pmem-ai 0.7.1-a → 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-a';
+const CURRENT_TEMPLATE_VERSION = '0.7.2';
 function verifyIntegrations(pmemPath, manifest) {
     if (!manifest)
         return;

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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 @@
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package/dist/core/query/ask.d.ts

@@ -0,0 +1,20 @@
+type MatchType = 'exact_id' | 'exact_title' | 'alias' | 'tag' | 'graph_expansion' | 'keyword_fallback';
+interface AskMatchV03 {
+    id: string;
+    title: string;
+    match_type: MatchType;
+    confidence: number;
+    graph_distance: number;
+    file: string;
+    edge_type?: string;
+    from_card?: string;
+}
+export interface AskResultV03 {
+    query: string;
+    matched: AskMatchV03[];
+    recommended_files: string[];
+    evidence_paths: string[];
+}
+export declare function askQuery(pmemPath: string, query: string): AskResultV03;
+export {};
+//# sourceMappingURL=ask.d.ts.map

package/dist/core/query/ask.d.ts.map

@@ -0,0 +1 @@
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package/dist/core/query/ask.js

@@ -0,0 +1,256 @@
+"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.askQuery = askQuery;
+const path = __importStar(require("path"));
+const fs_1 = require("../fs");
+const db_1 = require("../db");
+const manifest_1 = require("../manifest");
+function askQuery(pmemPath, query) {
+    const dbPath = path.join(pmemPath, 'pmem.db');
+    if (!(0, fs_1.fileExists)(dbPath)) {
+        throw new Error('No SQLite database found. Run `pmem rebuild` first.');
+    }
+    const db = (0, db_1.openDatabase)(pmemPath);
+    (0, db_1.createSchema)(db);
+    const normalizedQuery = query.toLowerCase().trim();
+    const queryTokens = tokenize(normalizedQuery);
+    const matches = [];
+    const seenIds = new Set();
+    // Step 1: Exact match — card ID
+    const idMatches = db.prepare("SELECT * FROM cards WHERE (id = ? OR id LIKE ?) AND is_deleted = 0").all(normalizedQuery, `%${normalizedQuery}%`);
+    for (const card of idMatches) {
+        if (seenIds.has(card.id))
+            continue;
+        seenIds.add(card.id);
+        matches.push({
+            id: card.id,
+            title: card.title,
+            match_type: card.id === normalizedQuery ? 'exact_id' : 'exact_title',
+            confidence: card.id === normalizedQuery ? 0.95 : 0.85,
+            graph_distance: 0,
+            file: card.file_path,
+        });
+    }
+    // Step 2: Exact match — aliases
+    const aliasMatches = db.prepare(`SELECT c.* FROM cards c
+     JOIN aliases a ON c.id = a.card_id
+     WHERE (a.normalized_alias = ? OR a.normalized_alias LIKE ?)
+       AND c.is_deleted = 0`).all(normalizedQuery, `%${normalizedQuery}%`);
+    for (const card of aliasMatches) {
+        if (seenIds.has(card.id))
+            continue;
+        seenIds.add(card.id);
+        matches.push({
+            id: card.id,
+            title: card.title,
+            match_type: 'alias',
+            confidence: 0.9,
+            graph_distance: 0,
+            file: card.file_path,
+        });
+    }
+    // Step 3: Exact match — tags
+    const tagMatches = db.prepare(`SELECT c.* FROM cards c
+     JOIN tags t ON c.id = t.card_id
+     WHERE t.normalized_tag = ?
+       AND c.is_deleted = 0`).all(normalizedQuery);
+    for (const card of tagMatches) {
+        if (seenIds.has(card.id))
+            continue;
+        seenIds.add(card.id);
+        matches.push({
+            id: card.id,
+            title: card.title,
+            match_type: 'tag',
+            confidence: 0.7,
+            graph_distance: 0,
+            file: card.file_path,
+        });
+    }
+    // Token-based tag matching
+    for (const token of queryTokens) {
+        const tokenTagMatches = db.prepare(`SELECT c.* FROM cards c
+       JOIN tags t ON c.id = t.card_id
+       WHERE t.normalized_tag LIKE ?
+         AND c.is_deleted = 0`).all(`%${token}%`);
+        for (const card of tokenTagMatches) {
+            if (seenIds.has(card.id))
+                continue;
+            seenIds.add(card.id);
+            matches.push({
+                id: card.id,
+                title: card.title,
+                match_type: 'tag',
+                confidence: 0.6,
+                graph_distance: 0,
+                file: card.file_path,
+            });
+        }
+    }
+    // Step 4: Graph expansion — 1-hop neighbors
+    const matchedIdsAtThisPoint = new Set(matches.map(m => m.id));
+    for (const match of matches) {
+        const edges = db.prepare("SELECT * FROM edges WHERE from_id = ? OR to_id = ?").all(match.id, match.id);
+        for (const edge of edges) {
+            const neighborId = edge.from_id === match.id ? edge.to_id : edge.from_id;
+            if (matchedIdsAtThisPoint.has(neighborId) || seenIds.has(neighborId))
+                continue;
+            seenIds.add(neighborId);
+            const neighborCard = db.prepare("SELECT * FROM cards WHERE id = ? AND is_deleted = 0").get(neighborId);
+            if (neighborCard) {
+                matches.push({
+                    id: neighborCard.id,
+                    title: neighborCard.title,
+                    match_type: 'graph_expansion',
+                    confidence: 0.6,
+                    graph_distance: 1,
+                    file: neighborCard.file_path,
+                    edge_type: edge.type,
+                    from_card: match.id,
+                });
+            }
+        }
+    }
+    // Step 5: Keyword fallback — FTS5 if available, else LIKE
+    const directMatchesBeforeFallback = matches.filter(m => m.match_type !== 'graph_expansion');
+    if (directMatchesBeforeFallback.length === 0) {
+        if ((0, db_1.hasFTS5)(db)) {
+            try {
+                const ftsResults = db.prepare("SELECT c.*, rank FROM card_fts JOIN cards c ON card_fts.card_id = c.id WHERE card_fts MATCH ? AND c.is_deleted = 0 ORDER BY rank").all(normalizedQuery);
+                for (const row of ftsResults) {
+                    if (seenIds.has(row.id))
+                        continue;
+                    seenIds.add(row.id);
+                    matches.push({
+                        id: row.id,
+                        title: row.title,
+                        match_type: 'keyword_fallback',
+                        confidence: Math.min(0.5, 1 / (1 + (row.rank || 1))),
+                        graph_distance: 0,
+                        file: row.file_path,
+                    });
+                }
+            }
+            catch {
+                // FTS5 query failed, fall through to LIKE fallback
+            }
+        }
+        // LIKE fallback
+        if (matches.filter(m => m.match_type === 'keyword_fallback').length === 0) {
+            const likePattern = `%${normalizedQuery}%`;
+            const likeResults = db.prepare("SELECT * FROM cards WHERE (title LIKE ? OR summary LIKE ?) AND is_deleted = 0").all(likePattern, likePattern);
+            for (const card of likeResults) {
+                if (seenIds.has(card.id))
+                    continue;
+                seenIds.add(card.id);
+                const titleLower = card.title.toLowerCase();
+                const tokenOverlap = queryTokens.filter(t => titleLower.includes(t)).length;
+                matches.push({
+                    id: card.id,
+                    title: card.title,
+                    match_type: 'keyword_fallback',
+                    confidence: Math.min(0.5, tokenOverlap / Math.max(1, queryTokens.length)),
+                    graph_distance: 0,
+                    file: card.file_path,
+                });
+            }
+        }
+    }
+    // Step 6: Rerank
+    const typeOrder = {
+        exact_id: 5,
+        exact_title: 4,
+        alias: 3,
+        tag: 2,
+        graph_expansion: 1,
+        keyword_fallback: 0,
+    };
+    matches.sort((a, b) => {
+        return ((typeOrder[b.match_type] - typeOrder[a.match_type]) ||
+            (b.confidence - a.confidence) ||
+            (a.graph_distance - b.graph_distance));
+    });
+    // Step 7: Deduplicate
+    const dedupedIds = new Set();
+    const deduped = [];
+    for (const m of matches) {
+        if (dedupedIds.has(m.id))
+            continue;
+        dedupedIds.add(m.id);
+        deduped.push(m);
+    }
+    // Build recommended_files and evidence_paths
+    const recommendedFiles = [];
+    for (const m of deduped.slice(0, 8)) {
+        recommendedFiles.push(m.file);
+    }
+    const manifest = (0, manifest_1.loadManifest)(pmemPath);
+    const config = manifest ? (0, manifest_1.resolveConfig)(manifest) : { evidence_types: ['decision', 'trace'] };
+    const evidenceTypes = config.evidence_types;
+    const evidencePaths = [];
+    for (const m of deduped) {
+        const card = db.prepare("SELECT type, file_path FROM cards WHERE id = ? AND is_deleted = 0").get(m.id);
+        if (card && evidenceTypes.includes(card.type)) {
+            evidencePaths.push(card.file_path);
+        }
+    }
+    return {
+        query,
+        matched: deduped,
+        recommended_files: recommendedFiles,
+        evidence_paths: evidencePaths,
+    };
+}
+function tokenize(text) {
+    const tokens = [];
+    const words = text.split(/[\s,，。、；;：:！!？?()（）\[\]【】{}]+/);
+    for (const word of words) {
+        if (word.length === 0)
+            continue;
+        if (/[一-鿿]/.test(word)) {
+            const cjkChars = word.match(/[一-鿿]/g) || [];
+            tokens.push(...cjkChars);
+            const nonCjk = word.replace(/[一-鿿]/g, '').trim();
+            if (nonCjk)
+                tokens.push(nonCjk.toLowerCase());
+        }
+        else {
+            tokens.push(word.toLowerCase());
+        }
+    }
+    return [...new Set(tokens)];
+}
+//# sourceMappingURL=ask.js.map

package/dist/core/query/ask.js.map

@@ -0,0 +1 @@
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package/dist/core/query/recall.d.ts

@@ -0,0 +1,21 @@
+export interface RecallQueryResult {
+    project: string;
+    stage?: string;
+    focus: string;
+    state: string[];
+    next: string;
+    mustRead: string[];
+    dirty_flags_count: number;
+    recent_updates: Array<{
+        action: string;
+        summary: string | null;
+        created_at: string;
+    }>;
+    active_modules: string[];
+    active_foundation: string[];
+}
+export declare function recallQuery(pmemPath: string, options?: {
+    budget?: number;
+    since?: string;
+}): RecallQueryResult;
+//# sourceMappingURL=recall.d.ts.map

package/dist/core/query/recall.d.ts.map

@@ -0,0 +1 @@
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