lemma-mcp 0.18.2 → 0.19.0

package/README.md

@@ -193,6 +193,7 @@ Lemma is local-first by design:
 ## Documentation
 
 - [Development Guide](docs/development/DEVELOPMENT.md) — Architecture, project structure, testing
+- [Roadmap](docs/development/ROADMAP.md) — Research-grounded plan + backward-compatibility contract
 - [Research](docs/research/README.md) — Academic papers that influenced Lemma's design
 - [Changelog](CHANGELOG.md) — Version history
 

package/dist/db/memory-store.d.ts

@@ -38,5 +38,5 @@ export declare function shouldRunDecay(lemmaDb: LemmaDB): boolean;
 export declare function markDecayRun(lemmaDb: LemmaDB): void;
 export declare function decayMemories(lemmaDb: LemmaDB): number;
 export declare function getMemoryStats(lemmaDb: LemmaDB, project?: string | null): MemoryStats;
-export declare function mergeMemories(lemmaDb: LemmaDB, ids: number[], title: string, fragment: string, description?: string): number | null;
+export declare function mergeMemories(lemmaDb: LemmaDB, ids: number[], title: string, fragment: string, description?: string, consolidate?: boolean): number | null;
 //# sourceMappingURL=memory-store.d.ts.map

package/dist/db/memory-store.d.ts.map

@@ -1 +1 @@
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package/dist/db/memory-store.js

@@ -1,6 +1,7 @@
 import crypto from "crypto";
 import { logger } from "../logger.js";
 import { sanitizeFtsQuery } from "./fts.js";
+import { loadConfig } from "../memory/config.js";
 function generateLegacyId() {
     return "m" + crypto.randomBytes(6).toString("hex");
 }
@@ -351,22 +352,44 @@ export function shouldRunDecay(lemmaDb) {
 export function markDecayRun(lemmaDb) {
     lemmaDb.prepareCached(`INSERT OR REPLACE INTO schema_version (version, applied_at) VALUES (-1, datetime('now'))`).run();
 }
+const FRAGMENT_TYPES = ["fact", "pattern", "lesson", "warning", "context"];
 export function decayMemories(lemmaDb) {
     if (!shouldRunDecay(lemmaDb)) {
         logger.info("Memory decay skipped (too recent)");
         return 0;
     }
+    const cfg = loadConfig();
+    const decayCfg = cfg.decay ?? { model: "linear", half_life_days: undefined };
     const { db } = lemmaDb;
     return db.transaction(() => {
-        const result = lemmaDb
-            .prepareCached(`UPDATE memories SET confidence = MAX(0, confidence - 0.002),
+        let changed = 0;
+        if (decayCfg.model === "ebbinghaus") {
+            // Exponential, type-aware retention keyed off the true elapsed time since
+            // the last decay run — so a long absence forgets more (Ebbinghaus), while
+            // access (access_count > 0 this window) fully resets the fragment.
+            const row = lemmaDb.prepareCached(`SELECT applied_at FROM schema_version WHERE version = -1`).get();
+            const lastMs = row ? new Date(row.applied_at).getTime() : Date.now() - DECAY_INTERVAL_HOURS * 3600 * 1000;
+            const elapsedDays = Math.max(0.5, (Date.now() - lastMs) / 86400000);
+            const halfLives = decayCfg.half_life_days ?? {};
+            for (const type of FRAGMENT_TYPES) {
+                const halfLife = halfLives[type] || 60;
+                const retention = Math.pow(0.5, elapsedDays / halfLife);
+                const r = lemmaDb.prepareCached(`UPDATE memories SET confidence = MAX(0, confidence * ?), updated_at = datetime('now')
+           WHERE access_count = 0 AND confidence > 0 AND type = ?`).run(retention, type);
+                changed += r.changes;
+            }
+        }
+        else {
+            // Linear (default, unchanged): flat −0.002 for every unaccessed fragment.
+            const result = lemmaDb.prepareCached(`UPDATE memories SET confidence = MAX(0, confidence - 0.002),
          updated_at = datetime('now')
-         WHERE access_count = 0 AND confidence > 0`)
-            .run();
+         WHERE access_count = 0 AND confidence > 0`).run();
+            changed = result.changes;
+        }
         lemmaDb.prepareCached("UPDATE memories SET access_count = 0").run();
         markDecayRun(lemmaDb);
-        logger.info("Memory decay complete", { decayed: result.changes });
-        return result.changes;
+        logger.info("Memory decay complete", { decayed: changed, model: decayCfg.model });
+        return changed;
     })();
 }
 export function getMemoryStats(lemmaDb, project) {
@@ -390,7 +413,7 @@ export function getMemoryStats(lemmaDb, project) {
         high_confidence: row.high_confidence,
     };
 }
-export function mergeMemories(lemmaDb, ids, title, fragment, description) {
+export function mergeMemories(lemmaDb, ids, title, fragment, description, consolidate = false) {
     if (ids.length === 0)
         return null;
     const { db } = lemmaDb;
@@ -411,11 +434,23 @@ export function mergeMemories(lemmaDb, ids, title, fragment, description) {
                 addRelation(lemmaDb, rel.source_id, newId, rel.type, rel.note ?? undefined);
             }
         }
-        const deleteStmt = lemmaDb.prepareCached("DELETE FROM memories WHERE id = ?");
-        for (const id of ids) {
-            deleteStmt.run(id);
+        if (consolidate) {
+            // Non-destructive: keep the sources but mark them superseded by the merged
+            // fragment and heavily down-weight them, so recall/injection ignores them
+            // yet nothing is lost and it's reversible (roadmap B3; SDFT; survey O4).
+            for (const id of ids) {
+                addRelation(lemmaDb, newId, id, "supersedes", "consolidated");
+                lemmaDb.prepareCached(`UPDATE memories SET confidence = MIN(confidence, 0.1), updated_at = datetime('now') WHERE id = ?`).run(id);
+            }
+            logger.info("Memories consolidated (non-destructive)", { sourceIds: ids, newId });
+        }
+        else {
+            const deleteStmt = lemmaDb.prepareCached("DELETE FROM memories WHERE id = ?");
+            for (const id of ids) {
+                deleteStmt.run(id);
+            }
+            logger.info("Memories merged", { sourceIds: ids, newId });
         }
-        logger.info("Memories merged", { sourceIds: ids, newId });
         return newId;
     })();
 }

package/dist/db/memory-store.js.map

@@ -1 +1 @@
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package/dist/intelligence/conflict.d.ts

@@ -2,5 +2,19 @@ import type { MemoryFragment } from "../types.js";
 import type { ConflictPair } from "./types.js";
 export declare function detectConflict(newFragment: MemoryFragment, existingFragments: MemoryFragment[], topN?: number): ConflictPair[];
 export declare function scanForConflicts(allFragments: MemoryFragment[]): ConflictPair[];
+export interface ConflictResolution {
+    winner_id: string;
+    loser_id: string;
+    winner_score: number;
+    loser_score: number;
+    rationale: string;
+}
+/**
+ * Propose which of two conflicting fragments should win, via a survey-O3
+ * heuristic: recency × confidence × support-count. This is advisory only — it
+ * suggests a `supersedes` link and a small spot-decay for the loser; it never
+ * deletes or auto-relates. The calling agent decides (roadmap B4, N4).
+ */
+export declare function resolveConflict(a: MemoryFragment, b: MemoryFragment): ConflictResolution;
 export declare function formatConflictResults(conflicts: ConflictPair[]): string;
 //# sourceMappingURL=conflict.d.ts.map

package/dist/intelligence/conflict.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"conflict.d.ts","sourceRoot":"","sources":["../../src/intelligence/conflict.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,aAAa,CAAC;AAClD,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,YAAY,CAAC;AA0E/C,wBAAgB,cAAc,CAC5B,WAAW,EAAE,cAAc,EAC3B,iBAAiB,EAAE,cAAc,EAAE,EACnC,IAAI,SAAI,GACP,YAAY,EAAE,CAuChB;AAED,wBAAgB,gBAAgB,CAAC,YAAY,EAAE,cAAc,EAAE,GAAG,YAAY,EAAE,CA0E/E;AAED,MAAM,WAAW,kBAAkB;IACjC,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,CAAC;IACjB,YAAY,EAAE,MAAM,CAAC;IACrB,WAAW,EAAE,MAAM,CAAC;IACpB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,CAAC,EAAE,cAAc,EAAE,CAAC,EAAE,cAAc,GAAG,kBAAkB,CAmBxF;AAED,wBAAgB,qBAAqB,CAAC,SAAS,EAAE,YAAY,EAAE,GAAG,MAAM,CAUvE"}

package/dist/intelligence/conflict.js

@@ -102,43 +102,100 @@ export function scanForConflicts(allFragments) {
     const conflicts = [];
     const signatures = new Map();
     const negationMap = new Map();
-    for (const frag of allFragments) {
-        signatures.set(frag.id, extractTopicSignature(frag.fragment));
+    // Tier-1 gate: an inverted index (term → fragment indices) so we only run the
+    // expensive overlap+signal check on pairs that share ≥1 topic term. Pairs
+    // sharing zero terms have overlap 0 and were always skipped, so the output is
+    // identical to the old O(n²) scan — just far fewer comparisons (SSR-Ada; C3).
+    const inverted = new Map();
+    for (let i = 0; i < allFragments.length; i++) {
+        const frag = allFragments[i];
+        const sig = extractTopicSignature(frag.fragment);
+        signatures.set(frag.id, sig);
         negationMap.set(frag.id, hasNegation(frag.fragment));
+        for (const term of sig) {
+            const list = inverted.get(term);
+            if (list)
+                list.push(i);
+            else
+                inverted.set(term, [i]);
+        }
     }
-    for (let i = 0; i < allFragments.length; i++) {
-        for (let j = i + 1; j < allFragments.length; j++) {
-            const a = allFragments[i];
-            const b = allFragments[j];
-            const overlap = topicOverlap(signatures.get(a.id), signatures.get(b.id));
-            if (overlap < 0.4)
-                continue;
-            const aNeg = negationMap.get(a.id);
-            const bNeg = negationMap.get(b.id);
-            let conflictScore = 0;
-            if (aNeg !== bNeg && overlap >= 0.5) {
-                conflictScore = 0.5 + (overlap - 0.5) * 0.5;
-            }
-            const signalScore = detectContradictionSignals(a.fragment, b.fragment);
-            conflictScore = Math.max(conflictScore, signalScore * overlap);
-            if (conflictScore >= 0.4) {
-                conflicts.push({
-                    memory_a_id: a.id,
-                    memory_a_title: a.title,
-                    memory_b_id: b.id,
-                    memory_b_title: b.title,
-                    reason: aNeg !== bNeg
-                        ? "Opposing sentiment on same topic"
-                        : "Contradiction signals detected",
-                    overlap_score: Math.round(conflictScore * 100) / 100,
-                });
+    // Generate the candidate pair set (deduped) from co-occurrence in the index.
+    const candidates = new Set();
+    const N = allFragments.length;
+    for (const idxs of inverted.values()) {
+        if (idxs.length < 2)
+            continue;
+        for (let x = 0; x < idxs.length; x++) {
+            for (let y = x + 1; y < idxs.length; y++) {
+                const i = idxs[x], j = idxs[y];
+                candidates.add(i < j ? i * N + j : j * N + i);
             }
         }
     }
+    // Tier-2: the expensive contradiction check, on candidates only. Sort the
+    // keys so pairs are visited in the same (i<j) order as the old scan, keeping
+    // the output byte-identical for equal-score ties.
+    const orderedKeys = [...candidates].sort((a, b) => a - b);
+    for (const key of orderedKeys) {
+        const i = Math.floor(key / N);
+        const j = key % N;
+        const a = allFragments[i];
+        const b = allFragments[j];
+        const overlap = topicOverlap(signatures.get(a.id), signatures.get(b.id));
+        if (overlap < 0.4)
+            continue;
+        const aNeg = negationMap.get(a.id);
+        const bNeg = negationMap.get(b.id);
+        let conflictScore = 0;
+        if (aNeg !== bNeg && overlap >= 0.5) {
+            conflictScore = 0.5 + (overlap - 0.5) * 0.5;
+        }
+        const signalScore = detectContradictionSignals(a.fragment, b.fragment);
+        conflictScore = Math.max(conflictScore, signalScore * overlap);
+        if (conflictScore >= 0.4) {
+            conflicts.push({
+                memory_a_id: a.id,
+                memory_a_title: a.title,
+                memory_b_id: b.id,
+                memory_b_title: b.title,
+                reason: aNeg !== bNeg
+                    ? "Opposing sentiment on same topic"
+                    : "Contradiction signals detected",
+                overlap_score: Math.round(conflictScore * 100) / 100,
+            });
+        }
+    }
     conflicts.sort((a, b) => b.overlap_score - a.overlap_score);
-    logger.flow("conflict", "full_scan", { fragment_count: allFragments.length, conflict_count: conflicts.length });
+    logger.flow("conflict", "full_scan", { fragment_count: allFragments.length, conflict_count: conflicts.length, candidate_pairs: candidates.size });
     return conflicts;
 }
+/**
+ * Propose which of two conflicting fragments should win, via a survey-O3
+ * heuristic: recency × confidence × support-count. This is advisory only — it
+ * suggests a `supersedes` link and a small spot-decay for the loser; it never
+ * deletes or auto-relates. The calling agent decides (roadmap B4, N4).
+ */
+export function resolveConflict(a, b) {
+    const score = (f) => {
+        const created = new Date(f.created).getTime();
+        const days = Number.isNaN(created) ? 180 : (Date.now() - created) / 86400000;
+        const recency = Math.max(0, 1 - days / 180);
+        const support = (f.relations || []).filter(r => r.type === "supports").length;
+        const supportScore = Math.min(support / 3, 1);
+        return (f.confidence ?? 0.5) * 0.5 + recency * 0.3 + supportScore * 0.2;
+    };
+    const sa = Math.round(score(a) * 100) / 100;
+    const sb = Math.round(score(b) * 100) / 100;
+    const [winner, loser, ws, ls] = sa >= sb ? [a, b, sa, sb] : [b, a, sb, sa];
+    return {
+        winner_id: winner.id,
+        loser_id: loser.id,
+        winner_score: ws,
+        loser_score: ls,
+        rationale: `recency×confidence×support favors [${winner.id}] (${ws} vs ${ls})`,
+    };
+}
 export function formatConflictResults(conflicts) {
     if (conflicts.length === 0)
         return "No conflicts detected.";

package/dist/intelligence/conflict.js.map

@@ -1 +1 @@
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package/dist/intelligence/index.d.ts

@@ -1,6 +1,8 @@
 export type { ProactiveSuggestion, ConflictPair, PatternDetection, ProjectProgress, TfidfVector, SuggestionType, SuggestionPriority } from "./types.js";
-export { detectConflict, scanForConflicts, formatConflictResults } from "./conflict.js";
+export { detectConflict, scanForConflicts, formatConflictResults, resolveConflict } from "./conflict.js";
+export type { ConflictResolution } from "./conflict.js";
 export { checkAfterMemoryAdd, checkAfterGuidePractice, checkAfterMemoryRead, runFullAnalysis, formatSuggestions, } from "./proactive.js";
+export { calculateQualityScore, qualityScoreReasons, isLowQuality, QUALITY_SUGGESTION_THRESHOLD, } from "./scoring.js";
 export { getProjectAnalytics, getAllProjectsAnalytics, formatProjectProgress, } from "./session-analytics.js";
 export { buildVectors, findSemanticSimilar, findSemanticSimilarPairs, semanticSearch, } from "./semantic.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/intelligence/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/intelligence/index.ts"],"names":[],"mappings":"AAAA,YAAY,EAAE,mBAAmB,EAAE,YAAY,EAAE,gBAAgB,EAAE,eAAe,EAAE,WAAW,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAExJ,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,qBAAqB,EAAE,MAAM,eAAe,CAAC;AAExF,OAAO,EACL,mBAAmB,EACnB,uBAAuB,EACvB,oBAAoB,EACpB,eAAe,EACf,iBAAiB,GAClB,MAAM,gBAAgB,CAAC;AAExB,OAAO,EACL,mBAAmB,EACnB,uBAAuB,EACvB,qBAAqB,GACtB,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EACL,YAAY,EACZ,mBAAmB,EACnB,wBAAwB,EACxB,cAAc,GACf,MAAM,eAAe,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/intelligence/index.ts"],"names":[],"mappings":"AAAA,YAAY,EAAE,mBAAmB,EAAE,YAAY,EAAE,gBAAgB,EAAE,eAAe,EAAE,WAAW,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAExJ,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,qBAAqB,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AACzG,YAAY,EAAE,kBAAkB,EAAE,MAAM,eAAe,CAAC;AAExD,OAAO,EACL,mBAAmB,EACnB,uBAAuB,EACvB,oBAAoB,EACpB,eAAe,EACf,iBAAiB,GAClB,MAAM,gBAAgB,CAAC;AAExB,OAAO,EACL,qBAAqB,EACrB,mBAAmB,EACnB,YAAY,EACZ,4BAA4B,GAC7B,MAAM,cAAc,CAAC;AAEtB,OAAO,EACL,mBAAmB,EACnB,uBAAuB,EACvB,qBAAqB,GACtB,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EACL,YAAY,EACZ,mBAAmB,EACnB,wBAAwB,EACxB,cAAc,GACf,MAAM,eAAe,CAAC"}

package/dist/intelligence/index.js

@@ -1,5 +1,6 @@
-export { detectConflict, scanForConflicts, formatConflictResults } from "./conflict.js";
+export { detectConflict, scanForConflicts, formatConflictResults, resolveConflict } from "./conflict.js";
 export { checkAfterMemoryAdd, checkAfterGuidePractice, checkAfterMemoryRead, runFullAnalysis, formatSuggestions, } from "./proactive.js";
+export { calculateQualityScore, qualityScoreReasons, isLowQuality, QUALITY_SUGGESTION_THRESHOLD, } from "./scoring.js";
 export { getProjectAnalytics, getAllProjectsAnalytics, formatProjectProgress, } from "./session-analytics.js";
 export { buildVectors, findSemanticSimilar, findSemanticSimilarPairs, semanticSearch, } from "./semantic.js";
 //# sourceMappingURL=index.js.map

package/dist/intelligence/index.js.map

@@ -1 +1 @@
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package/dist/intelligence/proactive.d.ts.map

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package/dist/intelligence/proactive.js

@@ -1,4 +1,5 @@
 import { logger } from "../logger.js";
+import { isLowQuality, qualityScoreReasons } from "./scoring.js";
 export function checkAfterMemoryAdd(fragment, allFragments, allGuides) {
     const suggestions = [];
     const patternHits = detectRecurringPatterns(fragment, allFragments);
@@ -168,6 +169,19 @@ export function runFullAnalysis(allFragments, allGuides) {
             suggested_action: `guide_distill for each hot fragment`,
         });
     }
+    const lowQuality = allFragments.filter(isLowQuality);
+    if (lowQuality.length > 0) {
+        const examples = lowQuality
+            .slice(0, 3)
+            .map(f => `[${f.id}] "${f.title}" (${qualityScoreReasons(f).join(", ")})`)
+            .join("; ");
+        suggestions.push({
+            type: "refine",
+            priority: lowQuality.length > 5 ? "high" : "medium",
+            message: `${lowQuality.length} memory(ies) score below the quality threshold (poor feedback/recall track record): ${examples}. Refine or prune them.`,
+            suggested_action: `memory_update / memory_feedback / memory_forget on the weakest fragments`,
+        });
+    }
     logger.flow("proactive", "full_analysis", { suggestions: suggestions.length });
     return suggestions;
 }

package/dist/intelligence/proactive.js.map

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package/dist/intelligence/scoring.d.ts

@@ -0,0 +1,40 @@
+import type { MemoryFragment } from "../types.js";
+/**
+ * Composite quality scoring for memory fragments (roadmap C2).
+ *
+ * The `quality_score` column has existed since schema v1 but was never
+ * populated — this module finally computes it, purely from a fragment's own
+ * counters (no LLM, no new state, no global rebuild). It blends trust
+ * (confidence), corroboration (feedback), reuse (access), maturity
+ * (refinement) and penalises decay (staleness) and rejection (negative hits).
+ *
+ * The score is only used to (a) fill the dormant column on the touch-points
+ * where a fragment is already being written, and (b) surface a *specific*
+ * refine suggestion for established-but-weak fragments. It never deletes or
+ * down-weights data on its own.
+ */
+/** Below this composite quality, an established fragment earns a refine suggestion. */
+export declare const QUALITY_SUGGESTION_THRESHOLD = 0.35;
+/**
+ * Composite quality of a fragment in [0,1], derived entirely from existing
+ * columns. The positive components sum to 1.0; a bounded negative-recall
+ * penalty (≤0.35) is then subtracted. The penalty is deliberately strong:
+ * Lemma's `confidence` decays only −0.02 per negative hit, so without it a
+ * repeatedly-rejected fragment would keep a high confidence and never drop
+ * below the suggestion threshold. A pristine, corroborated, frequently-reused
+ * fragment approaches 1.0; a rejected or stale one approaches 0.
+ */
+export declare function calculateQualityScore(frag: MemoryFragment): number;
+/**
+ * The specific counters that make a fragment low-quality — empty means the
+ * fragment has no track record worth judging yet (so a brand-new fragment is
+ * never punished for silence). Callers cite these verbatim so the suggestion
+ * names exact numbers (SSR / Self-Refine specificity), not a generic nudge.
+ */
+export declare function qualityScoreReasons(frag: MemoryFragment): string[];
+/**
+ * True when a fragment is both low-scoring AND has an established track record
+ * — the gate for emitting a refine suggestion.
+ */
+export declare function isLowQuality(frag: MemoryFragment): boolean;
+//# sourceMappingURL=scoring.d.ts.map

package/dist/intelligence/scoring.d.ts.map

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