@andespindola/brainlink 0.1.0-beta.13 → 0.1.0-beta.130

package/dist/application/dedupe-notes.js

@@ -0,0 +1,226 @@
+import { createHash } from 'node:crypto';
+import { createEmbeddingBuckets, createLocalEmbedding, cosineSimilarity } from '../domain/embeddings.js';
+import { parseMarkdownDocument } from '../domain/markdown.js';
+import { writeMarkdownFile, ensureVault, readMarkdownFiles } from '../infrastructure/file-system-vault.js';
+import { indexVault } from './index-vault.js';
+const tokenPattern = /[\p{L}\p{N}_-]+/gu;
+const frontmatterPattern = /^---\n[\s\S]*?\n---\n?/m;
+const rootHeadingPattern = /^#\s+.+\n+/m;
+const maxCandidatesPerBucket = 240;
+const normalizePath = (path) => path.replaceAll('\\', '/').replace(/^\.\//, '');
+const toComparableBody = (content) => content
+    .replace(frontmatterPattern, '')
+    .replace(rootHeadingPattern, '')
+    .replaceAll('\r\n', '\n')
+    .trim();
+const normalizeStrictContent = (content) => toComparableBody(content);
+const normalizeSemanticContent = (content) => toComparableBody(content)
+    .replace(/\s+/g, ' ')
+    .trim();
+const toHash = (value) => createHash('sha256').update(value, 'utf8').digest('hex');
+const toCandidateId = (leftPath, rightPath) => [normalizePath(leftPath), normalizePath(rightPath)].sort((left, right) => left.localeCompare(right)).join('|');
+const hasSharedTokens = (left, right) => {
+    const leftTokens = new Set((left.match(tokenPattern) ?? []).map((token) => token.toLowerCase()).filter((token) => token.length > 2));
+    const rightTokens = new Set((right.match(tokenPattern) ?? []).map((token) => token.toLowerCase()).filter((token) => token.length > 2));
+    if (leftTokens.size === 0 || rightTokens.size === 0) {
+        return false;
+    }
+    for (const token of leftTokens) {
+        if (rightTokens.has(token)) {
+            return true;
+        }
+    }
+    return false;
+};
+const relatedMarker = (targetTitle) => `Related: [[${targetTitle}]] priority: low #related-to`;
+const ensureRelatedEdgeLine = (content, targetTitle) => {
+    const linkPattern = new RegExp(`\\[\\[\\s*${targetTitle.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}\\s*(?:[\\]|#])?`, 'i');
+    if (linkPattern.test(content)) {
+        return content;
+    }
+    const trimmed = content.trimEnd();
+    return `${trimmed}\n\n${relatedMarker(targetTitle)}\n`;
+};
+const ensureMergedMarker = (content, targetTitle) => {
+    const marker = `Merged into [[${targetTitle}]]`;
+    if (content.includes(marker)) {
+        return content;
+    }
+    return `${content.trimEnd()}\n\n${marker} priority: low #related-to\n`;
+};
+const appendMergedContent = (baseContent, mergedTitle, mergedContent) => {
+    const marker = `## Merged Memory From [[${mergedTitle}]]`;
+    if (baseContent.includes(marker)) {
+        return baseContent;
+    }
+    const mergedBody = normalizeSemanticContent(mergedContent);
+    return `${baseContent.trimEnd()}\n\n${marker}\n\n${mergedBody}\n`;
+};
+const loadNoteRecords = async (vaultPath, agentId) => {
+    const absoluteVaultPath = await ensureVault(vaultPath);
+    const files = await readMarkdownFiles(vaultPath);
+    return files
+        .map((file) => {
+        const parsed = parseMarkdownDocument({
+            absolutePath: file.absolutePath,
+            vaultPath: absoluteVaultPath,
+            content: file.content,
+            createdAt: file.createdAt,
+            updatedAt: file.updatedAt
+        });
+        const strict = normalizeStrictContent(parsed.content);
+        const semantic = normalizeSemanticContent(parsed.content);
+        const embedding = createLocalEmbedding(`${parsed.title}\n${semantic}`);
+        return {
+            title: parsed.title,
+            path: normalizePath(parsed.path),
+            agentId: parsed.agentId,
+            content: parsed.content,
+            normalizedStrictContent: strict,
+            semanticContent: semantic,
+            embedding,
+            buckets: createEmbeddingBuckets(embedding, 20)
+        };
+    })
+        .filter((record) => (agentId ? record.agentId === agentId : true));
+};
+const pairToCandidate = (left, right, kind, score, reason) => ({
+    id: toCandidateId(left.path, right.path),
+    possibleDuplicate: true,
+    kind,
+    score: Number(score.toFixed(4)),
+    left: {
+        title: left.title,
+        path: left.path,
+        agentId: left.agentId
+    },
+    right: {
+        title: right.title,
+        path: right.path,
+        agentId: right.agentId
+    },
+    reason
+});
+const indexCandidatePairs = (notes) => {
+    const bucketMap = new Map();
+    notes.forEach((note, index) => {
+        note.buckets.forEach((bucket) => {
+            const current = bucketMap.get(bucket) ?? [];
+            if (current.length < maxCandidatesPerBucket) {
+                current.push(index);
+                bucketMap.set(bucket, current);
+            }
+        });
+    });
+    const pairKeys = new Set();
+    const pairs = [];
+    bucketMap.forEach((indexes) => {
+        for (let leftIndex = 0; leftIndex < indexes.length; leftIndex += 1) {
+            for (let rightIndex = leftIndex + 1; rightIndex < indexes.length; rightIndex += 1) {
+                const left = Math.min(indexes[leftIndex] ?? 0, indexes[rightIndex] ?? 0);
+                const right = Math.max(indexes[leftIndex] ?? 0, indexes[rightIndex] ?? 0);
+                const key = `${left}|${right}`;
+                if (!pairKeys.has(key)) {
+                    pairKeys.add(key);
+                    pairs.push([left, right]);
+                }
+            }
+        }
+    });
+    return pairs;
+};
+export const scanDuplicateNotes = async (vaultPath, options = {}) => {
+    const notes = await loadNoteRecords(vaultPath, options.agentId);
+    if (notes.length < 2) {
+        return [];
+    }
+    const minSemanticScore = options.minSemanticScore ?? 0.92;
+    const includeSemantic = options.includeSemantic !== false;
+    const seen = new Map();
+    const byHash = notes.reduce((state, note) => {
+        const key = toHash(note.normalizedStrictContent);
+        const current = state.get(key) ?? [];
+        current.push(note);
+        state.set(key, current);
+        return state;
+    }, new Map());
+    byHash.forEach((group) => {
+        if (group.length < 2) {
+            return;
+        }
+        const [base, ...rest] = group.sort((left, right) => left.path.localeCompare(right.path));
+        rest.forEach((note) => {
+            const candidate = pairToCandidate(base, note, 'exact', 1, 'Exact content hash match');
+            seen.set(candidate.id, candidate);
+        });
+    });
+    if (includeSemantic) {
+        const pairs = indexCandidatePairs(notes);
+        pairs.forEach(([leftIndex, rightIndex]) => {
+            const left = notes[leftIndex];
+            const right = notes[rightIndex];
+            if (!left || !right || left.path === right.path) {
+                return;
+            }
+            const id = toCandidateId(left.path, right.path);
+            if (seen.has(id)) {
+                return;
+            }
+            const score = cosineSimilarity(left.embedding, right.embedding);
+            const titleShared = hasSharedTokens(left.title, right.title);
+            const contentShared = hasSharedTokens(left.semanticContent, right.semanticContent);
+            if (score >= minSemanticScore && (titleShared || contentShared || score >= 0.975)) {
+                const candidate = pairToCandidate(left, right, 'semantic', score, 'High semantic similarity');
+                seen.set(id, candidate);
+            }
+        });
+    }
+    const focusPath = options.focusPath ? normalizePath(options.focusPath) : undefined;
+    const limited = Array.from(seen.values())
+        .filter((item) => (focusPath ? item.left.path === focusPath || item.right.path === focusPath : true))
+        .sort((left, right) => right.score - left.score || left.left.path.localeCompare(right.left.path))
+        .slice(0, Math.max(1, options.limit ?? 25));
+    return limited;
+};
+export const resolveDuplicateNotes = async (vaultPath, options) => {
+    const leftPath = normalizePath(options.leftPath);
+    const rightPath = normalizePath(options.rightPath);
+    if (leftPath === rightPath) {
+        throw new Error('leftPath and rightPath must be different notes.');
+    }
+    const notes = await loadNoteRecords(vaultPath);
+    const byPath = new Map(notes.map((note) => [note.path, note]));
+    const left = byPath.get(leftPath);
+    const right = byPath.get(rightPath);
+    if (!left || !right) {
+        throw new Error(`Duplicate resolution paths were not found in vault index source: ${leftPath}, ${rightPath}`);
+    }
+    const updates = new Map();
+    const leftRelated = ensureRelatedEdgeLine(left.content, right.title);
+    const rightRelated = ensureRelatedEdgeLine(right.content, left.title);
+    if (options.action === 'link') {
+        updates.set(left.path, leftRelated);
+        updates.set(right.path, rightRelated);
+    }
+    else if (options.action === 'ignore') {
+        updates.set(left.path, leftRelated);
+    }
+    else {
+        const mergedLeft = appendMergedContent(leftRelated, right.title, right.content);
+        const mergedRight = ensureMergedMarker(rightRelated, left.title);
+        updates.set(left.path, mergedLeft);
+        updates.set(right.path, mergedRight);
+    }
+    for (const [path, content] of updates) {
+        await writeMarkdownFile(vaultPath, path, content);
+    }
+    const shouldIndex = options.autoIndex !== false;
+    const index = shouldIndex ? await indexVault(vaultPath) : undefined;
+    return {
+        action: options.action,
+        leftPath,
+        rightPath,
+        updatedPaths: Array.from(updates.keys()).sort((leftValue, rightValue) => leftValue.localeCompare(rightValue)),
+        ...(index ? { index } : {})
+    };
+};

package/dist/application/frontend/client-css.js

@@ -25,6 +25,13 @@ body {
   font-family: Inter, ui-sans-serif, system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", sans-serif;
 }
 
+body {
+  display: flex;
+  flex-direction: column;
+  min-height: 100vh;
+  min-height: 100dvh;
+}
+
 button,
 input,
 select {
@@ -32,50 +39,73 @@ select {
 }
 
 .shell {
+  flex: 1 1 auto;
   width: 100%;
-  height: 100svh;
+  min-height: 0;
   overflow: hidden;
 }
 
 .workspace {
+  display: grid;
+  grid-template-rows: auto minmax(0, 1fr);
   position: relative;
+  width: 100%;
+  height: 100%;
   min-width: 0;
   min-height: 0;
 }
 
-#graph {
-  display: block;
+.graph-header {
+  z-index: 5;
+  display: flex;
+  align-items: center;
+  gap: 12px;
+  min-height: 72px;
+  padding: 10px 16px;
+  border-bottom: 1px solid var(--line);
+  background: linear-gradient(180deg, rgba(17, 21, 27, 0.96) 0%, rgba(17, 21, 27, 0.86) 100%);
+  backdrop-filter: blur(8px);
+}
+
+.brand-block {
+  display: grid;
+  gap: 2px;
+  min-width: max-content;
+}
+
+.brand-block strong {
+  font-size: 18px;
+}
+
+.graph-stage {
+  position: relative;
   width: 100%;
   height: 100%;
   background:
     radial-gradient(circle at 18% 20%, rgba(53, 208, 162, 0.12), transparent 28rem),
     linear-gradient(135deg, #0d0f12 0%, #12161c 55%, #0a0d10 100%);
-  cursor: grab;
+  overflow: hidden;
 }
 
-#graph:active {
-  cursor: grabbing;
+#graph,
+#graphGl {
+  display: block;
+  position: absolute;
+  inset: 0;
+  width: 100%;
+  height: 100%;
 }
 
-.topbar {
-  position: absolute;
-  top: 18px;
-  left: 18px;
-  right: 18px;
-  display: flex;
-  align-items: center;
-  justify-content: space-between;
-  gap: 18px;
-  pointer-events: none;
+#graph {
+  cursor: grab;
 }
 
-.topbar > div {
-  display: flex;
-  align-items: center;
+#graphGl {
+  pointer-events: none;
 }
 
-.topbar strong {
-  font-size: 18px;
+#graph:active {
+  cursor: grabbing;
 }
 
 .eyebrow {
@@ -84,13 +114,19 @@ select {
 }
 
 .search {
-  width: min(420px, 42vw);
-  pointer-events: auto;
+  flex: 1 1 320px;
+  min-width: 220px;
 }
 
 .agent-filter {
   width: min(220px, 28vw);
-  pointer-events: auto;
+}
+
+.header-actions {
+  display: flex;
+  align-items: center;
+  gap: 10px;
+  margin-left: auto;
 }
 
 .search input,
@@ -111,9 +147,6 @@ select {
 }
 
 .toolbar {
-  position: absolute;
-  left: 18px;
-  bottom: 18px;
   display: flex;
   gap: 8px;
 }
@@ -134,12 +167,9 @@ select {
 }
 
 .floating-metrics {
-  position: absolute;
-  top: 66px;
-  left: 18px;
   display: flex;
   gap: 10px;
-  pointer-events: none;
+  flex-wrap: wrap;
 }
 
 .metric-chip {
@@ -232,8 +262,8 @@ li small {
 }
 
 .content-dialog {
-  width: min(920px, calc(100vw - 32px));
-  max-height: calc(100svh - 32px);
+  width: min(1240px, calc(100vw - 24px));
+  max-height: calc(100svh - 20px);
   padding: 0;
   border: 1px solid var(--line);
   border-radius: 8px;
@@ -250,7 +280,7 @@ li small {
 .content-dialog article {
   display: grid;
   grid-template-rows: auto auto minmax(0, 1fr);
-  max-height: calc(100svh - 34px);
+  max-height: calc(100svh - 22px);
 }
 
 .content-dialog header {
@@ -326,7 +356,7 @@ li small {
 
 .content-meta-section ul,
 .content-meta-section .tags {
-  max-height: 140px;
+  max-height: 220px;
   overflow: auto;
   align-content: flex-start;
   padding-right: 4px;
@@ -340,33 +370,51 @@ li small {
   padding: 22px;
 }
 
+.app-footer {
+  flex: 0 0 28px;
+  height: 28px;
+  display: flex;
+  align-items: center;
+  justify-content: center;
+  background: transparent;
+}
+
+.app-footer small {
+  color: var(--muted);
+  font-size: 11px;
+  letter-spacing: 0.02em;
+}
+
 @media (max-width: 860px) {
-  .topbar {
+  .graph-header {
     align-items: stretch;
-    flex-direction: column;
+    flex-wrap: wrap;
+    padding: 10px 12px;
+    min-height: 0;
   }
 
   .search {
     width: 100%;
+    flex-basis: 100%;
+    order: 3;
   }
 
   .agent-filter {
     width: 100%;
   }
 
+  .header-actions {
+    width: 100%;
+    margin-left: 0;
+    justify-content: space-between;
+    order: 4;
+  }
+
   .content-dialog header {
     align-items: stretch;
     flex-direction: column;
   }
 
-  .floating-metrics {
-    top: 116px;
-    right: 18px;
-    left: 18px;
-    justify-content: flex-start;
-    flex-wrap: wrap;
-  }
-
   .metric-chip {
     min-width: 82px;
   }

package/dist/application/frontend/client-html.js

@@ -9,40 +9,49 @@ export const createClientHtml = () => `<!doctype html>
   <body>
     <main class="shell">
       <section class="workspace" aria-label="Knowledge graph">
-        <canvas id="graph" aria-label="Brainlink knowledge graph"></canvas>
-        <div class="topbar">
-          <div>
+        <header class="graph-header" aria-label="Graph actions">
+          <div class="brand-block">
             <strong>Brainlink</strong>
+            <span class="eyebrow">Knowledge Graph</span>
+          </div>
+          <div class="floating-metrics" aria-label="Graph totals">
+            <div class="metric-chip">
+              <strong id="nodeCount">0</strong>
+              <small>Notes</small>
+            </div>
+            <div class="metric-chip">
+              <strong id="edgeCount">0</strong>
+              <small>Links</small>
+            </div>
+            <div class="metric-chip">
+              <strong id="tagCount">0</strong>
+              <small>Tags</small>
+            </div>
           </div>
           <label class="search">
             <input id="search" type="search" placeholder="Filter notes, tags or paths" autocomplete="off" />
           </label>
-          <label class="agent-filter">
-            <select id="agent"></select>
-          </label>
-        </div>
-        <div class="floating-metrics" aria-label="Graph totals">
-          <div class="metric-chip">
-            <strong id="nodeCount">0</strong>
-            <small>Notes</small>
+          <div class="header-actions">
+            <label class="agent-filter">
+              <select id="agent"></select>
+            </label>
+            <div class="toolbar" aria-label="Graph controls">
+              <button id="zoomIn" type="button" title="Zoom in">+</button>
+              <button id="zoomOut" type="button" title="Zoom out">-</button>
+              <button id="fit" type="button" title="Focus central hub">◎</button>
+              <button id="reset" type="button" title="Reset view">⌂</button>
+            </div>
           </div>
-          <div class="metric-chip">
-            <strong id="edgeCount">0</strong>
-            <small>Links</small>
-          </div>
-          <div class="metric-chip">
-            <strong id="tagCount">0</strong>
-            <small>Tags</small>
-          </div>
-        </div>
-        <div class="toolbar" aria-label="Graph controls">
-          <button id="zoomIn" type="button" title="Zoom in">+</button>
-          <button id="zoomOut" type="button" title="Zoom out">-</button>
-          <button id="fit" type="button" title="Fit visible nodes">◎</button>
-          <button id="reset" type="button" title="Reset view">⌂</button>
+        </header>
+        <div class="graph-stage">
+          <canvas id="graphGl" aria-hidden="true"></canvas>
+          <canvas id="graph" aria-label="Brainlink knowledge graph"></canvas>
         </div>
       </section>
     </main>
+    <footer class="app-footer" aria-label="Copyright notice">
+      <small>Copyright © 2026 Substructa</small>
+    </footer>
     <dialog id="contentDialog" class="content-dialog" aria-labelledby="contentTitle">
       <article>
         <header>