pmem-ai 0.6.2 → 0.6.3

package/CHANGELOG.md

@@ -2,6 +2,40 @@
 
 All notable changes to pmem are documented here.
 
+## 0.6.3 - Relationship Auto-Discovery
+
+### Added
+
+- `pmem discover`: auto-discover project relationships across 6 languages (Node.js, Python, Rust, Go, C/C++, Java). Two-layer discovery: source file imports (regex, confidence 0.7) and package manager dependencies (package.json/Cargo.toml/go.mod/etc., confidence 0.7-0.85).
+- `pmem discover --dry-run`: preview discoveries without writing to database.
+- `pmem discover --lang <langs>`: filter to specific languages (auto-detect by default).
+- `pmem discover --pattern-file <path>`: custom language pattern JSON for additional ecosystems.
+- `pmem discover --min-confidence <0-1>`: threshold for edge creation (default 0.5).
+- `pmem related --format json`: structured output with confidence/source per edge, grouped by `high_confidence` vs `needs_review`.
+- `pmem related --source explicit|inferred|all`: filter edges by source.
+- `pmem update --confirm --accept-edges <ids>`: promote inferred edges to explicit (confidence 1.0).
+- `pmem update --confirm --reject-edges <ids>`: delete rejected inferred edges.
+- `pmem update --suggest` now includes low-confidence inferred edges as suggestions.
+- Agent-configurable language patterns via manifest `discover.additional_patterns`.
+
+### False-Positive Guard
+
+- `BUILTIN_MODULES` per-language skip list: Node.js core modules (`fs`, `path`, `crypto`, `child_process`, etc.), Python stdlib, Go stdlib, Java `java.*`/`javax.*`/`jakarta.*`/Spring/JUnit, C/C++ standard headers, Rust std crates. These are silently dropped from `discovered_edges` and `ambiguous` so the agent only sees actionable items.
+- New `AmbiguousRelation.kind = 'external_unmatched'` and `severity` field. Bare-name imports (npm packages, third-party libs) and dep-file entries with no matching card are classified as `severity: 'informational'`, distinct from `severity: 'actionable'` for internal project files missing a card.
+- Discover result `summary` now reports `actionable` and `external_refs` counts. Compact output shows actionable items first, then a collapsed count for informational ones.
+
+### Changed
+
+- `pmem rebuild` (incremental) now preserves inferred edges (only deletes/recreates explicit edges).
+- `pmem related` compact output shows `[inferred, 0.7]` tags on non-explicit edges.
+- `pmem trace` now shows edge source and confidence annotations.
+
+### Internal
+
+- New `src/core/discover/` module: `index.ts` (orchestration), `patterns.ts` (6-language registry), `detect.ts` (auto-detection).
+- New edge CRUD in `src/core/db.ts`: `deleteInferredEdges`, `getInferredEdges`, `getEdgesForCard`, `updateEdgeSource`, `deleteEdgesByIds`, `getOrphanEdges`, `deleteExplicitCardEdges`.
+- New types in `src/types.ts`: `DiscoverResult`, `DiscoveredEdge`, `AmbiguousRelation`, `LanguagePattern`, `ManifestDiscoverConfig`.
+
 ## 0.6.2 - Real-User Friction Fixes
 
 ### Added

package/README.md

@@ -12,6 +12,7 @@ Coding agents lose project context quickly. A repository has source files, docs,
 
 - `pmem recall` restores the hot project context.
 - `pmem ask "<query>"` finds relevant memory cards.
+- `pmem discover` auto-discovers project relationships (tech stack, file deps, imports) across 6 languages.
 - `pmem status` maps changed files back to affected cards.
 - `pmem update --suggest` tells an agent what memory likely needs attention.
 - `pmem verify` checks that Markdown cards and runtime indexes still agree.
@@ -27,7 +28,7 @@ The design is intentionally local and Git-friendly. Markdown cards remain the so
 - You want agents to update memory deliberately instead of auto-writing noisy logs.
 - You prefer local files over hosted memory services.
 
-It is not a vector database, MCP server, Graph UI, or remote multi-user service. v0.5 focuses on making the CLI product installable, understandable, and reliable as a Beta.
+It is not a vector database, MCP server, Graph UI, or remote multi-user service. v0.6 focuses on making the CLI agent-native with relationship discovery and polished workflows.
 
 ## Install
 
@@ -273,13 +274,17 @@ pmem init [project-name] [--guided]
 
 pmem recall [--budget N] [--format compact|json|paths|pack]
 pmem ask <query> [--format compact|json|paths|pack]
-pmem related <id> [--depth N] [--type <edge-type>]
+pmem discover [--dry-run] [--format compact|json] [--min-confidence 0.5]
+              [--lang auto|nodejs,python,rust,go,cpp,java]
+              [--pattern-file custom.json]
+pmem related <id> [--depth N] [--type <edge-type>] [--format compact|json] [--source explicit|inferred|all]
 pmem trace <id>
 
 pmem status [--since <timestamp>] [--format compact|json]
 pmem mark-dirty [-r <reason>] [--auto]
 pmem update [--auto|--suggest|--apply-suggestion <id>|--confirm|--force] \
   [-s <summary>] [-n <next>] [--format compact|json]
+  [--accept-edges <ids>] [--reject-edges <ids>]
 
 pmem distill [--suggest|--apply-suggestion <id>|--confirm|--suggest-splits]
 pmem rebuild [--changed|--full|--card <id>]
@@ -389,9 +394,13 @@ pmem verify
 - README, quick start, and [usage guide](docs/usage.md)
 - E2E suite, CI/CD, error UX, release checklist
 
-**v0.6 Agent-native Workflow Polish** — in development:
+**v0.6 Agent-native Workflow Polish** — shipped:
 - Non-interactive init (`--description`/`--stage`/`--next` flags, `--answers` file)
 - Claude Code slash commands (`/pmem-recall`, `/pmem-ask`, `/pmem-update`, `/pmem-distill`)
+- Relationship auto-discovery across 6 languages (`pmem discover`)
+- Inferred edge review and confirmation workflow
+- False-positive guard: language builtins and external packages filtered out
+- Actionable vs informational `ambiguous` classification (severity field)
 - Actionable empty states and error messages
 - Session fault tolerance
 - Integration verification enhanced

package/dist/commands/graph.d.ts

@@ -1,6 +1,9 @@
+import type { CliFormat } from '../types';
 export declare function relatedCommand(id: string, options?: {
     depth?: number;
     type?: string;
+    format?: CliFormat;
+    source?: 'explicit' | 'inferred' | 'mention' | 'all';
 }): void;
 export declare function traceCommand(id: string): void;
 //# sourceMappingURL=graph.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"graph.d.ts","sourceRoot":"","sources":["../../src/commands/graph.ts"],"names":[],"mappings":"AAOA,wBAAgB,cAAc,CAAC,EAAE,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE;IAAE,KAAK,CAAC,EAAE,MAAM,CAAC;IAAC,IAAI,CAAC,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,CAuH5F;AAED,wBAAgB,YAAY,CAAC,EAAE,EAAE,MAAM,GAAG,IAAI,CAgF7C"}
+{"version":3,"file":"graph.d.ts","sourceRoot":"","sources":["../../src/commands/graph.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAoB,SAAS,EAAE,MAAM,UAAU,CAAC;AAI5D,wBAAgB,cAAc,CAAC,EAAE,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE;IACnD,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,SAAS,CAAC;IACnB,MAAM,CAAC,EAAE,UAAU,GAAG,UAAU,GAAG,SAAS,GAAG,KAAK,CAAC;CACtD,GAAG,IAAI,CAyKP;AAED,wBAAgB,YAAY,CAAC,EAAE,EAAE,MAAM,GAAG,IAAI,CAiF7C"}

package/dist/commands/graph.js

@@ -44,28 +44,69 @@ function relatedCommand(id, options) {
     const pmemPath = path.join(cwd, PMEM_DIR);
     const depth = options?.depth ?? 1;
     const edgeTypeFilter = options?.type;
+    const fmt = options?.format ?? 'compact';
+    const sourceFilter = (options?.source && options.source !== 'all')
+        ? options.source
+        : undefined;
     const db = (0, db_1.openDatabase)(pmemPath);
     (0, db_1.createSchema)(db);
-    // Query card by ID
     const card = db.prepare('SELECT * FROM cards WHERE id = ? AND is_deleted = 0').get(id);
     if (!card) {
-        console.log(`Node "${id}" not found in database.`);
-        console.log(`Try: pmem ask "${id}" to search for related nodes.`);
+        if (fmt === 'json') {
+            console.log(JSON.stringify({ error: `Node "${id}" not found` }, null, 2));
+        }
+        else {
+            console.log(`Node "${id}" not found in database.`);
+            console.log(`Try: pmem ask "${id}" to search for related nodes.`);
+        }
         return;
     }
-    // Query direct edges
-    let directQuery = 'SELECT * FROM edges WHERE (from_id = ? OR to_id = ?)';
-    const directParams = [id, id];
+    let directEdges = (0, db_1.getEdgesForCard)(db, id, sourceFilter);
     if (edgeTypeFilter) {
-        directQuery += ' AND type = ?';
-        directParams.push(edgeTypeFilter);
+        directEdges = directEdges.filter(e => e.type === edgeTypeFilter);
     }
-    const directEdges = db.prepare(directQuery).all(...directParams);
-    // Helper to fetch a card by ID
     const getCard = (cardId) => {
         return db.prepare('SELECT * FROM cards WHERE id = ? AND is_deleted = 0').get(cardId);
     };
-    // Output node info
+    if (fmt === 'json') {
+        const edgesByType = {};
+        for (const edge of directEdges) {
+            const isOut = edge.from_id === id;
+            const targetId = isOut ? edge.to_id : edge.from_id;
+            const targetCard = getCard(targetId);
+            if (!edgesByType[edge.type]) {
+                edgesByType[edge.type] = [];
+            }
+            edgesByType[edge.type].push({
+                direction: isOut ? 'out' : 'in',
+                target_id: targetId,
+                target_title: targetCard?.title ?? targetId,
+                source: edge.source,
+                confidence: edge.confidence,
+            });
+        }
+        const highConfidence = [];
+        const needsReview = [];
+        for (const items of Object.values(edgesByType)) {
+            for (const item of items) {
+                if (item.source === 'inferred' && item.confidence < 0.7) {
+                    needsReview.push(item);
+                }
+                else {
+                    highConfidence.push(item);
+                }
+            }
+        }
+        console.log(JSON.stringify({
+            card: { id: card.id, type: card.type, title: card.title, status: card.status, file: card.file_path },
+            total_edges: directEdges.length,
+            high_confidence: highConfidence,
+            needs_review: needsReview,
+            edges_by_type: edgesByType,
+        }, null, 2));
+        return;
+    }
+    // Compact output
     console.log(`${card.id}`);
     console.log(`Type: ${card.type}`);
     console.log(`Title: ${card.title}`);
@@ -76,7 +117,6 @@ function relatedCommand(id, options) {
         console.log('\nNo related nodes.');
         return;
     }
-    // Group direct edges by type
     const grouped = new Map();
     for (const edge of directEdges) {
         const isOut = edge.from_id === id;
@@ -90,19 +130,21 @@ function relatedCommand(id, options) {
             targetId,
             targetTitle,
             direction: isOut ? 'out' : 'in',
+            source: edge.source,
+            confidence: edge.confidence,
         });
     }
     console.log('\nDirect Relations:');
     for (const [edgeType, targets] of grouped) {
         for (const t of targets) {
             const prefix = t.direction === 'in' ? '←' : '';
-            console.log(`  ${prefix}${edgeType}: ${t.targetId} (${t.targetTitle})`);
+            const srcTag = t.source === 'inferred' ? ` [${t.source}, ${t.confidence.toFixed(1)}]` : '';
+            console.log(`  ${prefix}${edgeType}: ${t.targetId} (${t.targetTitle})${srcTag}`);
         }
     }
     // BFS for multi-hop traversal when depth > 1
     if (depth > 1) {
         const visited = new Set([id]);
-        // Seed frontier with direct neighbors
         let frontier = new Set();
         for (const edge of directEdges) {
             const neighborId = edge.from_id === id ? edge.to_id : edge.from_id;
@@ -135,7 +177,7 @@ function relatedCommand(id, options) {
             }
             frontier = nextFrontier;
         }
-        const totalReachable = visited.size - 1; // excluding the target itself
+        const totalReachable = visited.size - 1;
         if (totalReachable > 0) {
             console.log(`\nExtended Network (depth ${depth}):`);
             console.log(`  ${totalReachable} reachable node(s) via ${totalExtendedEdges + directEdges.length} edge(s) across all hops`);
@@ -147,7 +189,6 @@ function traceCommand(id) {
     const pmemPath = path.join(cwd, PMEM_DIR);
     const db = (0, db_1.openDatabase)(pmemPath);
     (0, db_1.createSchema)(db);
-    // Query card by ID
     const card = db.prepare('SELECT * FROM cards WHERE id = ? AND is_deleted = 0').get(id);
     if (!card) {
         console.log(`Node "${id}" not found in database.`);
@@ -174,9 +215,9 @@ function traceCommand(id) {
             console.log(`    ${row.file_path}`);
         }
     }
-    // Find depends_on chain: edges where this node depends on others
+    // Find depends_on chain
     const dependsOn = db.prepare(`
-    SELECT e.to_id, c.title as to_title
+    SELECT e.to_id, c.title as to_title, e.source, e.confidence
     FROM edges e
     LEFT JOIN cards c ON c.id = e.to_id AND c.is_deleted = 0
     WHERE e.from_id = ? AND e.type = 'depends_on'
@@ -184,12 +225,13 @@ function traceCommand(id) {
     if (dependsOn.length > 0) {
         console.log('\nDepends On:');
         for (const row of dependsOn) {
-            console.log(`  - ${row.to_id}${row.to_title ? ` (${row.to_title})` : ''}`);
+            const srcTag = row.source === 'inferred' ? ` [${row.source}, ${row.confidence.toFixed(1)}]` : '';
+            console.log(`  - ${row.to_id}${row.to_title ? ` (${row.to_title})` : ''}${srcTag}`);
         }
     }
-    // Find depended_by: edges where other nodes depend on this node
+    // Find depended_by
     const dependedBy = db.prepare(`
-    SELECT e.from_id, c.title as from_title
+    SELECT e.from_id, c.title as from_title, e.source, e.confidence
     FROM edges e
     LEFT JOIN cards c ON c.id = e.from_id AND c.is_deleted = 0
     WHERE e.to_id = ? AND e.type = 'depends_on'
@@ -197,10 +239,11 @@ function traceCommand(id) {
     if (dependedBy.length > 0) {
         console.log('\nDepended On By:');
         for (const row of dependedBy) {
-            console.log(`  - ${row.from_id}${row.from_title ? ` (${row.from_title})` : ''}`);
+            const srcTag = row.source === 'inferred' ? ` [${row.source}, ${row.confidence.toFixed(1)}]` : '';
+            console.log(`  - ${row.from_id}${row.from_title ? ` (${row.from_title})` : ''}${srcTag}`);
         }
     }
-    // Read and display card body content (first 3000 chars after frontmatter)
+    // Read and display card body content
     const filePath = path.join(cwd, card.file_path);
     if ((0, fs_1.fileExists)(filePath)) {
         const content = (0, fs_1.readFile)(filePath);

package/dist/commands/graph.js.map

@@ -1 +1 @@
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+{"version":3,"file":"graph.js","sourceRoot":"","sources":["../../src/commands/graph.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAOA,wCA8KC;AAED,oCAiFC;AAxQD,2CAA6B;AAC7B,mCAAkD;AAClD,mCAAyE;AAGzE,MAAM,QAAQ,GAAG,OAAO,CAAC;AAEzB,SAAgB,cAAc,CAAC,EAAU,EAAE,OAK1C;IACC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;IAC1B,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;IAC1C,MAAM,KAAK,GAAG,OAAO,EAAE,KAAK,IAAI,CAAC,CAAC;IAClC,MAAM,cAAc,GAAG,OAAO,EAAE,IAAI,CAAC;IACrC,MAAM,GAAG,GAAG,OAAO,EAAE,MAAM,IAAI,SAAS,CAAC;IACzC,MAAM,YAAY,GAAG,CAAC,OAAO,EAAE,MAAM,IAAI,OAAO,CAAC,MAAM,KAAK,KAAK,CAAC;QAChE,CAAC,CAAC,OAAO,CAAC,MAAM;QAChB,CAAC,CAAC,SAAS,CAAC;IAEd,MAAM,EAAE,GAAG,IAAA,iBAAY,EAAC,QAAQ,CAAC,CAAC;IAClC,IAAA,iBAAY,EAAC,EAAE,CAAC,CAAC;IAEjB,MAAM,IAAI,GAAG,EAAE,CAAC,OAAO,CAAC,qDAAqD,CAAC,CAAC,GAAG,CAAC,EAAE,CAAwB,CAAC;IAC9G,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,IAAI,GAAG,KAAK,MAAM,EAAE,CAAC;YACnB,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,aAAa,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC5E,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,GAAG,CAAC,SAAS,EAAE,0BAA0B,CAAC,CAAC;YACnD,OAAO,CAAC,GAAG,CAAC,kBAAkB,EAAE,gCAAgC,CAAC,CAAC;QACpE,CAAC;QACD,OAAO;IACT,CAAC;IAED,IAAI,WAAW,GAAG,IAAA,oBAAe,EAAC,EAAE,EAAE,EAAE,EAAE,YAAY,CAAc,CAAC;IACrE,IAAI,cAAc,EAAE,CAAC;QACnB,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,cAAc,CAAC,CAAC;IACnE,CAAC;IAED,MAAM,OAAO,GAAG,CAAC,MAAc,EAAuB,EAAE;QACtD,OAAO,EAAE,CAAC,OAAO,CAAC,qDAAqD,CAAC,CAAC,GAAG,CAAC,MAAM,CAAwB,CAAC;IAC9G,CAAC,CAAC;IAEF,IAAI,GAAG,KAAK,MAAM,EAAE,CAAC;QACnB,MAAM,WAAW,GAMX,EAAE,CAAC;QAET,KAAK,MAAM,IAAI,IAAI,WAAW,EAAE,CAAC;YAC/B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,KAAK,EAAE,CAAC;YAClC,MAAM,QAAQ,GAAG,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC;YACnD,MAAM,UAAU,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;YAErC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;gBAC5B,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC;YAC9B,CAAC;YACD,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC;gBAC1B,SAAS,EAAE,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI;gBAC/B,SAAS,EAAE,QAAQ;gBACnB,YAAY,EAAE,UAAU,EAAE,KAAK,IAAI,QAAQ;gBAC3C,MAAM,EAAE,IAAI,CAAC,MAAM;gBACnB,UAAU,EAAE,IAAI,CAAC,UAAU;aAC5B,CAAC,CAAC;QACL,CAAC;QAED,MAAM,cAAc,GAA+B,EAAE,CAAC;QACtD,MAAM,WAAW,GAA+B,EAAE,CAAC;QAEnD,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,MAAM,CAAC,WAAW,CAAC,EAAE,CAAC;YAC/C,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;gBACzB,IAAI,IAAI,CAAC,MAAM,KAAK,UAAU,IAAI,IAAI,CAAC,UAAU,GAAG,GAAG,EAAE,CAAC;oBACxD,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBACzB,CAAC;qBAAM,CAAC;oBACN,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBAC5B,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC;YACzB,IAAI,EAAE,EAAE,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,EAAE;YACpG,WAAW,EAAE,WAAW,CAAC,MAAM;YAC/B,eAAe,EAAE,cAAc;YAC/B,YAAY,EAAE,WAAW;YACzB,aAAa,EAAE,WAAW;SAC3B,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QACb,OAAO;IACT,CAAC;IAED,iBAAiB;IACjB,OAAO,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;IAC1B,OAAO,CAAC,GAAG,CAAC,SAAS,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC;IAClC,OAAO,CAAC,GAAG,CAAC,UAAU,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC;IACpC,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;QAChB,OAAO,CAAC,GAAG,CAAC,WAAW,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;IACxC,CAAC;IAED,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC7B,OAAO,CAAC,GAAG,CAAC,qBAAqB,CAAC,CAAC;QACnC,OAAO;IACT,CAAC;IAED,MAAM,OAAO,GAAG,IAAI,GAAG,EAAoH,CAAC;IAC5I,KAAK,MAAM,IAAI,IAAI,WAAW,EAAE,CAAC;QAC/B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,KAAK,EAAE,CAAC;QAClC,MAAM,QAAQ,GAAG,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC;QACnD,MAAM,UAAU,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;QACrC,MAAM,WAAW,GAAG,UAAU,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC;QAE7D,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAC5B,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;QAC7B,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAE,CAAC,IAAI,CAAC;YAC3B,QAAQ;YACR,WAAW;YACX,SAAS,EAAE,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI;YAC/B,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,UAAU,EAAE,IAAI,CAAC,UAAU;SAC5B,CAAC,CAAC;IACL,CAAC;IAED,OAAO,CAAC,GAAG,CAAC,qBAAqB,CAAC,CAAC;IACnC,KAAK,MAAM,CAAC,QAAQ,EAAE,OAAO,CAAC,IAAI,OAAO,EAAE,CAAC;QAC1C,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;YACxB,MAAM,MAAM,GAAG,CAAC,CAAC,SAAS,KAAK,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YAC/C,MAAM,MAAM,GAAG,CAAC,CAAC,MAAM,KAAK,UAAU,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YAC3F,OAAO,CAAC,GAAG,CAAC,KAAK,MAAM,GAAG,QAAQ,KAAK,CAAC,CAAC,QAAQ,KAAK,CAAC,CAAC,WAAW,IAAI,MAAM,EAAE,CAAC,CAAC;QACnF,CAAC;IACH,CAAC;IAED,6CAA6C;IAC7C,IAAI,KAAK,GAAG,CAAC,EAAE,CAAC;QACd,MAAM,OAAO,GAAG,IAAI,GAAG,CAAS,CAAC,EAAE,CAAC,CAAC,CAAC;QACtC,IAAI,QAAQ,GAAG,IAAI,GAAG,EAAU,CAAC;QACjC,KAAK,MAAM,IAAI,IAAI,WAAW,EAAE,CAAC;YAC/B,MAAM,UAAU,GAAG,IAAI,CAAC,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC;YACnE,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC;gBAC7B,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC;gBA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package/dist/commands/rebuild.js

@@ -148,8 +148,8 @@ function rebuildCommand(options = {}) {
                 is_candidate: isCandidate,
             };
             (0, db_1.upsertCard)(db, cardRow);
-            // Clear existing relations before re-inserting
-            (0, db_1.deleteCardEdges)(db, fm.id);
+            // Clear existing explicit relations before re-inserting (preserve inferred edges)
+            (0, db_1.deleteExplicitCardEdges)(db, fm.id);
             (0, db_1.deleteCardAliases)(db, fm.id);
             (0, db_1.deleteCardTags)(db, fm.id);
             (0, db_1.deleteCardPaths)(db, fm.id);

package/dist/commands/rebuild.js.map

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

@@ -8,6 +8,8 @@ export declare function updateCommand(options: {
     applySuggestion?: string;
     format?: string;
     includeHistory?: boolean;
+    acceptEdges?: string;
+    rejectEdges?: string;
 }): void;
 export declare function markDirtyCommand(reason: string, options?: {
     auto?: boolean;

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;CAC1B,GAAG,IAAI,CAyCP;AAED,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,GAAE;IAAE,IAAI,CAAC,EAAE,OAAO,CAAA;CAAO,GAAG,IAAI,CA8FvF"}
+{"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,CA8FvF"}

package/dist/commands/update.js

@@ -56,6 +56,11 @@ function updateCommand(options) {
         console.log('No manifest found. Run `pmem init` first.');
         return;
     }
+    // --accept-edges / --reject-edges: manage inferred edges
+    if (options.acceptEdges || options.rejectEdges) {
+        manageEdges(pmemPath, options.acceptEdges, options.rejectEdges);
+        return;
+    }
     // --suggest: show intelligent update suggestions
     if (options.suggest) {
         suggestActions(pmemPath, options.format, options.includeHistory);
@@ -581,7 +586,8 @@ function generateSuggestions(pmemPath, includeHistory = false) {
     };
 }
 function suggestActions(pmemPath, format, includeHistory) {
-    const report = generateSuggestions(pmemPath, includeHistory);
+    let report = generateSuggestions(pmemPath, includeHistory);
+    report = enrichWithEdgeSuggestions(pmemPath, report);
     if (format === 'json') {
         console.log(JSON.stringify({
             summary: report.summary,
@@ -804,4 +810,114 @@ Continue as planned.
     }
     process.exit(0);
 }
+// === v0.6.3: Edge Confirmation Management ===
+function manageEdges(pmemPath, acceptRaw, rejectRaw) {
+    const dbPath = path.join(pmemPath, 'pmem.db');
+    if (!(0, fs_1.fileExists)(dbPath)) {
+        console.log('No SQLite database. Run `pmem rebuild` first.');
+        process.exit(2);
+    }
+    const db = (0, db_1.openDatabase)(pmemPath);
+    // Accept edges: upgrade from inferred to explicit
+    if (acceptRaw) {
+        const ids = parseEdgeIds(acceptRaw);
+        if (ids.length > 0) {
+            const changed = (0, db_1.updateEdgeSource)(db, ids, 'explicit', 1.0);
+            console.log(`Accepted ${changed} edge(s): upgraded source to explicit, confidence to 1.0.`);
+        }
+    }
+    // Reject edges: delete them
+    if (rejectRaw) {
+        const ids = parseEdgeIds(rejectRaw);
+        if (ids.length > 0) {
+            const deleted = (0, db_1.deleteEdgesByIds)(db, ids);
+            console.log(`Rejected ${deleted} edge(s): deleted.`);
+        }
+    }
+    (0, db_1.closeDatabase)();
+    if (!acceptRaw && !rejectRaw) {
+        // Show current inferred edges for review
+        const db2 = (0, db_1.openDatabase)(pmemPath);
+        const inferred = (0, db_1.getInferredEdges)(db2);
+        if (inferred.length === 0) {
+            console.log('No inferred edges to review.');
+        }
+        else {
+            console.log(`Inferred edges (${inferred.length} total):\n`);
+            const getCardTitle = (cid) => {
+                try {
+                    const row = db2.prepare('SELECT title FROM cards WHERE id = ?').get(cid);
+                    return row?.title ?? cid;
+                }
+                catch {
+                    return cid;
+                }
+            };
+            for (const edge of inferred) {
+                console.log(`  [${edge.id}] ${edge.from_id} → ${edge.to_id}`);
+                console.log(`      type: ${edge.type}, confidence: ${edge.confidence.toFixed(1)}, source: ${edge.source}`);
+            }
+            console.log('\nTo accept: pmem update --confirm --accept-edges <id1,id2>');
+            console.log('To reject: pmem update --confirm --reject-edges <id1,id2>');
+        }
+        (0, db_1.closeDatabase)();
+    }
+}
+function parseEdgeIds(raw) {
+    return raw
+        .split(',')
+        .map(s => parseInt(s.trim(), 10))
+        .filter(n => !isNaN(n) && n > 0);
+}
+// Add edge-related suggestions to the suggestion report.
+// All inferred edges are surfaced (not just low-confidence), so the agent
+// can review and decide which to accept / reject. Confidence and source are
+// included as `sources[]` entries to drive the agent's judgment.
+function enrichWithEdgeSuggestions(pmemPath, report) {
+    const dbPath = path.join(pmemPath, 'pmem.db');
+    if (!(0, fs_1.fileExists)(dbPath))
+        return report;
+    try {
+        const db = (0, db_1.openDatabase)(pmemPath);
+        const inferred = (0, db_1.getInferredEdges)(db);
+        if (inferred.length === 0)
+            return report;
+        for (const edge of inferred) {
+            const isLow = edge.confidence < 0.7;
+            const reasonTag = isLow
+                ? `inferred_edge_low_confidence: ${edge.from_id} → ${edge.to_id}`
+                : `inferred_edge_review: ${edge.from_id} → ${edge.to_id}`;
+            const detailReason = isLow
+                ? `inferred_${edge.type}_confidence_${edge.confidence.toFixed(1)}`
+                : `inferred_${edge.type}_confidence_${edge.confidence.toFixed(1)}_source_${edge.source}`;
+            report.groups.current_suggestions.push({
+                target: edge.from_id,
+                reason: reasonTag,
+                matched_file: null,
+                count: 1,
+                severity: isLow ? 'warning' : 'info',
+                blocks_verify: false,
+                is_duplicate: false,
+                is_historical: false,
+                created_at_first: edge.created_at || new Date().toISOString(),
+                created_at_last: edge.created_at || new Date().toISOString(),
+                sources: [{
+                        scope: 'edge',
+                        target: `${edge.from_id} → ${edge.to_id}`,
+                        reason: detailReason,
+                        created_at: edge.created_at || new Date().toISOString(),
+                        session_id: null,
+                    }],
+                edge_ids: edge.id !== undefined ? [edge.id] : [],
+                edge_tuple: `${edge.from_id} → ${edge.to_id}`,
+            });
+        }
+        report.summary.info += inferred.length;
+        report.summary.affected_cards = new Set(inferred.map(e => e.from_id)).size + report.summary.affected_cards;
+        return report;
+    }
+    catch {
+        return report;
+    }
+}
 //# sourceMappingURL=update.js.map