@velvetmonkey/flywheel-memory 2.0.42 → 2.0.44

package/dist/index.js

@@ -3058,7 +3058,7 @@ var DEFAULT_WATCHER_CONFIG = {
   flushMs: 1e3,
   batchSize: 50,
   usePolling: false,
-  pollInterval: 3e4
+  pollInterval: 1e4
 };
 function parseWatcherConfig() {
   const debounceMs = parseInt(process.env.FLYWHEEL_DEBOUNCE_MS || "");
@@ -3627,9 +3627,12 @@ function getSuppressedCount(stateDb2) {
   return row.count;
 }
 function getSuppressedEntities(stateDb2) {
-  return stateDb2.db.prepare(
-    "SELECT entity, false_positive_rate FROM wikilink_suppressions ORDER BY false_positive_rate DESC"
-  ).all();
+  return stateDb2.db.prepare(`
+    SELECT s.entity, s.false_positive_rate,
+      COALESCE((SELECT COUNT(*) FROM wikilink_feedback WHERE entity = s.entity), 0) as total
+    FROM wikilink_suppressions s
+    ORDER BY s.false_positive_rate DESC
+  `).all();
 }
 function computeBoostFromAccuracy(accuracy, sampleCount) {
   if (sampleCount < FEEDBACK_BOOST_MIN_SAMPLES) return 0;
@@ -3784,6 +3787,9 @@ function processImplicitFeedback(stateDb2, notePath, currentContent) {
     }
   });
   transaction();
+  if (removed.length > 0) {
+    updateSuppressionList(stateDb2);
+  }
   return removed;
 }
 var TIER_LABELS = [
@@ -5372,16 +5378,186 @@ function getCooccurrenceBoost(entityName, matchedEntities, cooccurrenceIndex2, r
   return Math.min(boost, MAX_COOCCURRENCE_BOOST);
 }
 
-// src/core/write/wikilinks.ts
+// src/core/write/edgeWeights.ts
 var moduleStateDb4 = null;
-function setWriteStateDb(stateDb2) {
+function setEdgeWeightStateDb(stateDb2) {
   moduleStateDb4 = stateDb2;
+}
+function buildPathToTargetsMap(stateDb2) {
+  const map = /* @__PURE__ */ new Map();
+  const rows = stateDb2.db.prepare(
+    "SELECT path, name_lower, aliases_json FROM entities"
+  ).all();
+  for (const row of rows) {
+    const targets = /* @__PURE__ */ new Set();
+    targets.add(row.name_lower);
+    if (row.aliases_json) {
+      try {
+        const aliases = JSON.parse(row.aliases_json);
+        for (const alias of aliases) {
+          targets.add(alias.toLowerCase());
+        }
+      } catch {
+      }
+    }
+    map.set(row.path, targets);
+  }
+  return map;
+}
+function pathToFallbackTarget(filePath) {
+  return filePath.replace(/\.md$/, "").split("/").pop()?.toLowerCase() ?? filePath.toLowerCase();
+}
+function recomputeEdgeWeights(stateDb2) {
+  const start = Date.now();
+  const edges = stateDb2.db.prepare(
+    "SELECT note_path, target FROM note_links"
+  ).all();
+  if (edges.length === 0) {
+    return { edges_updated: 0, duration_ms: Date.now() - start, total_weighted: 0, avg_weight: 0, strong_count: 0, top_changes: [] };
+  }
+  const survivalMap = /* @__PURE__ */ new Map();
+  const historyRows = stateDb2.db.prepare(
+    "SELECT note_path, target, edits_survived FROM note_link_history"
+  ).all();
+  for (const row of historyRows) {
+    survivalMap.set(`${row.note_path}\0${row.target}`, row.edits_survived);
+  }
+  const pathToTargets = buildPathToTargetsMap(stateDb2);
+  const targetToPaths = /* @__PURE__ */ new Map();
+  for (const [entityPath, targets] of pathToTargets) {
+    for (const target of targets) {
+      let paths = targetToPaths.get(target);
+      if (!paths) {
+        paths = /* @__PURE__ */ new Set();
+        targetToPaths.set(target, paths);
+      }
+      paths.add(entityPath);
+    }
+  }
+  const sessionRows = stateDb2.db.prepare(
+    `SELECT session_id, note_paths FROM tool_invocations
+     WHERE note_paths IS NOT NULL AND note_paths != '[]'`
+  ).all();
+  const sessionPaths = /* @__PURE__ */ new Map();
+  for (const row of sessionRows) {
+    try {
+      const paths = JSON.parse(row.note_paths);
+      if (!Array.isArray(paths) || paths.length === 0) continue;
+      let existing = sessionPaths.get(row.session_id);
+      if (!existing) {
+        existing = /* @__PURE__ */ new Set();
+        sessionPaths.set(row.session_id, existing);
+      }
+      for (const p of paths) {
+        existing.add(p);
+      }
+    } catch {
+    }
+  }
+  const coSessionCount = /* @__PURE__ */ new Map();
+  const sourceActivityCount = /* @__PURE__ */ new Map();
+  for (const [, paths] of sessionPaths) {
+    const sessionTargets = /* @__PURE__ */ new Set();
+    for (const p of paths) {
+      const targets = pathToTargets.get(p);
+      if (targets) {
+        for (const t of targets) sessionTargets.add(t);
+      } else {
+        sessionTargets.add(pathToFallbackTarget(p));
+      }
+    }
+    for (const edge of edges) {
+      if (paths.has(edge.note_path)) {
+        const srcKey = edge.note_path;
+        sourceActivityCount.set(srcKey, (sourceActivityCount.get(srcKey) ?? 0) + 1);
+        if (sessionTargets.has(edge.target)) {
+          const edgeKey = `${edge.note_path}\0${edge.target}`;
+          coSessionCount.set(edgeKey, (coSessionCount.get(edgeKey) ?? 0) + 1);
+        }
+      }
+    }
+  }
+  const oldWeights = /* @__PURE__ */ new Map();
+  const oldRows = stateDb2.db.prepare(
+    "SELECT note_path, target, weight FROM note_links"
+  ).all();
+  for (const row of oldRows) {
+    oldWeights.set(`${row.note_path}\0${row.target}`, row.weight);
+  }
+  const now = Date.now();
+  const update = stateDb2.db.prepare(
+    "UPDATE note_links SET weight = ?, weight_updated_at = ? WHERE note_path = ? AND target = ?"
+  );
+  const changes = [];
+  const tx = stateDb2.db.transaction(() => {
+    for (const edge of edges) {
+      const edgeKey = `${edge.note_path}\0${edge.target}`;
+      const editsSurvived = survivalMap.get(edgeKey) ?? 0;
+      const coSessions = coSessionCount.get(edgeKey) ?? 0;
+      const sourceAccess = sourceActivityCount.get(edge.note_path) ?? 0;
+      const weight = 1 + editsSurvived * 0.5 + Math.min(coSessions * 0.5, 3) + Math.min(sourceAccess * 0.2, 2);
+      const roundedWeight = Math.round(weight * 1e3) / 1e3;
+      const oldWeight = oldWeights.get(edgeKey) ?? 1;
+      const delta = roundedWeight - oldWeight;
+      if (Math.abs(delta) >= 1e-3) {
+        changes.push({
+          note_path: edge.note_path,
+          target: edge.target,
+          old_weight: oldWeight,
+          new_weight: roundedWeight,
+          delta: Math.round(delta * 1e3) / 1e3,
+          edits_survived: editsSurvived,
+          co_sessions: coSessions,
+          source_access: sourceAccess
+        });
+      }
+      update.run(roundedWeight, now, edge.note_path, edge.target);
+    }
+  });
+  tx();
+  changes.sort((a, b) => Math.abs(b.delta) - Math.abs(a.delta));
+  const top_changes = changes.slice(0, 10);
+  const stats = stateDb2.db.prepare(`
+    SELECT
+      COUNT(*) as total_weighted,
+      AVG(weight) as avg_weight,
+      SUM(CASE WHEN weight > 3.0 THEN 1 ELSE 0 END) as strong_count
+    FROM note_links
+    WHERE weight > 1.0
+  `).get();
+  return {
+    edges_updated: edges.length,
+    duration_ms: Date.now() - start,
+    total_weighted: stats?.total_weighted ?? 0,
+    avg_weight: Math.round((stats?.avg_weight ?? 0) * 100) / 100,
+    strong_count: stats?.strong_count ?? 0,
+    top_changes
+  };
+}
+function getEntityEdgeWeightMap(stateDb2) {
+  const rows = stateDb2.db.prepare(`
+    SELECT LOWER(target) as target_lower, AVG(weight) as avg_weight
+    FROM note_links
+    WHERE weight > 1.0
+    GROUP BY LOWER(target)
+  `).all();
+  const map = /* @__PURE__ */ new Map();
+  for (const row of rows) {
+    map.set(row.target_lower, row.avg_weight);
+  }
+  return map;
+}
+
+// src/core/write/wikilinks.ts
+var moduleStateDb5 = null;
+function setWriteStateDb(stateDb2) {
+  moduleStateDb5 = stateDb2;
   setGitStateDb(stateDb2);
   setHintsStateDb(stateDb2);
   setRecencyStateDb(stateDb2);
 }
 function getWriteStateDb() {
-  return moduleStateDb4;
+  return moduleStateDb5;
 }
 var moduleConfig = null;
 var ALL_IMPLICIT_PATTERNS = ["proper-nouns", "single-caps", "quoted-terms", "camel-case", "acronyms"];
@@ -5436,9 +5612,9 @@ var DEFAULT_EXCLUDE_FOLDERS = [
 ];
 async function initializeEntityIndex(vaultPath2) {
   try {
-    if (moduleStateDb4) {
+    if (moduleStateDb5) {
       try {
-        const dbIndex = getEntityIndexFromDb(moduleStateDb4);
+        const dbIndex = getEntityIndexFromDb(moduleStateDb5);
         if (dbIndex._metadata.total_entities > 0) {
           entityIndex = dbIndex;
           indexReady = true;
@@ -5466,9 +5642,9 @@ async function rebuildIndex(vaultPath2) {
   lastLoadedAt = Date.now();
   const entityDuration = Date.now() - startTime;
   console.error(`[Flywheel] Entity index built: ${entityIndex._metadata.total_entities} entities in ${entityDuration}ms`);
-  if (moduleStateDb4) {
+  if (moduleStateDb5) {
     try {
-      moduleStateDb4.replaceAllEntities(entityIndex);
+      moduleStateDb5.replaceAllEntities(entityIndex);
       console.error(`[Flywheel] Saved entities to StateDb`);
     } catch (e) {
       console.error(`[Flywheel] Failed to save entities to StateDb: ${e}`);
@@ -5505,14 +5681,14 @@ function isEntityIndexReady() {
   return indexReady && entityIndex !== null;
 }
 function checkAndRefreshIfStale() {
-  if (!moduleStateDb4 || !indexReady) return;
+  if (!moduleStateDb5 || !indexReady) return;
   try {
-    const metadata = getStateDbMetadata(moduleStateDb4);
+    const metadata = getStateDbMetadata(moduleStateDb5);
     if (!metadata.entitiesBuiltAt) return;
     const dbBuiltAt = new Date(metadata.entitiesBuiltAt).getTime();
     if (dbBuiltAt > lastLoadedAt) {
       console.error("[Flywheel] Entity index stale, reloading from StateDb...");
-      const dbIndex = getEntityIndexFromDb(moduleStateDb4);
+      const dbIndex = getEntityIndexFromDb(moduleStateDb5);
       if (dbIndex._metadata.total_entities > 0) {
         entityIndex = dbIndex;
         lastLoadedAt = Date.now();
@@ -5554,11 +5730,11 @@ function processWikilinks(content, notePath, existingContent) {
   }
   let entities = getAllEntities(entityIndex);
   console.error(`[Flywheel:DEBUG] Processing wikilinks with ${entities.length} entities`);
-  if (moduleStateDb4) {
+  if (moduleStateDb5) {
     const folder = notePath ? notePath.split("/")[0] : void 0;
     entities = entities.filter((e) => {
       const name = getEntityName2(e);
-      return !isSuppressed(moduleStateDb4, name, folder);
+      return !isSuppressed(moduleStateDb5, name, folder);
     });
   }
   const sortedEntities = sortEntitiesByPriority(entities, notePath);
@@ -5638,8 +5814,8 @@ function maybeApplyWikilinks(content, skipWikilinks, notePath, existingContent)
   checkAndRefreshIfStale();
   const result = processWikilinks(content, notePath, existingContent);
   if (result.linksAdded > 0) {
-    if (moduleStateDb4 && notePath) {
-      trackWikilinkApplications(moduleStateDb4, notePath, result.linkedEntities);
+    if (moduleStateDb5 && notePath) {
+      trackWikilinkApplications(moduleStateDb5, notePath, result.linkedEntities);
     }
     const implicitCount = result.implicitEntities?.length ?? 0;
     const implicitInfo = implicitCount > 0 ? ` + ${implicitCount} implicit: ${result.implicitEntities.join(", ")}` : "";
@@ -5993,6 +6169,11 @@ function scoreEntity(entity, contentTokens, contentStems, config) {
   }
   return score;
 }
+function getEdgeWeightBoostScore(entityName, map) {
+  const avgWeight = map.get(entityName.toLowerCase());
+  if (!avgWeight) return 0;
+  return Math.min((avgWeight - 1) * 2, 4);
+}
 async function suggestRelatedLinks(content, options = {}) {
   const {
     maxSuggestions = 3,
@@ -6036,7 +6217,8 @@ async function suggestRelatedLinks(content, options = {}) {
   }
   const linkedEntities = excludeLinked ? extractLinkedEntities(content) : /* @__PURE__ */ new Set();
   const noteFolder = notePath ? notePath.split("/")[0] : void 0;
-  const feedbackBoosts = moduleStateDb4 ? getAllFeedbackBoosts(moduleStateDb4, noteFolder) : /* @__PURE__ */ new Map();
+  const feedbackBoosts = moduleStateDb5 ? getAllFeedbackBoosts(moduleStateDb5, noteFolder) : /* @__PURE__ */ new Map();
+  const edgeWeightMap = moduleStateDb5 ? getEntityEdgeWeightMap(moduleStateDb5) : /* @__PURE__ */ new Map();
   const scoredEntities = [];
   const directlyMatchedEntities = /* @__PURE__ */ new Set();
   const entitiesWithContentMatch = /* @__PURE__ */ new Set();
@@ -6052,6 +6234,12 @@ async function suggestRelatedLinks(content, options = {}) {
     if (linkedEntities.has(entityName.toLowerCase())) {
       continue;
     }
+    if (moduleStateDb5 && !disabled.has("feedback")) {
+      const noteFolder2 = notePath ? notePath.split("/").slice(0, -1).join("/") : void 0;
+      if (isSuppressed(moduleStateDb5, entityName, noteFolder2)) {
+        continue;
+      }
+    }
     const contentScore = disabled.has("exact_match") && disabled.has("stem_match") ? 0 : scoreEntity(entity, contentTokens, contentStems, config);
     let score = contentScore;
     if (contentScore > 0) {
@@ -6069,6 +6257,8 @@ async function suggestRelatedLinks(content, options = {}) {
     score += layerHubBoost;
     const layerFeedbackAdj = disabled.has("feedback") ? 0 : feedbackBoosts.get(entityName) ?? 0;
     score += layerFeedbackAdj;
+    const layerEdgeWeightBoost = disabled.has("edge_weight") ? 0 : getEdgeWeightBoostScore(entityName, edgeWeightMap);
+    score += layerEdgeWeightBoost;
     if (score > 0) {
       directlyMatchedEntities.add(entityName);
     }
@@ -6086,7 +6276,8 @@ async function suggestRelatedLinks(content, options = {}) {
           recencyBoost: layerRecencyBoost,
           crossFolderBoost: layerCrossFolderBoost,
           hubBoost: layerHubBoost,
-          feedbackAdjustment: layerFeedbackAdj
+          feedbackAdjustment: layerFeedbackAdj,
+          edgeWeightBoost: layerEdgeWeightBoost
         }
       });
     }
@@ -6098,6 +6289,10 @@ async function suggestRelatedLinks(content, options = {}) {
       if (!disabled.has("length_filter") && entityName.length > MAX_ENTITY_LENGTH) continue;
       if (!disabled.has("article_filter") && isLikelyArticleTitle(entityName)) continue;
       if (linkedEntities.has(entityName.toLowerCase())) continue;
+      if (moduleStateDb5 && !disabled.has("feedback")) {
+        const noteFolder2 = notePath ? notePath.split("/").slice(0, -1).join("/") : void 0;
+        if (isSuppressed(moduleStateDb5, entityName, noteFolder2)) continue;
+      }
       const boost = getCooccurrenceBoost(entityName, directlyMatchedEntities, cooccurrenceIndex, recencyIndex);
       if (boost > 0) {
         const existing = scoredEntities.find((e) => e.name === entityName);
@@ -6119,7 +6314,8 @@ async function suggestRelatedLinks(content, options = {}) {
           const crossFolderBoost = disabled.has("cross_folder") ? 0 : notePath && entity.path ? getCrossFolderBoost(entity.path, notePath) : 0;
           const hubBoost = disabled.has("hub_boost") ? 0 : getHubBoost(entity);
           const feedbackAdj = disabled.has("feedback") ? 0 : feedbackBoosts.get(entityName) ?? 0;
-          const totalBoost = boost + typeBoost + contextBoost + recencyBoostVal + crossFolderBoost + hubBoost + feedbackAdj;
+          const edgeWeightBoost = disabled.has("edge_weight") ? 0 : getEdgeWeightBoostScore(entityName, edgeWeightMap);
+          const totalBoost = boost + typeBoost + contextBoost + recencyBoostVal + crossFolderBoost + hubBoost + feedbackAdj + edgeWeightBoost;
           if (totalBoost >= adaptiveMinScore) {
             scoredEntities.push({
               name: entityName,
@@ -6134,7 +6330,8 @@ async function suggestRelatedLinks(content, options = {}) {
                 recencyBoost: recencyBoostVal,
                 crossFolderBoost,
                 hubBoost,
-                feedbackAdjustment: feedbackAdj
+                feedbackAdjustment: feedbackAdj,
+                edgeWeightBoost
               }
             });
           }
@@ -6160,6 +6357,10 @@ async function suggestRelatedLinks(content, options = {}) {
           existing.score += boost;
           existing.breakdown.semanticBoost = boost;
         } else if (!linkedEntities.has(match.entityName.toLowerCase())) {
+          if (moduleStateDb5 && !disabled.has("feedback")) {
+            const noteFolder2 = notePath ? notePath.split("/").slice(0, -1).join("/") : void 0;
+            if (isSuppressed(moduleStateDb5, match.entityName, noteFolder2)) continue;
+          }
           const entityWithType = entitiesWithTypes.find(
             (et) => et.entity.name === match.entityName
           );
@@ -6172,7 +6373,8 @@ async function suggestRelatedLinks(content, options = {}) {
           const layerHubBoost = disabled.has("hub_boost") ? 0 : getHubBoost(entity);
           const layerCrossFolderBoost = disabled.has("cross_folder") ? 0 : notePath && entity.path ? getCrossFolderBoost(entity.path, notePath) : 0;
           const layerFeedbackAdj = disabled.has("feedback") ? 0 : feedbackBoosts.get(match.entityName) ?? 0;
-          const totalScore = boost + layerTypeBoost + layerContextBoost + layerHubBoost + layerCrossFolderBoost + layerFeedbackAdj;
+          const layerEdgeWeightBoost = disabled.has("edge_weight") ? 0 : getEdgeWeightBoostScore(match.entityName, edgeWeightMap);
+          const totalScore = boost + layerTypeBoost + layerContextBoost + layerHubBoost + layerCrossFolderBoost + layerFeedbackAdj + layerEdgeWeightBoost;
           if (totalScore >= adaptiveMinScore) {
             scoredEntities.push({
               name: match.entityName,
@@ -6188,7 +6390,8 @@ async function suggestRelatedLinks(content, options = {}) {
                 crossFolderBoost: layerCrossFolderBoost,
                 hubBoost: layerHubBoost,
                 feedbackAdjustment: layerFeedbackAdj,
-                semanticBoost: boost
+                semanticBoost: boost,
+                edgeWeightBoost: layerEdgeWeightBoost
               }
             });
             entitiesWithContentMatch.add(match.entityName);
@@ -6213,15 +6416,15 @@ async function suggestRelatedLinks(content, options = {}) {
     }
     return 0;
   });
-  if (moduleStateDb4 && notePath) {
+  if (moduleStateDb5 && notePath) {
     try {
       const now = Date.now();
-      const insertStmt = moduleStateDb4.db.prepare(`
+      const insertStmt = moduleStateDb5.db.prepare(`
         INSERT OR IGNORE INTO suggestion_events
           (timestamp, note_path, entity, total_score, breakdown_json, threshold, passed, strictness, applied, pipeline_event_id)
         VALUES (?, ?, ?, ?, ?, ?, ?, ?, 0, NULL)
       `);
-      const persistTransaction = moduleStateDb4.db.transaction(() => {
+      const persistTransaction = moduleStateDb5.db.transaction(() => {
         for (const e of relevantEntities) {
           insertStmt.run(
             now,
@@ -6262,13 +6465,15 @@ async function suggestRelatedLinks(content, options = {}) {
   if (topSuggestions.length === 0) {
     return emptyResult;
   }
-  const suffix = "\u2192 " + topSuggestions.map((name) => `[[${name}]]`).join(", ");
+  const MIN_SUFFIX_SCORE = 12;
+  const suffixEntries = topEntries.filter((e) => e.score >= MIN_SUFFIX_SCORE);
+  const suffix = suffixEntries.length > 0 ? "\u2192 " + suffixEntries.map((e) => `[[${e.name}]]`).join(", ") : "";
   const result = {
     suggestions: topSuggestions,
     suffix
   };
   if (detail) {
-    const feedbackStats = moduleStateDb4 ? getEntityStats(moduleStateDb4) : [];
+    const feedbackStats = moduleStateDb5 ? getEntityStats(moduleStateDb5) : [];
     const feedbackMap = new Map(feedbackStats.map((s) => [s.entity, s]));
     result.detailed = topEntries.map((e) => {
       const fb = feedbackMap.get(e.name);
@@ -6287,9 +6492,9 @@ async function suggestRelatedLinks(content, options = {}) {
   return result;
 }
 function detectAliasCollisions(noteName, aliases = []) {
-  if (!moduleStateDb4) return [];
+  if (!moduleStateDb5) return [];
   const collisions = [];
-  const nameAsAlias = getEntitiesByAlias(moduleStateDb4, noteName);
+  const nameAsAlias = getEntitiesByAlias(moduleStateDb5, noteName);
   for (const entity of nameAsAlias) {
     if (entity.name.toLowerCase() === noteName.toLowerCase()) continue;
     collisions.push({
@@ -6303,7 +6508,7 @@ function detectAliasCollisions(noteName, aliases = []) {
     });
   }
   for (const alias of aliases) {
-    const existingByName = getEntityByName(moduleStateDb4, alias);
+    const existingByName = getEntityByName(moduleStateDb5, alias);
     if (existingByName && existingByName.name.toLowerCase() !== noteName.toLowerCase()) {
       collisions.push({
         term: alias,
@@ -6315,7 +6520,7 @@ function detectAliasCollisions(noteName, aliases = []) {
         }
       });
     }
-    const existingByAlias = getEntitiesByAlias(moduleStateDb4, alias);
+    const existingByAlias = getEntitiesByAlias(moduleStateDb5, alias);
     for (const entity of existingByAlias) {
       if (entity.name.toLowerCase() === noteName.toLowerCase()) continue;
       if (existingByName && existingByName.name.toLowerCase() === entity.name.toLowerCase()) continue;
@@ -6339,8 +6544,8 @@ function suggestAliases(noteName, existingAliases = [], category) {
   function isSafe(alias) {
     if (existingLower.has(alias.toLowerCase())) return false;
     if (alias.toLowerCase() === noteName.toLowerCase()) return false;
-    if (!moduleStateDb4) return true;
-    const existing = getEntityByName(moduleStateDb4, alias);
+    if (!moduleStateDb5) return true;
+    const existing = getEntityByName(moduleStateDb5, alias);
     return !existing;
   }
   const inferredCategory = category || inferCategoryFromName(noteName);
@@ -6382,8 +6587,8 @@ function inferCategoryFromName(name) {
 }
 async function checkPreflightSimilarity(noteName) {
   const result = { similarEntities: [] };
-  if (!moduleStateDb4) return result;
-  const exact = getEntityByName(moduleStateDb4, noteName);
+  if (!moduleStateDb5) return result;
+  const exact = getEntityByName(moduleStateDb5, noteName);
   if (exact) {
     result.existingEntity = {
       name: exact.name,
@@ -6393,7 +6598,7 @@ async function checkPreflightSimilarity(noteName) {
   }
   const ftsNames = /* @__PURE__ */ new Set();
   try {
-    const searchResults = searchEntitiesDb(moduleStateDb4, noteName, 5);
+    const searchResults = searchEntitiesDb(moduleStateDb5, noteName, 5);
     for (const sr of searchResults) {
       if (sr.name.toLowerCase() === noteName.toLowerCase()) continue;
       ftsNames.add(sr.name.toLowerCase());
@@ -6414,7 +6619,7 @@ async function checkPreflightSimilarity(noteName) {
         if (match.similarity < 0.85) continue;
         if (match.entityName.toLowerCase() === noteName.toLowerCase()) continue;
         if (ftsNames.has(match.entityName.toLowerCase())) continue;
-        const entity = getEntityByName(moduleStateDb4, match.entityName);
+        const entity = getEntityByName(moduleStateDb5, match.entityName);
         if (entity) {
           result.similarEntities.push({
             name: entity.name,
@@ -9202,123 +9407,6 @@ function suggestEntityAliases(stateDb2, folder) {
   return suggestions;
 }
 
-// src/core/write/edgeWeights.ts
-var moduleStateDb5 = null;
-function setEdgeWeightStateDb(stateDb2) {
-  moduleStateDb5 = stateDb2;
-}
-function buildPathToTargetsMap(stateDb2) {
-  const map = /* @__PURE__ */ new Map();
-  const rows = stateDb2.db.prepare(
-    "SELECT path, name_lower, aliases_json FROM entities"
-  ).all();
-  for (const row of rows) {
-    const targets = /* @__PURE__ */ new Set();
-    targets.add(row.name_lower);
-    if (row.aliases_json) {
-      try {
-        const aliases = JSON.parse(row.aliases_json);
-        for (const alias of aliases) {
-          targets.add(alias.toLowerCase());
-        }
-      } catch {
-      }
-    }
-    map.set(row.path, targets);
-  }
-  return map;
-}
-function pathToFallbackTarget(filePath) {
-  return filePath.replace(/\.md$/, "").split("/").pop()?.toLowerCase() ?? filePath.toLowerCase();
-}
-function recomputeEdgeWeights(stateDb2) {
-  const start = Date.now();
-  const edges = stateDb2.db.prepare(
-    "SELECT note_path, target FROM note_links"
-  ).all();
-  if (edges.length === 0) {
-    return { edges_updated: 0, duration_ms: Date.now() - start };
-  }
-  const survivalMap = /* @__PURE__ */ new Map();
-  const historyRows = stateDb2.db.prepare(
-    "SELECT note_path, target, edits_survived FROM note_link_history"
-  ).all();
-  for (const row of historyRows) {
-    survivalMap.set(`${row.note_path}\0${row.target}`, row.edits_survived);
-  }
-  const pathToTargets = buildPathToTargetsMap(stateDb2);
-  const targetToPaths = /* @__PURE__ */ new Map();
-  for (const [entityPath, targets] of pathToTargets) {
-    for (const target of targets) {
-      let paths = targetToPaths.get(target);
-      if (!paths) {
-        paths = /* @__PURE__ */ new Set();
-        targetToPaths.set(target, paths);
-      }
-      paths.add(entityPath);
-    }
-  }
-  const sessionRows = stateDb2.db.prepare(
-    `SELECT session_id, note_paths FROM tool_invocations
-     WHERE note_paths IS NOT NULL AND note_paths != '[]'`
-  ).all();
-  const sessionPaths = /* @__PURE__ */ new Map();
-  for (const row of sessionRows) {
-    try {
-      const paths = JSON.parse(row.note_paths);
-      if (!Array.isArray(paths) || paths.length === 0) continue;
-      let existing = sessionPaths.get(row.session_id);
-      if (!existing) {
-        existing = /* @__PURE__ */ new Set();
-        sessionPaths.set(row.session_id, existing);
-      }
-      for (const p of paths) {
-        existing.add(p);
-      }
-    } catch {
-    }
-  }
-  const coSessionCount = /* @__PURE__ */ new Map();
-  const sourceActivityCount = /* @__PURE__ */ new Map();
-  for (const [, paths] of sessionPaths) {
-    const sessionTargets = /* @__PURE__ */ new Set();
-    for (const p of paths) {
-      const targets = pathToTargets.get(p);
-      if (targets) {
-        for (const t of targets) sessionTargets.add(t);
-      } else {
-        sessionTargets.add(pathToFallbackTarget(p));
-      }
-    }
-    for (const edge of edges) {
-      if (paths.has(edge.note_path)) {
-        const srcKey = edge.note_path;
-        sourceActivityCount.set(srcKey, (sourceActivityCount.get(srcKey) ?? 0) + 1);
-        if (sessionTargets.has(edge.target)) {
-          const edgeKey = `${edge.note_path}\0${edge.target}`;
-          coSessionCount.set(edgeKey, (coSessionCount.get(edgeKey) ?? 0) + 1);
-        }
-      }
-    }
-  }
-  const now = Date.now();
-  const update = stateDb2.db.prepare(
-    "UPDATE note_links SET weight = ?, weight_updated_at = ? WHERE note_path = ? AND target = ?"
-  );
-  const tx = stateDb2.db.transaction(() => {
-    for (const edge of edges) {
-      const edgeKey = `${edge.note_path}\0${edge.target}`;
-      const editsSurvived = survivalMap.get(edgeKey) ?? 0;
-      const coSessions = coSessionCount.get(edgeKey) ?? 0;
-      const sourceAccess = sourceActivityCount.get(edge.note_path) ?? 0;
-      const weight = 1 + editsSurvived * 0.5 + Math.min(coSessions * 0.5, 3) + Math.min(sourceAccess * 0.2, 2);
-      update.run(Math.round(weight * 1e3) / 1e3, now, edge.note_path, edge.target);
-    }
-  });
-  tx();
-  return { edges_updated: edges.length, duration_ms: Date.now() - start };
-}
-
 // src/tools/read/system.ts
 function registerSystemTools(server2, getIndex, setIndex, getVaultPath, setConfig, getStateDb) {
   const RefreshIndexOutputSchema = {
@@ -12852,7 +12940,7 @@ Example: vault_add_to_section({ path: "daily/2026-02-15.md", section: "Log", con
             wikilinkInfo: wikilinkInfo || "none"
           };
           let suggestInfo;
-          if (suggestOutgoingLinks && !skipWikilinks) {
+          if (suggestOutgoingLinks && !skipWikilinks && processedContent.length >= 100) {
             const result = await suggestRelatedLinks(processedContent, { maxSuggestions, notePath });
             if (result.suffix) {
               processedContent = processedContent + " " + result.suffix;
@@ -12971,7 +13059,7 @@ Example: vault_add_to_section({ path: "daily/2026-02-15.md", section: "Log", con
           }
           let workingReplacement = validationResult.content;
           let { content: processedReplacement } = maybeApplyWikilinks(workingReplacement, skipWikilinks, notePath);
-          if (suggestOutgoingLinks && !skipWikilinks) {
+          if (suggestOutgoingLinks && !skipWikilinks && processedReplacement.length >= 100) {
             const result = await suggestRelatedLinks(processedReplacement, { maxSuggestions, notePath });
             if (result.suffix) {
               processedReplacement = processedReplacement + " " + result.suffix;
@@ -13352,7 +13440,7 @@ function registerNoteTools(server2, vaultPath2, getIndex) {
         }
         let { content: processedContent, wikilinkInfo } = maybeApplyWikilinks(effectiveContent, skipWikilinks, notePath);
         let suggestInfo;
-        if (suggestOutgoingLinks && !skipWikilinks) {
+        if (suggestOutgoingLinks && !skipWikilinks && processedContent.length >= 100) {
           const result = await suggestRelatedLinks(processedContent, { maxSuggestions, notePath });
           if (result.suffix) {
             processedContent = processedContent + " " + result.suffix;
@@ -15774,10 +15862,11 @@ function registerWikilinkFeedbackTools(server2, getStateDb) {
         days_back: z21.number().optional().describe("Days to look back (default: 30)"),
         granularity: z21.enum(["day", "week"]).optional().describe("Time bucket granularity for layer_timeseries (default: day)"),
         timestamp_before: z21.number().optional().describe("Earlier timestamp for snapshot_diff"),
-        timestamp_after: z21.number().optional().describe("Later timestamp for snapshot_diff")
+        timestamp_after: z21.number().optional().describe("Later timestamp for snapshot_diff"),
+        skip_status_update: z21.boolean().optional().describe("Skip marking application as removed (caller will trigger implicit detection via file edit)")
       }
     },
-    async ({ mode, entity, note_path, context, correct, limit, days_back, granularity, timestamp_before, timestamp_after }) => {
+    async ({ mode, entity, note_path, context, correct, limit, days_back, granularity, timestamp_before, timestamp_after, skip_status_update }) => {
       const stateDb2 = getStateDb();
       if (!stateDb2) {
         return {
@@ -15805,6 +15894,11 @@ function registerWikilinkFeedbackTools(server2, getStateDb) {
               isError: true
             };
           }
+          if (!correct && note_path && !skip_status_update) {
+            stateDb2.db.prepare(
+              `UPDATE wikilink_applications SET status = 'removed' WHERE entity = ? AND note_path = ? COLLATE NOCASE`
+            ).run(entity, note_path);
+          }
           const suppressionUpdated = updateSuppressionList(stateDb2) > 0;
           result = {
             mode: "report",
@@ -17829,7 +17923,15 @@ async function runPostIndexWork(index) {
             if (edgeWeightAgeMs >= 60 * 60 * 1e3) {
               const result = recomputeEdgeWeights(stateDb);
               lastEdgeWeightRebuildAt = Date.now();
-              tracker.end({ rebuilt: true, edges: result.edges_updated, duration_ms: result.duration_ms });
+              tracker.end({
+                rebuilt: true,
+                edges: result.edges_updated,
+                duration_ms: result.duration_ms,
+                total_weighted: result.total_weighted,
+                avg_weight: result.avg_weight,
+                strong_count: result.strong_count,
+                top_changes: result.top_changes
+              });
               serverLog("watcher", `Edge weights: ${result.edges_updated} edges in ${result.duration_ms}ms`);
             } else {
               tracker.end({ rebuilt: false, age_ms: edgeWeightAgeMs });
@@ -18114,9 +18216,27 @@ async function runPostIndexWork(index) {
             }
           }
         }
-        tracker.end({ removals: feedbackResults });
-        if (feedbackResults.length > 0) {
-          serverLog("watcher", `Implicit feedback: ${feedbackResults.length} removals detected`);
+        const additionResults = [];
+        if (stateDb && linkDiffs.length > 0) {
+          const checkApplication = stateDb.db.prepare(
+            `SELECT 1 FROM wikilink_applications WHERE LOWER(entity) = LOWER(?) AND note_path = ? AND status = 'applied'`
+          );
+          for (const diff of linkDiffs) {
+            for (const target of diff.added) {
+              if (checkApplication.get(target, diff.file)) continue;
+              const entity = entitiesAfter.find(
+                (e) => e.nameLower === target || (e.aliases ?? []).some((a) => a.toLowerCase() === target)
+              );
+              if (entity) {
+                recordFeedback(stateDb, entity.name, "implicit:manual_added", diff.file, true);
+                additionResults.push({ entity: entity.name, file: diff.file });
+              }
+            }
+          }
+        }
+        tracker.end({ removals: feedbackResults, additions: additionResults });
+        if (feedbackResults.length > 0 || additionResults.length > 0) {
+          serverLog("watcher", `Implicit feedback: ${feedbackResults.length} removals, ${additionResults.length} manual additions detected`);
         }
         tracker.start("tag_scan", { files: filteredEvents.length });
         const tagDiffs = [];

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@velvetmonkey/flywheel-memory",
-  "version": "2.0.42",
-  "description": "MCP server that gives Claude full read/write access to your Obsidian vault. 42 tools for search, backlinks, graph queries, mutations, and hybrid semantic search.",
+  "version": "2.0.44",
+  "description": "MCP server that gives Claude full read/write access to your Obsidian vault. Select from 42 tools for search, backlinks, graph queries, mutations, and hybrid semantic search.",
   "type": "module",
   "main": "dist/index.js",
   "bin": {
@@ -52,7 +52,7 @@
   },
   "dependencies": {
     "@modelcontextprotocol/sdk": "^1.25.1",
-    "@velvetmonkey/vault-core": "^2.0.42",
+    "@velvetmonkey/vault-core": "^2.0.44",
     "better-sqlite3": "^11.0.0",
     "chokidar": "^4.0.0",
     "gray-matter": "^4.0.3",