pmem-ai 0.7.1 → 0.7.3

package/CHANGELOG.md

@@ -2,6 +2,46 @@
 
 All notable changes to pmem are documented here.
 
+## v0.7.3 — `rebuild --full` Edge Cleanup (closes #6)
+
+### Fixed
+
+- **`pmem rebuild --full` left orphan + stale edges after card split/delete** (issue #6, three concrete bugs):
+  1. *Orphan inbound edges*: When a target card was deleted but other cards' frontmatter still named it (or the user had edited their own `related:` to `[]`), the explicit edges survived `--full`. `clearAllTables` ran but the v0.7.0-a snapshot+restore step then resurrected them. Now `--full` post-cleans any edge whose `from_id` or `to_id` no longer has a `cards` row, and the snapshot+restore step skips managed sources (`explicit`/`inferred`/`mention`) so they cannot be resurrected.
+  2. *Stale `depends_on` / `related`*: When a card's `depends_on` array was reduced (e.g. `[A, X, Y]` → `[X]`), the rebuild loop's per-card `deleteExplicitCardEdges` correctly removed the old rows, but the snapshot+restore step put them back. The smart snapshot+restore filter (see above) now refuses to re-insert managed-source edges, so the diff takes effect.
+  3. *Stale inferred `next_step_of`*: Same mechanism for `source='inferred'` task→module edges. In addition, the rebuild loop now also calls a new per-card `deleteInferredCardEdges` so *incremental* rebuilds re-derive inferred edges from the current `related` frontmatter — previously only `--full` cleared them, and only by accident via `clearAllTables`.
+- **Workaround SQL from the issue is no longer required.** All three manual `sqlite3` cleanup statements in the issue body become no-ops after `--full`.
+
+### Added
+
+- `deleteInferredCardEdges(db, cardId)` and `deleteOrphanEdges(db)` helpers in `src/core/db.ts`.
+- 3 new integration tests in `src/commands/rebuild.test.ts` covering all three bugs and a regression test that confirms manually-inserted (`source='manual'`) edges still round-trip through `--full`.
+
+### Version
+
+Bumped from 0.7.2 → 0.7.3.
+
+## 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 @@
+{"version":3,"file":"milestone.js","sourceRoot":"","sources":["../../src/commands/milestone.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAQA,4CAyIC;AAjJD,2CAA6B;AAC7B,iDAAyC;AACzC,mCAAgE;AAChE,+CAA6E;AAC7E,mCAAmF;AAEnF,MAAM,QAAQ,GAAG,OAAO,CAAC;AAEzB,SAAgB,gBAAgB,CAAC,OAAe,EAAE,UAA8C,EAAE;IAChG,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;IAC1B,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;IAE1C,IAAI,CAAC,IAAA,eAAU,EAAC,QAAQ,CAAC,EAAE,CAAC;QAC1B,OAAO,CAAC,GAAG,CAAC,kDAAkD,CAAC,CAAC;QAChE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,MAAM,QAAQ,GAAG,IAAA,uBAAY,EAAC,QAAQ,CAAC,CAAC;IACxC,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,CAAC,GAAG,CAAC,2CAA2C,CAAC,CAAC;QACzD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,MAAM,MAAM,GAAG,IAAA,wBAAa,EAAC,QAAQ,CAAC,CAAC;IAEvC,oDAAoD;IACpD,MAAM,YAAY,GAAG,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,IAAI,MAAM,CAAC,SAAS,CAAC,WAAW,CAAC,IAAI,QAAQ,CAAC;IAC5F,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,YAAY,CAAC,CAAC;IACnD,IAAA,cAAS,EAAC,QAAQ,CAAC,CAAC;IAEpB,MAAM,YAAY,GAAG,OAAO,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAC/C,MAAM,WAAW,GAAG,cAAc,YAAY,EAAE,CAAC;IAEjD,MAAM,OAAO,GAAG,OAAO,CAAC,OAAO,IAAI,oBAAoB,OAAO,EAAE,CAAC;IACjE,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,IAAI,IAAI,YAAY,EAAE,CAAC;IAE9C,0BAA0B;IAC1B,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,IAAA,wBAAQ,EAAC,yBAAyB,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;QACtG,IAAI,MAAM,EAAE,CAAC;YACX,IAAI,CAAC;gBACH,MAAM,MAAM,GAAG,IAAA,wBAAQ,EAAC,2BAA2B,GAAG,EAAE,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC3G,OAAO,GAAG,0BAA0B,GAAG,mBAAmB,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC;YACnF,CAAC;YAAC,MAAM,CAAC;gBACP,IAAI,CAAC;oBACH,MAAM,OAAO,GAAG,IAAA,wBAAQ,EAAC,oBAAoB,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;oBACjF,OAAO,GAAG,uBAAuB,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,eAAe,GAAG,qCAAqC,GAAG,kBAAkB,CAAC;gBACnI,CAAC;gBAAC,MAAM,CAAC;oBACP,wBAAwB;gBAC1B,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAAC,MAAM,CAAC;QACP,iBAAiB;IACnB,CAAC;IAED,MAAM,aAAa,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,aAAa,WAAW,KAAK,CAAC,CAAC;IAEzE,IAAI,IAAA,eAAU,EAAC,aAAa,CAAC,EAAE,CAAC;QAC9B,OAAO,CAAC,GAAG,CAAC,kCAAkC,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,aAAa,CAAC,EAAE,CAAC,CAAC;QACnF,OAAO,CAAC,GAAG,CAAC,gDAAgD,CAAC,CAAC;QAC9D,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,IAAA,gBAAW,EAAC,aAAa,EAAE;MACvB,WAAW;;;WAGN,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;kBAC/B,GAAG;;;eAGN,OAAO;;;EAGpB,OAAO;;;WAGE,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;EAC/C,OAAO;;;CAGR,CAAC,CAAC;IAED,OAAO,CAAC,GAAG,CAAC,uBAAuB,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,aAAa,CAAC,EAAE,CAAC,CAAC;IACxE,OAAO,CAAC,GAAG,CAAC,cAAc,OAAO,EAAE,CAAC,CAAC;IACrC,OAAO,CAAC,GAAG,CAAC,SAAS,WAAW,EAAE,CAAC,CAAC;IAEpC,2EAA2E;IAC3E,qBAAqB,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAC;IAElD,mDAAmD;IACnD,IAAI,UAAU,GAAG,KAAK,CAAC;IACvB,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SAAS,CAAC,CAAC;IAC9C,IAAI,IAAA,eAAU,EAAC,MAAM,CAAC,EAAE,CAAC;QACvB,IAAI,CAAC;YACH,MAAM,EAAE,GAAG,IAAA,iBAAY,EAAC,QAAQ,CAAC,CAAC;YAClC,IAAA,iBAAY,EAAC,EAAE,CAAC,CAAC;YAEjB,gCAAgC;YAChC,MAAM,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;YAChD,cAAc,CAAC,EAAE,IAAI,EAAE,WAAW,EAAE,CAAC,CAAC;YACtC,UAAU,GAAG,IAAI,CAAC;YAElB,wEAAwE;YACxE,oEAAoE;YACpE,MAAM,kBAAkB,GAAG,YAAY,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;YAC5D,MAAM,YAAY,GAAG,EAAE,CAAC,OAAO,CAC7B;;;8BAGsB,CACvB,CAAC,GAAG,CACH,YAAY,YAAY,GAAG,EAC3B,KAAK,kBAAkB,GAAG,CACF,CAAC;YAE3B,MAAM,GAAG,GAAG,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;YACrC,KAAK,MAAM,EAAE,IAAI,YAAY,EAAE,CAAC;gBAC9B,IAAA,eAAU,EAAC,EAAE,EAAE;oBACb,OAAO,EAAE,WAAW;oBACpB,KAAK,EAAE,EAAE,CAAC,EAAE;oBACZ,IAAI,EAAE,YAAY;oBAClB,MAAM,EAAE,UAAU;oBAClB,UAAU,EAAE,GAAG;oBACf,UAAU,EAAE,GAAG;oBACf,UAAU,EAAE,GAAG;iBAChB,CAAC,CAAC;YACL,CAAC;YACD,IAAI,YAAY,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAC5B,OAAO,CAAC,GAAG,CAAC,eAAe,YAAY,CAAC,MAAM,qBAAqB,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YAC/G,CAAC;YAED,IAAA,kBAAa,GAAE,CAAC;QAClB,CAAC;QAAC,MAAM,CAAC;YACP,gCAAgC;QAClC,CAAC;IACH,CAAC;IAED,wFAAwF;IACxF,IAAI,CAAC,UAAU,EAAE,CAAC;QAChB,OAAO,CAAC,GAAG,CAAC,yDAAyD,CAAC,CAAC;IACzE,CAAC;IACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC;AAED;;;GAGG;AACH,SAAS,qBAAqB,CAAC,QAAa,EAAE,MAAW,EAAE,QAAgB;IACzE,IAAI,OAAO,GAAG,KAAK,CAAC;IAEpB,6CAA6C;IAC7C,IAAI,QAAQ,CAAC,MAAM,IAAI,KAAK,CAAC,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAC,UAAU,CAAC,EAAE,CAAC;QACjE,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE,CAAC;YACtD,QAAQ,CAAC,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;YAC7C,OAAO,GAAG,IAAI,CAAC;QACjB,CAAC;QACD,sCAAsC;QACtC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC;YAC/B,QAAQ,CAAC,MAAM,CAAC,SAAS,GAAG,EAAE,CAAC;QACjC,CAAC;QACD,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,SAAS,CAAC,WAAW,CAAC,EAAE,CAAC;YAC5C,QAAQ,CAAC,MAAM,CAAC,SAAS,CAAC,WAAW,CAAC,GAAG,QAAQ,CAAC;YAClD,OAAO,GAAG,IAAI,CAAC;QACjB,CAAC;IACH,CAAC;IAED,2DAA2D;IAC3D,IAAI,QAAQ,CAAC,WAAW,EAAE,UAAU,EAAE,CAAC;QACrC,MAAM,OAAO,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package/dist/commands/rebuild.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"rebuild.d.ts","sourceRoot":"","sources":["../../src/commands/rebuild.ts"],"names":[],"mappings":"AAWA,UAAU,cAAc;IACtB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AASD,wBAAgB,cAAc,CAAC,OAAO,GAAE,cAAmB,GAAG,IAAI,CAmajE;AA8BD;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,EAAE,CAQ3D"}
+{"version":3,"file":"rebuild.d.ts","sourceRoot":"","sources":["../../src/commands/rebuild.ts"],"names":[],"mappings":"AAWA,UAAU,cAAc;IACtB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AASD,wBAAgB,cAAc,CAAC,OAAO,GAAE,cAAmB,GAAG,IAAI,CAidjE;AA8BD;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,EAAE,CAQ3D"}

package/dist/commands/rebuild.js

@@ -217,9 +217,15 @@ function rebuildCommand(options = {}) {
                 is_candidate: isCandidate,
             };
             (0, db_1.upsertCard)(db, cardRow);
-            // Clear existing explicit and mention relations before re-inserting (preserve inferred edges)
+            // Clear existing explicit, mention, and inferred relations before
+            // re-inserting from the current frontmatter. v0.7.3 (issue #6):
+            // inferred edges (e.g. task→module next_step_of) must also be
+            // re-derived per card — otherwise an incremental rebuild that
+            // re-targets a task's `related` to a different module would
+            // leave the stale inferred edge to the old module in place.
             (0, db_1.deleteExplicitCardEdges)(db, fm.id);
             (0, db_1.deleteMentionEdges)(db, fm.id);
+            (0, db_1.deleteInferredCardEdges)(db, fm.id);
             (0, db_1.deleteCardAliases)(db, fm.id);
             (0, db_1.deleteCardTags)(db, fm.id);
             (0, db_1.deleteCardPaths)(db, fm.id);
@@ -310,25 +316,63 @@ function rebuildCommand(options = {}) {
     });
     // Execute all SQLite writes in a single transaction
     doRebuild();
-    // v0.7.0-a: restore manually inserted edges that were not re-created
-    // by the rebuild loop (preserved across --full rebuilds)
+    // v0.7.3 (issue #6): prune orphan edges after a --full rebuild.
+    // The rebuild loop inserts explicit edges (depends_on, related) from
+    // each card's current frontmatter without checking that the target
+    // card still has a file. If a target card was deleted but the
+    // declaring card's frontmatter still names it (or a card was just
+    // renamed and the caller hasn't yet propagated the rename), those
+    // edges would otherwise dangle and trip `pmem verify`'s
+    // orphan_edges / too_many_relations checks.
+    if (isFull) {
+        (0, db_1.deleteOrphanEdges)(db);
+    }
+    // v0.7.0-a (revised in v0.7.3, issue #6): restore edges that the
+    // rebuild loop did not and could not have re-derived. We now
+    // restrict restoration to:
+    //   - sources the rebuild loop does NOT manage (anything other than
+    //     'explicit', 'inferred', 'mention'). These are typically manual
+    //     SQL inserts that should survive a full rebuild.
+    //   - edges whose both endpoints still exist in the cards table.
+    //     Orphan edges (e.g. pointing to a deleted card) are NOT
+    //     restored, since they would just be pruned again by
+    //     `deleteOrphanEdges` and the user wants them gone.
+    // Without these filters, the snapshot+restore step would resurrect
+    // every `depends_on` / `related_to` / `next_step_of` edge that the
+    // user had just removed from a card's frontmatter — the original
+    // root cause of issue #6.
     if (isFull && snappedEdges.length > 0) {
         const restoreEdgeTx = db.transaction(() => {
+            // Build a set of currently-existing card IDs so the restore loop
+            // can skip edges whose endpoints no longer exist.
+            const existingCardIds = new Set(db.prepare("SELECT id FROM cards WHERE is_deleted = 0").all().map(r => r.id));
             // Build set of current edge keys: "from_id|to_id|type|source"
             const currentKeys = new Set();
             const currentEdges = db.prepare("SELECT from_id, to_id, type, source FROM edges").all();
             for (const e of currentEdges) {
                 currentKeys.add(`${e.from_id}|${e.to_id}|${e.type}|${e.source}`);
             }
+            // Sources managed by the rebuild loop — restoring any of these
+            // would re-introduce the very stale edges we just deleted from
+            // the loop's deleteExplicitCardEdges/deleteMentionEdges/
+            // deleteInferredCardEdges pass.
+            const managedSources = new Set(['explicit', 'inferred', 'mention']);
             const restoreStmt = db.prepare("INSERT OR IGNORE INTO edges (from_id, to_id, type, source, confidence, created_at, updated_at) VALUES (?, ?, ?, ?, ?, ?, ?)");
             let restoredCount = 0;
             const now = new Date().toISOString();
             for (const e of snappedEdges) {
+                // Skip managed sources — they should be re-derived from
+                // current frontmatter, not resurrected from the snapshot.
+                if (managedSources.has(e.source))
+                    continue;
+                // Skip orphan edges — both endpoints must still be cards.
+                if (!existingCardIds.has(e.from_id) || !existingCardIds.has(e.to_id))
+                    continue;
                 const key = `${e.from_id}|${e.to_id}|${e.type}|${e.source}`;
-                if (!currentKeys.has(key)) {
-                    restoreStmt.run(e.from_id, e.to_id, e.type, e.source, e.confidence, e.created_at ?? now, e.updated_at ?? now);
-                    restoredCount++;
-                }
+                if (currentKeys.has(key))
+                    continue;
+                restoreStmt.run(e.from_id, e.to_id, e.type, e.source, e.confidence, e.created_at ?? now, e.updated_at ?? now);
+                restoredCount++;
             }
             if (restoredCount > 0) {
                 preservedEdges = restoredCount;

package/dist/commands/rebuild.js.map

@@ -1 +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 @@
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