pmem-ai 0.7.5 → 0.7.6-a

package/CHANGELOG.md

@@ -2,6 +2,40 @@
 
 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
+
+- **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 @@
-{"version":3,"file":"module.d.ts","sourceRoot":"","sources":["../../src/commands/module.ts"],"names":[],"mappings":"AAIA,wBAAgB,kBAAkB,CAAC,OAAO,EAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAA;CAAE,GAAG,IAAI,CAoCvF"}
+{"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;AA4gBD;;;;;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)) {
@@ -316,17 +331,38 @@ function rebuildCommand(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);
+                    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:
@@ -418,6 +454,9 @@ function rebuildCommand(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)();
 }
 /**

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 @@
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