pmem-ai 0.7.6 → 0.8.0

package/CHANGELOG.md

@@ -2,6 +2,20 @@
 
 All notable changes to pmem are documented here.
 
+## v0.7.6-a — Stale Card Cleanup & missing_card_file Fix (2026-06-29)
+
+### Fixed
+
+- **`missing_card_file` rebuild dead loop (#12)**: `pmem verify` previously reported `missing_card_file` and suggested `pmem rebuild`, but incremental rebuild only processed existing `.md` files on disk and never cleaned up DB rows for deleted cards — creating an unresolvable loop. Incremental rebuild now detects stale DB cards whose source files no longer exist, marks them `is_deleted = 1`, and cleans up their edges/aliases/tags/paths.
+- **`deleteOrphanEdges` now runs unconditionally**: Previously only called during `--full` rebuild; now runs in all rebuild modes since stale card cleanup can create new orphan edges in incremental mode.
+- **`--fix` / `--fix-stale` directly handle `missing_card_file`**: Before calling rebuild, these options now directly remove stale card rows from the database, providing an immediate repair path without waiting for index rebuild.
+
+### Changed
+
+- **Verify fix hint updated**: `missing_card_file` now suggests `"pmem rebuild (incremental rebuild will clean up stale card references)"` instead of just `"pmem rebuild"`.
+- **`card_id` added to `missing_card_file` verify issues**: Enables direct DB cleanup by `--fix` / `--fix-stale`.
+- **Rebuild summary reports cleaned stale cards**: `"Cleaned N stale card(s) (source files deleted)"` when applicable.
+
 ## v0.7.6 — Agent Contract & Write-Path Integrity (2026-06-28)
 
 ### Added

package/README.md

@@ -215,16 +215,18 @@ Do not edit SQLite directly. Edit Markdown cards or use pmem workflow commands,
 
 ### Recall And Ask
 
-Use `recall` for the current project state:
+Use `recall` for the current project state. v0.8 (upcoming on `main` branch, not yet released to npm) adds budget modes: `brief` returns L0 + read-if-needed paths, `normal` is the default agent context, and `deep` preserves more detail when budget allows.
 
 ```bash
 pmem recall --budget 2000
+pmem recall --mode brief --budget 500
 ```
 
-Use `ask` for targeted retrieval:
+Use `ask` for targeted retrieval. v0.8 (upcoming on `main` branch, not yet released to npm) uses the Hybrid Recall Engine: exact IDs, aliases, tags, source file paths, always-on FTS5/BM25, graph expansion, recency, and stale/dirty penalties are fused into a deterministic score. Add `--explain` to see why each card was recalled.
 
 ```bash
 pmem ask "sqlite runtime" --format compact
+pmem ask "src/core/query/recall.ts" --explain --limit 5
 pmem ask "release checklist" --format json
 ```
 
@@ -382,8 +384,8 @@ pmem init [project-name] [--guided] [--description <text>] [--stage <text>] [--n
 pmem context <task> [--budget N] [--format compact|json]
 pmem capture [--auto] [-s <summary>] [-n <next>] [--full] [--force]
 
-pmem recall [--budget N] [--format compact|json|paths|pack] [--since <duration>]
-pmem ask <query> [--format compact|json|paths|pack]
+pmem recall [--budget N] [--mode brief|normal|deep] [--format compact|json|paths|pack] [--since <duration>]
+pmem ask <query> [--format compact|json|paths|pack] [--explain] [--limit N]
 pmem discover [--dry-run] [--format compact|json] [--min-confidence <n>]
               [--lang auto|nodejs,python,rust,go,cpp,java]
               [--pattern-file <path>]

package/dist/commands/ask.d.ts

@@ -1,3 +1,7 @@
 import type { CliFormat } from '../types';
-export declare function askCommand(query: string, format?: CliFormat): void;
+export interface AskCommandOptions {
+    explain?: boolean;
+    limit?: number;
+}
+export declare function askCommand(query: string, format?: CliFormat, options?: AskCommandOptions): void;
 //# sourceMappingURL=ask.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"ask.d.ts","sourceRoot":"","sources":["../../src/commands/ask.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,SAAS,EAAoB,MAAM,UAAU,CAAC;AAyB5D,wBAAgB,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,GAAE,SAAqB,GAAG,IAAI,CA0S7E"}
+{"version":3,"file":"ask.d.ts","sourceRoot":"","sources":["../../src/commands/ask.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,UAAU,CAAC;AAI1C,MAAM,WAAW,iBAAiB;IAChC,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,wBAAgB,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,GAAE,SAAqB,EAAE,OAAO,GAAE,iBAAsB,GAAG,IAAI,CAkF9G"}

package/dist/commands/ask.js

@@ -36,11 +36,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.askCommand = askCommand;
 const path = __importStar(require("path"));
 const fs_1 = require("../core/fs");
-const db_1 = require("../core/db");
 const format_1 = require("../core/format");
-const manifest_1 = require("../core/manifest");
+const ask_1 = require("../core/query/ask");
 const PMEM_DIR = '.pmem';
-function askCommand(query, format = 'compact') {
+function askCommand(query, format = 'compact', options = {}) {
     const cwd = process.cwd();
     const pmemPath = path.join(cwd, PMEM_DIR);
     const dbPath = path.join(pmemPath, 'pmem.db');
@@ -52,222 +51,30 @@ function askCommand(query, format = 'compact') {
         console.log('No SQLite database found. Run `pmem rebuild` first.');
         return;
     }
-    let db;
+    let result;
     try {
-        db = (0, db_1.openDatabase)(pmemPath);
-        (0, db_1.createSchema)(db);
+        result = (0, ask_1.askQuery)(pmemPath, query, {
+            explain: options.explain,
+            limit: options.limit,
+        });
     }
     catch (err) {
         if (err?.message?.includes('not a valid SQLite database')) {
             console.log(err.message);
             return;
         }
-        console.log(`Failed to open database: ${err?.message || err}`);
+        console.log(`Ask query failed: ${err?.message || err}`);
         console.log('Run `pmem rebuild --full` to rebuild the database.');
         return;
     }
-    const normalizedQuery = query.toLowerCase().trim();
-    const queryTokens = tokenize(normalizedQuery);
-    const matches = [];
-    const seenIds = new Set();
-    // Step 1: Exact match — card ID
-    const idMatches = db.prepare("SELECT * FROM cards WHERE (id = ? OR id LIKE ?) AND is_deleted = 0").all(normalizedQuery, `%${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, `%${normalizedQuery}%`);
-    for (const card of aliasMatches) {
-        if (seenIds.has(card.id))
-            continue;
-        seenIds.add(card.id);
-        matches.push({
-            id: card.id,
-            title: card.title,
-            match_type: 'alias',
-            confidence: 0.9,
-            graph_distance: 0,
-            file: card.file_path,
-        });
-    }
-    // Step 3: Exact match — tags
-    const tagMatches = db.prepare(`SELECT c.* FROM cards c
-     JOIN tags t ON c.id = t.card_id
-     WHERE t.normalized_tag = ?
-       AND c.is_deleted = 0`).all(normalizedQuery);
-    for (const card of tagMatches) {
-        if (seenIds.has(card.id))
-            continue;
-        seenIds.add(card.id);
-        matches.push({
-            id: card.id,
-            title: card.title,
-            match_type: 'tag',
-            confidence: 0.7,
-            graph_distance: 0,
-            file: card.file_path,
-        });
-    }
-    // Also try tag matching with individual query tokens
-    for (const token of queryTokens) {
-        const tokenTagMatches = db.prepare(`SELECT c.* FROM cards c
-       JOIN tags t ON c.id = t.card_id
-       WHERE t.normalized_tag LIKE ?
-         AND c.is_deleted = 0`).all(`%${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 from matched cards
-    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
-    if (matches.filter(m => m.match_type !== 'graph_expansion').length === 0) {
-        // Filter out expansions for the "no direct matches" check
-        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 (used if FTS5 unavailable or FTS5 returned no results)
-            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);
-                    // Simple relevance: count token overlap in title
-                    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 (keep first/highest-ranked match per id)
-    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);
-        }
-    }
-    const result = {
-        query,
-        matched: deduped,
-        recommended_files: recommendedFiles,
-        evidence_paths: evidencePaths,
-    };
-    // Build guidance for empty results
-    const askMessage = deduped.length > 0
-        ? `Found ${deduped.length} match(es).`
+    const askMessage = result.matched.length > 0
+        ? `Found ${result.matched.length} match(es).`
         : 'No matching memory cards found.';
-    const askNextSteps = deduped.length > 0 ? [] : [
+    const askNextSteps = result.matched.length > 0 ? [] : [
         'Try a different query keyword',
         'Run `pmem recall` for full project context',
         'Check that cards have relevant aliases and tags',
     ];
-    // Output
     if (format === 'json') {
         console.log(JSON.stringify({
             ...result,
@@ -275,46 +82,47 @@ function askCommand(query, format = 'compact') {
             next_steps: askNextSteps,
         }, null, 2));
     }
-    else {
-        // Adapt to formatOutput's expected shape
-        const formatCompat = {
-            query: result.query,
-            matched: result.matched.map(m => ({
-                id: m.id,
-                title: m.title,
-                matchType: m.match_type,
-                match_type: m.match_type,
-                confidence: m.confidence,
-                graphDistance: m.graph_distance,
-                graph_distance: m.graph_distance,
-                file: m.file,
-                edgeType: m.edge_type,
-                edge_type: m.edge_type,
-                fromCard: m.from_card,
-            })),
-            recommended_files: result.recommended_files,
-            evidencePaths: result.evidence_paths,
-        };
-        console.log((0, format_1.formatOutput)(formatCompat, format, 2000));
+    else if (format === 'paths' || format === 'pack') {
+        console.log((0, format_1.formatOutput)(result, format, 2000));
     }
-}
-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 {
+        const lines = [`Query: ${result.query}`, ''];
+        if (result.matched.length === 0) {
+            lines.push('No matching memory cards found.');
+            lines.push('');
+            for (const step of askNextSteps)
+                lines.push(`  - ${step}`);
         }
         else {
-            tokens.push(word.toLowerCase());
+            lines.push('Matched:');
+            for (const m of result.matched) {
+                const score = m.score !== undefined ? ` (${m.score})` : '';
+                const stale = m.stale ? ' ⚠stale' : '';
+                let annotation = '';
+                if (options.explain && m.reasons && m.reasons.length > 0) {
+                    const parts = m.reasons.map(r => `${r.channel}:${r.detail}`);
+                    annotation = ` [${parts.join('; ')}]`;
+                }
+                else {
+                    const via = m.match_type === 'graph_expansion' && m.from_card
+                        ? `via ${m.from_card}`
+                        : m.match_type;
+                    annotation = ` [${via}]`;
+                }
+                lines.push(`  - ${m.id}${score}${annotation}${stale}: "${m.title}"`);
+            }
+            lines.push('');
+            lines.push('Recommended:');
+            for (const f of result.recommended_files)
+                lines.push(`  ${f}`);
+            if (result.evidence_paths.length > 0) {
+                lines.push('');
+                lines.push('Evidence:');
+                for (const f of result.evidence_paths.slice(0, 8))
+                    lines.push(`  ${f}`);
+            }
         }
+        console.log(lines.join('\n'));
     }
-    return [...new Set(tokens)];
 }
 //# sourceMappingURL=ask.js.map

package/dist/commands/ask.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ask.js","sourceRoot":"","sources":["../../src/commands/ask.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAaA,gCAkFC;AA/FD,2CAA6B;AAC7B,mCAAwC;AACxC,2CAA8C;AAC9C,2CAA6C;AAG7C,MAAM,QAAQ,GAAG,OAAO,CAAC;AAOzB,SAAgB,UAAU,CAAC,KAAa,EAAE,SAAoB,SAAS,EAAE,UAA6B,EAAE;IACtG,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;IAC1B,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;IAC1C,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SAAS,CAAC,CAAC;IAE9C,IAAI,CAAC,IAAA,eAAU,EAAC,QAAQ,CAAC,EAAE,CAAC;QAC1B,OAAO,CAAC,GAAG,CAAC,kDAAkD,CAAC,CAAC;QAChE,OAAO;IACT,CAAC;IAED,IAAI,CAAC,IAAA,eAAU,EAAC,MAAM,CAAC,EAAE,CAAC;QACxB,OAAO,CAAC,GAAG,CAAC,qDAAqD,CAAC,CAAC;QACnE,OAAO;IACT,CAAC;IAED,IAAI,MAAM,CAAC;IACX,IAAI,CAAC;QACH,MAAM,GAAG,IAAA,cAAQ,EAAC,QAAQ,EAAE,KAAK,EAAE;YACjC,OAAO,EAAE,OAAO,CAAC,OAAO;YACxB,KAAK,EAAE,OAAO,CAAC,KAAK;SACrB,CAAC,CAAC;IACL,CAAC;IAAC,OAAO,GAAQ,EAAE,CAAC;QAClB,IAAI,GAAG,EAAE,OAAO,EAAE,QAAQ,CAAC,6BAA6B,CAAC,EAAE,CAAC;YAC1D,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;YACzB,OAAO;QACT,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,qBAAqB,GAAG,EAAE,OAAO,IAAI,GAAG,EAAE,CAAC,CAAC;QACxD,OAAO,CAAC,GAAG,CAAC,oDAAoD,CAAC,CAAC;QAClE,OAAO;IACT,CAAC;IAED,MAAM,UAAU,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC;QAC1C,CAAC,CAAC,SAAS,MAAM,CAAC,OAAO,CAAC,MAAM,aAAa;QAC7C,CAAC,CAAC,iCAAiC,CAAC;IACtC,MAAM,YAAY,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;QACpD,+BAA+B;QAC/B,4CAA4C;QAC5C,iDAAiD;KAClD,CAAC;IAEF,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;QACtB,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC;YACzB,GAAG,MAAM;YACT,OAAO,EAAE,UAAU;YACnB,UAAU,EAAE,YAAY;SACzB,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;IACf,CAAC;SAAM,IAAI,MAAM,KAAK,OAAO,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;QACnD,OAAO,CAAC,GAAG,CAAC,IAAA,qBAAY,EAAC,MAAM,EAAE,MAAM,EAAE,IAAI,CAAC,CAAC,CAAC;IAClD,CAAC;SAAM,CAAC;QACN,MAAM,KAAK,GAAa,CAAC,UAAU,MAAM,CAAC,KAAK,EAAE,EAAE,EAAE,CAAC,CAAC;QACvD,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,iCAAiC,CAAC,CAAC;YAC9C,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACf,KAAK,MAAM,IAAI,IAAI,YAAY;gBAAE,KAAK,CAAC,IAAI,CAAC,OAAO,IAAI,EAAE,CAAC,CAAC;QAC7D,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;YACvB,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;gBAC/B,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;gBAC3D,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC;gBACvC,IAAI,UAAU,GAAG,EAAE,CAAC;gBACpB,IAAI,OAAO,CAAC,OAAO,IAAI,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;oBACzD,MAAM,KAAK,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;oBAC7D,UAAU,GAAG,KAAK,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;gBACxC,CAAC;qBAAM,CAAC;oBACN,MAAM,GAAG,GAAG,CAAC,CAAC,UAAU,KAAK,iBAAiB,IAAI,CAAC,CAAC,SAAS;wBAC3D,CAAC,CAAC,OAAO,CAAC,CAAC,SAAS,EAAE;wBACtB,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC;oBACjB,UAAU,GAAG,KAAK,GAAG,GAAG,CAAC;gBAC3B,CAAC;gBACD,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,EAAE,GAAG,KAAK,GAAG,UAAU,GAAG,KAAK,MAAM,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC;YACvE,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACf,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;YAC3B,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,iBAAiB;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;YAC/D,IAAI,MAAM,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACrC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACf,KAAK,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;gBACxB,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,cAAc,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC;oBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;YAC1E,CAAC;QACH,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;IAChC,CAAC;AACH,CAAC"}

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,CAYjE;AAmfD;;;;;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,CAYjE;AAqjBD;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,EAAE,CAQ3D"}

package/dist/commands/rebuild.js

@@ -136,6 +136,11 @@ function rebuildLocked(pmemPath, options) {
     let skipped = 0;
     let updated = 0;
     let snappedEdges = [];
+    // v0.8: FTS rows collected during the card loop, written after createFTS5.
+    // For skipped (hash-match) cards we still collect so a missing FTS row can
+    // be backfilled — the card_fts table did not exist before v0.8.
+    const ftsRows = [];
+    const ftsSkippedIds = [];
     // Pre-scan all card IDs for wikilink validation (so [[card-id]] refs
     // resolve even when the target card hasn't been processed yet)
     const validCardIds = new Set();
@@ -201,6 +206,17 @@ function rebuildLocked(pmemPath, options) {
                     if (card && !card.updated_at) {
                         db.prepare('UPDATE cards SET updated_at = ? WHERE file_path = ?').run(resolveUpdatedAt(fm.updated, file), relPath);
                     }
+                    // v0.8 FTS backfill: card content unchanged, but its FTS row may
+                    // not exist yet (table introduced in v0.8). Collect for backfill.
+                    ftsRows.push({
+                        id: fm.id,
+                        title,
+                        summary: extractCardSummary(fm, parsed.bodyText),
+                        body: parsed.bodyText,
+                        aliases: fm.aliases ?? [],
+                        tags: fm.tags ?? [],
+                    });
+                    ftsSkippedIds.push(fm.id);
                     skipped++;
                     continue;
                 }
@@ -232,6 +248,14 @@ function rebuildLocked(pmemPath, options) {
                 is_candidate: isCandidate,
             };
             (0, db_1.upsertCard)(db, cardRow);
+            ftsRows.push({
+                id: fm.id,
+                title,
+                summary: cardRow.summary,
+                body: parsed.bodyText,
+                aliases: fm.aliases ?? [],
+                tags: fm.tags ?? [],
+            });
             // 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
@@ -331,17 +355,39 @@ function rebuildLocked(pmemPath, options) {
     });
     // Execute all SQLite writes in a single transaction
     doRebuild();
-    // 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);
+    // v0.7.6-a (issue #12): clean up stale DB cards whose source .md files
+    // have been deleted from disk. The rebuild loop only processes files
+    // that exist — it never removes DB rows for deleted files — so an
+    // incremental rebuild would otherwise dead-loop on `missing_card_file`
+    // verify warnings with no way to resolve them short of `--full`.
+    //
+    // Wrapped in a transaction so a crash mid-cleanup leaves the DB in a
+    // consistent state (all-or-nothing per stale card batch).
+    let cleanedStaleCards = 0;
+    {
+        const cleanupTx = db.transaction(() => {
+            const staleCards = db.prepare("SELECT id, file_path FROM cards WHERE is_deleted = 0").all();
+            for (const card of staleCards) {
+                const absPath = path.join(cwd, card.file_path);
+                if (!(0, fs_1.fileExists)(absPath)) {
+                    db.prepare("UPDATE cards SET is_deleted = 1 WHERE id = ?").run(card.id);
+                    // Bidirectional edge cleanup — covers both outgoing and incoming edges
+                    // for the deleted card, matching the verify.ts cleanupMissingCards pattern.
+                    db.prepare("DELETE FROM edges WHERE from_id = ? OR to_id = ?").run(card.id, card.id);
+                    (0, db_1.deleteCardAliases)(db, card.id);
+                    (0, db_1.deleteCardTags)(db, card.id);
+                    (0, db_1.deleteCardPaths)(db, card.id);
+                    (0, db_1.deleteCardFts)(db, card.id);
+                    cleanedStaleCards++;
+                }
+            }
+        });
+        cleanupTx();
     }
+    // v0.7.3 (issue #6): prune orphan edges after rebuild.
+    // v0.7.7 (issue #12): run unconditionally — stale card cleanup above
+    // can create new orphan edges even in incremental mode.
+    (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:
@@ -397,6 +443,21 @@ function rebuildLocked(pmemPath, options) {
     }
     // Create FTS5 virtual table for full-text search (outside transaction)
     (0, db_1.createFTS5)(db);
+    // v0.8: populate FTS index. Updated cards always refresh; skipped cards
+    // only backfill when their FTS row is missing. Full rebuild starts clean.
+    {
+        const ftsSkipped = new Set(ftsSkippedIds);
+        const ftsTx = db.transaction(() => {
+            if (isFull)
+                (0, db_1.clearCardFts)(db);
+            for (const row of ftsRows) {
+                if (!isFull && ftsSkipped.has(row.id) && (0, db_1.cardFtsRowExists)(db, row.id))
+                    continue;
+                (0, db_1.refreshCardFts)(db, row);
+            }
+        });
+        ftsTx();
+    }
     // Write legacy graph.json for backward compatibility
     const allContent = cardFiles.map(f => (0, fs_1.readFile)(f) || '').join('');
     const sourceHash = (0, hash_1.computeHash)(allContent);
@@ -433,6 +494,9 @@ function rebuildLocked(pmemPath, options) {
     const dbEdgeCount = db.prepare("SELECT COUNT(*) as cnt FROM edges").get().cnt;
     console.log(`${modeLabel}: ${processed} cards processed, ${skipped} skipped (hash match), ${updated} updated`);
     console.log(`Graph: ${nodes.length} nodes, ${dbEdgeCount} edges`);
+    if (cleanedStaleCards > 0) {
+        console.log(`Cleaned ${cleanedStaleCards} stale card(s) (source files deleted)`);
+    }
     (0, db_1.closeDatabase)();
 }
 /**