardFilePath)) {
+                                const content = (0, fs_1.readFile)(cardFilePath);
+                                if (content) {
+                                    const match = content.match(/^---\n([\s\S]*?)\n---/);
+                                    if (match) {
+                                        const frontmatterText = match[1];
+                                        const nowStr = new Date().toISOString();
+                                        let newFmText = frontmatterText;
+                                        const regex = /^last_verified:.*$/m;
+                                        if (regex.test(frontmatterText)) {
+                                            newFmText = frontmatterText.replace(regex, `last_verified: "${nowStr}"`);
+                                        }
+                                        else {
+                                            newFmText = frontmatterText.trimEnd() + `\nlast_verified: "${nowStr}"`;
+                                        }
+                                        const newContent = content.replace(/^---\n([\s\S]*?)\n---/, `---\n${newFmText}\n---`);
+                                        (0, fs_1.writeFile)(cardFilePath, newContent);
+                                        refreshed.push(cardId);
+                                    }
+                                }
+                            }
+                        }
+                    }
+                    if (refreshed.length > 0) {
+                        console.log(`Refreshed last_verified for: ${refreshed.join(', ')}`);
+                    }
+                }
+                catch {
+                    // skip cards that can't be refreshed
+                }
+            }
+        }
+        // Rebuild indexes — picks up frontmatter changes from --refresh-verified above
         console.log('Rebuilding indexes...');
         (0, rebuild_1.rebuildCommand)();
         console.log('\n✓ Memory updated.');