pmem-ai 0.7.5 → 0.7.6

package/CHANGELOG.md

@@ -2,6 +2,26 @@
 
 All notable changes to pmem are documented here.
 
+## v0.7.6 — Agent Contract & Write-Path Integrity (2026-06-28)
+
+### Added
+
+- **Lock Protocol**: `pmem rebuild` and `pmem update --confirm` acquire `.pmem/.lock` during index mutations. `pmem verify` acquires the lock before reading the SQLite index. Concurrent verify during an active rebuild emits `active_lock` (info) and defers freshness checks instead of producing transient `stale_index` warnings. Stale locks (>60s, from crashed processes) are auto-cleaned on acquisition and can be manually cleaned with `pmem verify --fix-locks`. Reentrant: nested calls (e.g. `update --confirm` → `rebuildCommand`) share the same lock without deadlock.
+- **`pmem relations <id> --format json`**: Inspect a card's edge graph with `outgoing`/`incoming` edges, `summary_by_type`, `summary_by_source`, and `pruning_candidates` (edges with `source: inferred` or `confidence < 0.5`).
+- **`too_many_relations` verify output**: When a card exceeds its relation threshold, `pmem verify` now includes `top_edges` (up to 10 lowest-confidence edges) and `pruning_candidates` in the issue, so agents can identify which relations to prune.
+- **`content_trust: "untrusted_project_data"`**: All MCP card objects carry this annotation per agent contract.
+
+### Fixed
+
+- **Rebuild/verify race (#9)**: `pmem verify` no longer produces false `stale_index`/`missing_database` warnings when run during an active `pmem rebuild`. Lock acquisition gates all DB reads.
+- **Test pollution (#9)**: `src/core/next.test.ts` no longer mutates global `process.cwd()`, preventing collateral failures in `src/mcp/security.test.ts` under Node's concurrent test runner.
+- **Write-path contract (#10)**: `pmem update --confirm` preserves all existing card content — it writes only to `.pmem/state.md`, `.pmem/next.md`, and trace files. Agent-authored frontmatter fields are merged without removing user content.
+
+### Changed
+
+- **Build artifacts excluded from repo**: `dist/` added to `.gitignore` and removed from git tracking (264 files). CI/pack/publish all run `npm run build` before packaging.
+- **Skills updated**: `code-task.md`, `update.md`, and `distill.md` now document lock protocol behavior and verify output interpretation.
+
 ## v0.7.5 — Context Restoration Release (2026-06-26)
 
 ### Added

package/README.md

@@ -228,6 +228,16 @@ pmem ask "sqlite runtime" --format compact
 pmem ask "release checklist" --format json
 ```
 
+### Relations
+
+Use `relations` to inspect a card's edge graph and find pruning candidates:
+
+```bash
+pmem relations module.auth --format json
+```
+
+The JSON output includes `outgoing` / `incoming` edge lists, `summary_by_type`, `summary_by_source`, and `pruning_candidates` — edges with `source: inferred` or `confidence < 0.5` that are safe to prune. This helps agents reduce noise when a card accumulates too many low-quality relations.
+
 ### Dirty, Update, Distill
 
 The memory update flow is intentionally confirmation-first:
@@ -249,6 +259,29 @@ pmem sync -s "<summary>" -n "<next step>"
 
 `distill` consolidates trace cards into stable cards when enough evidence accumulates.
 
+### Lock Protocol (v0.7.6)
+
+`pmem rebuild` and `pmem update --confirm` acquire `.pmem/.lock` during index mutations. `pmem verify` acquires the lock before reading the SQLite index.
+
+When an agent runs `pmem verify` during an active rebuild:
+- It emits an `active_lock` info note (not a warning/error) and defers all index freshness checks.
+- The output says `clean (index checks deferred)` with Score 100/100.
+- No transient `stale_index` or `missing_database` warnings are emitted — those checks are skipped because another process holds the lock.
+
+If a `pmem` process crashes, the lock may become stale (>60s). Run:
+
+```bash
+pmem verify --fix-locks    # clean the stale lock
+```
+
+Agent guidance:
+- If `pmem verify` reports `active_lock`, wait and retry — do not treat it as a failure.
+- If it reports `stale_lock`, run `pmem verify --fix-locks` before proceeding.
+
+### Verify Output: too_many_relations
+
+When a card exceeds its relation threshold, `pmem verify` emits `too_many_relations` with `top_edges` (up to 10 lowest-confidence edges) and `pruning_candidates` (edges with `source: inferred` or `confidence < 0.5`). Agents can use `pruning_candidates` to suggest which relations to remove, or run `pmem relations <id> --format json` for a full inspection.
+
 ### Module & Decision Inference (v0.7.5)
 
 To automate codebase module and decision mapping:
@@ -355,6 +388,7 @@ pmem discover [--dry-run] [--format compact|json] [--min-confidence <n>]
               [--lang auto|nodejs,python,rust,go,cpp,java]
               [--pattern-file <path>]
 pmem related <id> [--depth N] [--type <edge-type>] [--format compact|json] [--source explicit|inferred|mention|all]
+pmem relations <id> [--format json]
 pmem trace <id>
 
 pmem status [--since <timestamp>] [--format compact|json]

package/dist/commands/decision.d.ts

@@ -1,5 +1,8 @@
-export declare function decisionInferCommand(options: {
+export interface DecisionInferOptions {
     write?: boolean;
     fromTraces?: boolean;
-}): void;
+    format?: 'compact' | 'json';
+    threshold?: number;
+}
+export declare function decisionInferCommand(options: DecisionInferOptions): void;
 //# sourceMappingURL=decision.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"decision.d.ts","sourceRoot":"","sources":["../../src/commands/decision.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,oBAAoB;IACnC,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,MAAM,CAAC,EAAE,SAAS,GAAG,MAAM,CAAC;IAC5B,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAkDD,wBAAgB,oBAAoB,CAAC,OAAO,EAAE,oBAAoB,GAAG,IAAI,CA+CxE"}

package/dist/commands/decision.js

@@ -37,20 +37,65 @@ exports.decisionInferCommand = decisionInferCommand;
 const path = __importStar(require("path"));
 const fs_1 = require("../core/fs");
 const decisionInfer_1 = require("../core/decisionInfer");
+const HINT = 'decision infer scans .pmem/traces/*.md for H2 sections named `## Decision` or `## Decisions`.';
+function buildNextActions(state) {
+    const actions = [];
+    if (state === 'candidates_found') {
+        actions.push({
+            command: 'pmem decision infer --write',
+            reason: 'Apply inferred decisions as draft cards',
+            blocking: false,
+        });
+    }
+    actions.push({
+        command: 'pmem capture',
+        reason: 'Add more trace cards with explicit `## Decision` sections',
+        blocking: false,
+    });
+    return actions;
+}
+function printCompactNoCandidates(diagnostics) {
+    console.log('No decisions could be inferred from the current project traces.');
+    console.log('');
+    console.log('Diagnostics:');
+    console.log(`  trace_dir_exists:          ${diagnostics.trace_dir_exists}`);
+    console.log(`  traces_scanned:            ${diagnostics.traces_scanned}`);
+    console.log(`  traces_with_decisions:     ${diagnostics.traces_with_decisions}`);
+    console.log(`  decision_lines_found:      ${diagnostics.decision_lines_found}`);
+    console.log(`  candidates_above_threshold:${diagnostics.candidates_above_threshold}`);
+    console.log('');
+    console.log(`Hint: ${HINT}`);
+}
 function decisionInferCommand(options) {
     const cwd = process.cwd();
     const pmemPath = path.join(cwd, '.pmem');
+    const format = options.format ?? 'compact';
     if (!(0, fs_1.fileExists)(pmemPath)) {
         console.error('Error: No .pmem directory found. Run `pmem init` first.');
         process.exit(2);
     }
-    const inferred = (0, decisionInfer_1.inferDecisions)(pmemPath);
-    if (inferred.length === 0) {
-        console.log('No decisions could be inferred from the current project traces.');
+    const result = (0, decisionInfer_1.inferDecisions)(pmemPath, { threshold: options.threshold });
+    const { decisions, diagnostics } = result;
+    const state = decisions.length === 0 ? 'no_candidates' : 'candidates_found';
+    if (format === 'json') {
+        const output = {
+            command: 'decision infer',
+            state,
+            decisions,
+            diagnostics,
+            next_actions: buildNextActions(state),
+            hint: HINT,
+        };
+        console.log(JSON.stringify(output, null, 2));
+        return;
+    }
+    // Compact mode (default)
+    if (decisions.length === 0) {
+        printCompactNoCandidates(diagnostics);
         return;
     }
     if (options.write) {
-        const written = (0, decisionInfer_1.writeInferredDecisions)(pmemPath, inferred);
+        const written = (0, decisionInfer_1.writeInferredDecisions)(pmemPath, decisions);
         console.log(`Successfully wrote ${written.length} inferred decision card(s):`);
         for (const p of written) {
             console.log(`- ${path.relative(cwd, p)}`);
@@ -58,8 +103,8 @@ function decisionInferCommand(options) {
         console.log('Next: run `pmem rebuild` to rebuild indexes.');
     }
     else {
-        const candidatePath = (0, decisionInfer_1.writeDecisionCandidates)(pmemPath, inferred);
-        console.log(`Inferred ${inferred.length} decision candidate(s).`);
+        const candidatePath = (0, decisionInfer_1.writeDecisionCandidates)(pmemPath, decisions);
+        console.log(`Inferred ${decisions.length} decision candidate(s).`);
         console.log(`Candidate list written to: ${path.relative(cwd, candidatePath)}`);
         console.log('Run `pmem decision infer --write` to promote them to formal cards.');
     }

package/dist/commands/decision.js.map

@@ -1 +1 @@
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+{"version":3,"file":"decision.js","sourceRoot":"","sources":["../../src/commands/decision.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AA2DA,oDA+CC;AA1GD,2CAA6B;AAC7B,mCAAwC;AACxC,yDAAwJ;AAwBxJ,MAAM,IAAI,GACR,+FAA+F,CAAC;AAElG,SAAS,gBAAgB,CAAC,KAA2C;IACnE,MAAM,OAAO,GAAiB,EAAE,CAAC;IACjC,IAAI,KAAK,KAAK,kBAAkB,EAAE,CAAC;QACjC,OAAO,CAAC,IAAI,CAAC;YACX,OAAO,EAAE,6BAA6B;YACtC,MAAM,EAAE,yCAAyC;YACjD,QAAQ,EAAE,KAAK;SAChB,CAAC,CAAC;IACL,CAAC;IACD,OAAO,CAAC,IAAI,CAAC;QACX,OAAO,EAAE,cAAc;QACvB,MAAM,EAAE,2DAA2D;QACnE,QAAQ,EAAE,KAAK;KAChB,CAAC,CAAC;IACH,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,wBAAwB,CAAC,WAAyC;IACzE,OAAO,CAAC,GAAG,CAAC,iEAAiE,CAAC,CAAC;IAC/E,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;IAChB,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC;IAC5B,OAAO,CAAC,GAAG,CAAC,gCAAgC,WAAW,CAAC,gBAAgB,EAAE,CAAC,CAAC;IAC5E,OAAO,CAAC,GAAG,CAAC,gCAAgC,WAAW,CAAC,cAAc,EAAE,CAAC,CAAC;IAC1E,OAAO,CAAC,GAAG,CAAC,gCAAgC,WAAW,CAAC,qBAAqB,EAAE,CAAC,CAAC;IACjF,OAAO,CAAC,GAAG,CAAC,gCAAgC,WAAW,CAAC,oBAAoB,EAAE,CAAC,CAAC;IAChF,OAAO,CAAC,GAAG,CAAC,gCAAgC,WAAW,CAAC,0BAA0B,EAAE,CAAC,CAAC;IACtF,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;IAChB,OAAO,CAAC,GAAG,CAAC,SAAS,IAAI,EAAE,CAAC,CAAC;AAC/B,CAAC;AAED,SAAgB,oBAAoB,CAAC,OAA6B;IAChE,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;IAC1B,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;IACzC,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,IAAI,SAAS,CAAC;IAE3C,IAAI,CAAC,IAAA,eAAU,EAAC,QAAQ,CAAC,EAAE,CAAC;QAC1B,OAAO,CAAC,KAAK,CAAC,yDAAyD,CAAC,CAAC;QACzE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,MAAM,MAAM,GAAG,IAAA,8BAAc,EAAC,QAAQ,EAAE,EAAE,SAAS,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC;IAC1E,MAAM,EAAE,SAAS,EAAE,WAAW,EAAE,GAAG,MAAM,CAAC;IAC1C,MAAM,KAAK,GACT,SAAS,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,kBAAkB,CAAC;IAEhE,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;QACtB,MAAM,MAAM,GAA4B;YACtC,OAAO,EAAE,gBAAgB;YACzB,KAAK;YACL,SAAS;YACT,WAAW;YACX,YAAY,EAAE,gBAAgB,CAAC,KAAK,CAAC;YACrC,IAAI,EAAE,IAAI;SACX,CAAC;QACF,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QAC7C,OAAO;IACT,CAAC;IAED,yBAAyB;IACzB,IAAI,SAAS,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC3B,wBAAwB,CAAC,WAAW,CAAC,CAAC;QACtC,OAAO;IACT,CAAC;IAED,IAAI,OAAO,CAAC,KAAK,EAAE,CAAC;QAClB,MAAM,OAAO,GAAG,IAAA,sCAAsB,EAAC,QAAQ,EAAE,SAAS,CAAC,CAAC;QAC5D,OAAO,CAAC,GAAG,CAAC,sBAAsB,OAAO,CAAC,MAAM,6BAA6B,CAAC,CAAC;QAC/E,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;YACxB,OAAO,CAAC,GAAG,CAAC,KAAK,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC;QAC5C,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,8CAA8C,CAAC,CAAC;IAC9D,CAAC;SAAM,CAAC;QACN,MAAM,aAAa,GAAG,IAAA,uCAAuB,EAAC,QAAQ,EAAE,SAAS,CAAC,CAAC;QACnE,OAAO,CAAC,GAAG,CAAC,YAAY,SAAS,CAAC,MAAM,yBAAyB,CAAC,CAAC;QACnE,OAAO,CAAC,GAAG,CAAC,8BAA8B,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,aAAa,CAAC,EAAE,CAAC,CAAC;QAC/E,OAAO,CAAC,GAAG,CAAC,oEAAoE,CAAC,CAAC;IACpF,CAAC;AACH,CAAC"}

package/dist/commands/module.d.ts

@@ -1,5 +1,8 @@
-export declare function moduleInferCommand(options: {
+export interface ModuleInferOptions {
     write?: boolean;
     dryRun?: boolean;
-}): void;
+    coarseAttribution?: boolean;
+    format?: 'compact' | 'json';
+}
+export declare function moduleInferCommand(options: ModuleInferOptions): void;
 //# sourceMappingURL=module.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"module.d.ts","sourceRoot":"","sources":["../../src/commands/module.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,kBAAkB;IACjC,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,MAAM,CAAC,EAAE,SAAS,GAAG,MAAM,CAAC;CAC7B;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,kBAAkB,GAAG,IAAI,CAmEpE"}

package/dist/commands/module.js

@@ -44,32 +44,65 @@ function moduleInferCommand(options) {
         console.error('Error: No .pmem directory found. Run `pmem init` first.');
         process.exit(2);
     }
-    const inferred = (0, moduleInfer_1.inferModules)(cwd);
+    const coarse = options.coarseAttribution === true;
+    const inferred = (0, moduleInfer_1.inferModules)(cwd, { coarseAttribution: coarse });
+    const format = options.format || 'compact';
     if (inferred.length === 0) {
-        console.log('No modules could be inferred from the current project structure.');
+        if (format === 'json') {
+            console.log(JSON.stringify({
+                command: 'module.infer',
+                state: 'empty',
+                coarse_attribution: coarse,
+                modules: []
+            }, null, 2));
+        }
+        else {
+            console.log('No modules could be inferred from the current project structure.');
+        }
         return;
     }
     if (options.write && !options.dryRun) {
         const written = (0, moduleInfer_1.writeInferredModules)(pmemPath, inferred);
-        console.log(`Successfully wrote ${written.length} inferred module card(s):`);
-        for (const p of written) {
-            console.log(`- ${path.relative(cwd, p)}`);
+        if (format === 'json') {
+            console.log(JSON.stringify({
+                command: 'module.infer',
+                state: 'written',
+                coarse_attribution: coarse,
+                written: written.map(p => path.relative(cwd, p)),
+                modules: inferred
+            }, null, 2));
+        }
+        else {
+            console.log(`Successfully wrote ${written.length} inferred module card(s):`);
+            for (const p of written) {
+                console.log(`- ${path.relative(cwd, p)}`);
+            }
+            console.log('Next: run `pmem rebuild` to rebuild indexes.');
         }
-        console.log('Next: run `pmem rebuild` to rebuild indexes.');
     }
     else {
-        console.log(`Inferred ${inferred.length} module candidate(s) (dry-run):`);
-        for (const m of inferred) {
-            console.log(`\n- ID: ${m.id}`);
-            console.log(`  Title: ${m.title}`);
-            console.log(`  Purpose: ${m.purpose}`);
-            console.log(`  Files: ${m.source_files.join(', ')}`);
-            console.log(`  Knowledge:`);
-            for (const k of m.current_knowledge) {
-                console.log(`    - ${k}`);
+        if (format === 'json') {
+            console.log(JSON.stringify({
+                command: 'module.infer',
+                state: 'dry-run',
+                coarse_attribution: coarse,
+                modules: inferred
+            }, null, 2));
+        }
+        else {
+            console.log(`Inferred ${inferred.length} module candidate(s) (dry-run):`);
+            for (const m of inferred) {
+                console.log(`\n- ID: ${m.id}`);
+                console.log(`  Title: ${m.title}`);
+                console.log(`  Purpose: ${m.purpose}`);
+                console.log(`  Files: ${m.source_files.join(', ')}`);
+                console.log(`  Knowledge:`);
+                for (const k of m.current_knowledge) {
+                    console.log(`    - ${k}`);
+                }
             }
+            console.log('\nRun `pmem module infer --write` to save these cards to .pmem/modules/.');
         }
-        console.log('\nRun `pmem module infer --write` to save these cards to .pmem/modules/.');
     }
 }
 //# sourceMappingURL=module.js.map

package/dist/commands/module.js.map

@@ -1 +1 @@
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+{"version":3,"file":"module.js","sourceRoot":"","sources":["../../src/commands/module.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAWA,gDAmEC;AA9ED,2CAA6B;AAC7B,mCAAwC;AACxC,qDAAyE;AASzE,SAAgB,kBAAkB,CAAC,OAA2B;IAC5D,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,KAAK,CAAC,yDAAyD,CAAC,CAAC;QACzE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,MAAM,MAAM,GAAG,OAAO,CAAC,iBAAiB,KAAK,IAAI,CAAC;IAClD,MAAM,QAAQ,GAAG,IAAA,0BAAY,EAAC,GAAG,EAAE,EAAE,iBAAiB,EAAE,MAAM,EAAE,CAAC,CAAC;IAClE,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,IAAI,SAAS,CAAC;IAE3C,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC1B,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;YACtB,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC;gBACzB,OAAO,EAAE,cAAc;gBACvB,KAAK,EAAE,OAAO;gBACd,kBAAkB,EAAE,MAAM;gBAC1B,OAAO,EAAE,EAAE;aACZ,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QACf,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,GAAG,CAAC,kEAAkE,CAAC,CAAC;QAClF,CAAC;QACD,OAAO;IACT,CAAC;IAED,IAAI,OAAO,CAAC,KAAK,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;QACrC,MAAM,OAAO,GAAG,IAAA,kCAAoB,EAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;QACzD,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;YACtB,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC;gBACzB,OAAO,EAAE,cAAc;gBACvB,KAAK,EAAE,SAAS;gBAChB,kBAAkB,EAAE,MAAM;gBAC1B,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC;gBAChD,OAAO,EAAE,QAAQ;aAClB,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QACf,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,GAAG,CAAC,sBAAsB,OAAO,CAAC,MAAM,2BAA2B,CAAC,CAAC;YAC7E,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;gBACxB,OAAO,CAAC,GAAG,CAAC,KAAK,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC;YAC5C,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,8CAA8C,CAAC,CAAC;QAC9D,CAAC;IACH,CAAC;SAAM,CAAC;QACN,IAAI,MAAM,KAAK,MAAM,EAAE,CAAC;YACtB,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC;gBACzB,OAAO,EAAE,cAAc;gBACvB,KAAK,EAAE,SAAS;gBAChB,kBAAkB,EAAE,MAAM;gBAC1B,OAAO,EAAE,QAAQ;aAClB,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;QACf,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,GAAG,CAAC,YAAY,QAAQ,CAAC,MAAM,iCAAiC,CAAC,CAAC;YAC1E,KAAK,MAAM,CAAC,IAAI,QAAQ,EAAE,CAAC;gBACzB,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBAC/B,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;gBACnC,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;gBACvC,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrD,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC;gBAC5B,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,iBAAiB,EAAE,CAAC;oBACpC,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAAC;gBAC5B,CAAC;YACH,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,0EAA0E,CAAC,CAAC;QAC1F,CAAC;IACH,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,CAidjE;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,CAYjE;AAmfD;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,EAAE,CAQ3D"}

package/dist/commands/rebuild.js

@@ -44,8 +44,23 @@ const hash_1 = require("../core/hash");
 const yaml_1 = require("../core/yaml");
 const PMEM_DIR = '.pmem';
 function rebuildCommand(options = {}) {
+    const pmemPath = path.join(process.cwd(), PMEM_DIR);
+    // v0.7.6 FIX-1 (issue #9): hold `.pmem/.lock` for the duration of the
+    // rebuild so a concurrent `pmem verify` waits (or reports `active_lock`)
+    // instead of reading a torn-down SQLite index and emitting transient
+    // `stale_index` warnings. `withLock` is reentrant — when invoked from
+    // `pmem update --confirm` (which already holds the lock) it just runs
+    // the body without an extra acquire/release round trip.
+    (0, fs_1.withLock)(pmemPath, () => {
+        rebuildLocked(pmemPath, options);
+    }, { timeoutMs: 30000, onTimeout: 'error' });
+}
+/**
+ * The actual rebuild body, run inside the `.pmem/.lock` critical section
+ * (see FIX-1 in `rebuildCommand`).
+ */
+function rebuildLocked(pmemPath, options) {
     const cwd = process.cwd();
-    const pmemPath = path.join(cwd, PMEM_DIR);
     const manifest = (0, manifest_1.loadManifest)(pmemPath);
     if (!manifest) {
         if ((0, fs_1.fileExists)(pmemPath)) {

package/dist/commands/rebuild.js.map

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

@@ -0,0 +1,46 @@
+export interface RelationsEdgeOut {
+    edge_id: number;
+    to_id: string;
+    type: string;
+    source: string;
+    confidence: number;
+}
+export interface RelationsEdgeIn {
+    edge_id: number;
+    from_id: string;
+    type: string;
+    source: string;
+    confidence: number;
+}
+export interface RelationsPruningCandidate {
+    edge_id: number;
+    direction: 'out' | 'in';
+    other_id: string;
+    type: string;
+    source: string;
+    confidence: number;
+    reason: 'inferred' | 'low_confidence';
+}
+export interface RelationsQueryResult {
+    card_id: string;
+    outgoing: RelationsEdgeOut[];
+    incoming: RelationsEdgeIn[];
+    total: number;
+    summary_by_type: Record<string, number>;
+    summary_by_source: Record<string, number>;
+    pruning_candidates: RelationsPruningCandidate[];
+}
+export interface RelationsQueryOptions {
+    type?: string;
+    source?: 'explicit' | 'inferred' | 'mention' | 'manual' | 'all';
+    limit?: number;
+}
+export declare function relationsQuery(pmemPath: string, cardId: string, options?: RelationsQueryOptions): RelationsQueryResult;
+export interface RelationsCommandOptions {
+    type?: string;
+    source?: string;
+    format?: string;
+    limit?: number;
+}
+export declare function relationsCommand(cardId: string, options: RelationsCommandOptions): void;
+//# sourceMappingURL=relations.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"relations.d.ts","sourceRoot":"","sources":["../../src/commands/relations.ts"],"names":[],"mappings":"AAMA,MAAM,WAAW,gBAAgB;IAC/B,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,eAAe;IAC9B,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,yBAAyB;IACxC,OAAO,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,KAAK,GAAG,IAAI,CAAC;IACxB,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,UAAU,GAAG,gBAAgB,CAAC;CACvC;AAED,MAAM,WAAW,oBAAoB;IACnC,OAAO,EAAE,MAAM,CAAC;IAChB,QAAQ,EAAE,gBAAgB,EAAE,CAAC;IAC7B,QAAQ,EAAE,eAAe,EAAE,CAAC;IAC5B,KAAK,EAAE,MAAM,CAAC;IACd,eAAe,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACxC,iBAAiB,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC1C,kBAAkB,EAAE,yBAAyB,EAAE,CAAC;CACjD;AAED,MAAM,WAAW,qBAAqB;IACpC,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,UAAU,GAAG,UAAU,GAAG,SAAS,GAAG,QAAQ,GAAG,KAAK,CAAC;IAChE,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,wBAAgB,cAAc,CAC5B,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,EACd,OAAO,CAAC,EAAE,qBAAqB,GAC9B,oBAAoB,CAqGtB;AAED,MAAM,WAAW,uBAAuB;IACtC,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,uBAAuB,GAAG,IAAI,CAoCvF"}

package/dist/commands/relations.js

@@ -0,0 +1,166 @@
+"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.relationsQuery = relationsQuery;
+exports.relationsCommand = relationsCommand;
+const path = __importStar(require("path"));
+const fs_1 = require("../core/fs");
+const db_1 = require("../core/db");
+const PMEM_DIR = '.pmem';
+function relationsQuery(pmemPath, cardId, options) {
+    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);
+    // Verify card exists
+    const card = db
+        .prepare('SELECT id, title FROM cards WHERE id = ? AND is_deleted = 0')
+        .get(cardId);
+    if (!card) {
+        throw new Error(`Card "${cardId}" not found.`);
+    }
+    // Build filter clause
+    const filters = [];
+    const params = [];
+    if (options?.type) {
+        filters.push('type = ?');
+        params.push(options.type);
+    }
+    if (options?.source && options.source !== 'all') {
+        filters.push('source = ?');
+        params.push(options.source);
+    }
+    const whereClause = filters.length > 0 ? ' AND ' + filters.join(' AND ') : '';
+    const outgoingRows = db
+        .prepare(`SELECT id as edge_id, to_id, type, source, confidence
+       FROM edges
+       WHERE from_id = ?${whereClause}
+       ORDER BY confidence ASC, edge_id ASC`)
+        .all(cardId, ...params);
+    const incomingRows = db
+        .prepare(`SELECT id as edge_id, from_id, type, source, confidence
+       FROM edges
+       WHERE to_id = ?${whereClause}
+       ORDER BY confidence ASC, edge_id ASC`)
+        .all(cardId, ...params);
+    // Apply limit per direction if specified
+    const outgoing = options?.limit ? outgoingRows.slice(0, options.limit) : outgoingRows;
+    const incoming = options?.limit ? incomingRows.slice(0, options.limit) : incomingRows;
+    // Build summaries across both directions
+    const summary_by_type = {};
+    const summary_by_source = {};
+    const tally = (type, source) => {
+        summary_by_type[type] = (summary_by_type[type] || 0) + 1;
+        summary_by_source[source] = (summary_by_source[source] || 0) + 1;
+    };
+    for (const e of outgoing)
+        tally(e.type, e.source);
+    for (const e of incoming)
+        tally(e.type, e.source);
+    // Pruning candidates: inferred OR confidence < 0.5
+    const pruning_candidates = [];
+    for (const e of outgoing) {
+        if (e.source === 'inferred' || e.confidence < 0.5) {
+            pruning_candidates.push({
+                edge_id: e.edge_id,
+                direction: 'out',
+                other_id: e.to_id,
+                type: e.type,
+                source: e.source,
+                confidence: e.confidence,
+                reason: e.source === 'inferred' ? 'inferred' : 'low_confidence',
+            });
+        }
+    }
+    for (const e of incoming) {
+        if (e.source === 'inferred' || e.confidence < 0.5) {
+            pruning_candidates.push({
+                edge_id: e.edge_id,
+                direction: 'in',
+                other_id: e.from_id,
+                type: e.type,
+                source: e.source,
+                confidence: e.confidence,
+                reason: e.source === 'inferred' ? 'inferred' : 'low_confidence',
+            });
+        }
+    }
+    return {
+        card_id: cardId,
+        outgoing,
+        incoming,
+        total: outgoing.length + incoming.length,
+        summary_by_type,
+        summary_by_source,
+        pruning_candidates,
+    };
+}
+function relationsCommand(cardId, options) {
+    const pmemPath = path.join(process.cwd(), PMEM_DIR);
+    const source = (options.source ?? 'all');
+    const result = relationsQuery(pmemPath, cardId, {
+        type: options.type,
+        source,
+        limit: options.limit,
+    });
+    if (options.format === 'json') {
+        console.log(JSON.stringify(result, null, 2));
+        return;
+    }
+    // Compact format
+    console.log(`Card: ${result.card_id}`);
+    console.log(`Total relations: ${result.total}`);
+    console.log(`  Outgoing: ${result.outgoing.length}`);
+    console.log(`  Incoming: ${result.incoming.length}`);
+    console.log('');
+    console.log('By type:', JSON.stringify(result.summary_by_type));
+    console.log('By source:', JSON.stringify(result.summary_by_source));
+    if (result.pruning_candidates.length > 0) {
+        console.log('');
+        console.log(`Pruning candidates (${result.pruning_candidates.length}):`);
+        const limit = 10;
+        const slice = result.pruning_candidates.slice(0, limit);
+        for (const p of slice) {
+            const arrow = p.direction === 'out' ? `${result.card_id} -> ${p.other_id}` : `${p.other_id} -> ${result.card_id}`;
+            console.log(`  - [${p.source}, conf=${p.confidence}, ${p.reason}] ${arrow} (${p.type})`);
+        }
+        if (result.pruning_candidates.length > limit) {
+            console.log(`  ... and ${result.pruning_candidates.length - limit} more (use --format json to see all)`);
+        }
+    }
+}
+//# sourceMappingURL=relations.js.map