@andespindola/brainlink 0.1.0-beta.150 → 0.1.0-beta.151

package/CHANGELOG.md

@@ -14,6 +14,9 @@
 - Added default MCP startup bootstrap behavior controlled by `brainlink_policy.autoBootstrapOnStartup`.
 - Added CLI MCP policy presets through `blink agent policy --preset fully-auto|strict`.
 - Added write-time non-orphan enforcement by auto-linking notes without wiki edges to agent hub notes.
+- Changed graph indexing to keep every non-self Markdown wiki link as a weighted graph edge so the default star graph represents complete note connectivity.
+- Added `blink index --full` and MCP `brainlink_index` `full=true` for complete source reindexing without clearing the existing index first.
+- Improved index migration so stale graph link model metadata automatically triggers a complete source reindex.
 - Added MCP `brainlink_policy` presets (`fully-auto`, `strict`) for one-call policy switching.
 - Added MCP write connectivity metadata in `brainlink_add_note`/`brainlink_add_file` responses.
 - Added MCP `brainlink_recommendations` tool for plug-and-play workflow guidance.

package/README.md

@@ -538,7 +538,7 @@ Available tools:
 - `brainlink_add_file`: ingest a local file as a note and reindex.
 - `brainlink_volatile_add`: write temporary agent-decided memory with TTL; volatile sections are included in context and never create durable graph edges.
 - `brainlink_volatile_clear`: clear temporary memory for the current vault/agent namespace.
-- `brainlink_index`: rebuild the vault index.
+- `brainlink_index`: rebuild the vault index. Pass `full=true` for a complete source reindex.
 - `brainlink_stats`: read indexed vault statistics.
 - `brainlink_validate`: validate broken links and orphan notes.
 - `brainlink_sync`: run index, stats, validation, broken-link and orphan checks in one call.
@@ -563,7 +563,7 @@ Agents can raise the importance of a relationship by putting priority markers on
 Related: [[Incident Runbook]] #critical
 ```
 
-Indexed edges expose `weight` and `priority` (`low`, `normal`, `high`, `critical`) through CLI JSON, HTTP graph APIs and `brainlink_graph`. Brainlink promotes only representative graph links per note: high-priority and high-weight links win, structural hub links such as `Memory Hub`, `Knowledge Root`, `MOC` and map notes are suppressed when stronger direct links exist, and old indexes are rebuilt automatically when their graph link model version is missing or stale.
+Indexed edges expose `weight` and `priority` (`low`, `normal`, `high`, `critical`) through CLI JSON, HTTP graph APIs and `brainlink_graph`. Brainlink indexes every non-self Markdown `[[wiki link]]` as a graph edge, including structural hub links such as `Memory Hub`, `Knowledge Root`, `MOC` and map notes. Old indexes are rebuilt automatically when their graph link model version is missing or stale.
 
 ## Graph UI
 
@@ -589,8 +589,8 @@ When native GUI is used, the GUI window automatically closes when the `blink ser
 The graph UI shows:
 
 - notes as nodes
-- representative `[[wiki links]]` as weighted edges
-- star layout centered on the primary hub, without rewriting or flattening underlying relationships
+- all non-self `[[wiki links]]` as weighted edges
+- default star layout centered on the primary hub, without rewriting or flattening underlying relationships
 - details opened in a non-modal side panel (tags, outgoing links, backlinks, full Markdown content), so zoom and pan remain available while inspecting data
 - neutral graph nodes with segment/group metadata
 - agent selector (id-only labels) for isolated views
@@ -777,9 +777,12 @@ When action is not `merge`, Brainlink still creates a low-priority related edge
 ```bash
 blink index
 blink index --vault ./vault
+blink index --vault ./vault --full
 ```
 
-Rebuilds the local index from Markdown files.
+Rebuilds the local index from Markdown files. By default, unchanged notes reuse existing indexed chunks for speed.
+Use `--full` to force a complete source reindex of every Markdown note. Full reindex builds the replacement index before persisting it, so existing context is not cleared first.
+Brainlink also performs this complete source reindex automatically when it detects that the stored graph link model is older than the current model.
 
 ### `bench`
 

package/dist/application/index-vault.js

@@ -85,8 +85,8 @@ const readChangedDocuments = async (absoluteVaultPath, changedSummaries) => {
     })));
     return new Map(parsed.map((document) => [document.path, document]));
 };
-export const indexVault = async (vaultPath) => {
-    return indexVaultWithOptions(vaultPath, {});
+export const indexVault = async (vaultPath, options = {}) => {
+    return indexVaultWithOptions(vaultPath, options);
 };
 export const indexVaultWithOptions = async (vaultPath, options) => {
     const startedAt = process.hrtime.bigint();
@@ -113,6 +113,7 @@ export const indexVaultWithOptions = async (vaultPath, options) => {
         markdownFiles: summaries.length,
         hasPreviousState: previousState != null
     });
+    const fullReindex = options.full === true;
     const index = openFileIndex(absoluteVaultPath);
     try {
         const existingIndexedDocuments = await index.getIndexedDocuments();
@@ -120,10 +121,13 @@ export const indexVaultWithOptions = async (vaultPath, options) => {
         const currentSnapshot = toSnapshot(summaries);
         const currentSnapshotMap = createSnapshotMap(currentSnapshot);
         const previousSnapshotMap = createSnapshotMap(previousState?.files ?? []);
+        const graphLinkModelChanged = previousState != null &&
+            previousState.graphLinkModelVersion !== graphLinkModelVersion;
+        const fullSourceReindex = fullReindex || graphLinkModelChanged;
         const settingsChanged = previousState == null ||
             previousState.chunkSize !== config.chunkSize ||
             previousState.embeddingProvider !== config.embeddingProvider ||
-            previousState.graphLinkModelVersion !== graphLinkModelVersion;
+            graphLinkModelChanged;
         const packSettingsChanged = previousState == null ||
             previousState.searchPackRowChunkSize !== config.searchPack.rowChunkSize ||
             previousState.searchPackCompressionLevel !== config.searchPack.compressionLevel ||
@@ -132,7 +136,8 @@ export const indexVaultWithOptions = async (vaultPath, options) => {
         for (let index = 0; index < summaries.length; index += 1) {
             const summary = summaries[index];
             const previous = previousSnapshotMap.get(summary.relativePath);
-            const changed = settingsChanged ||
+            const changed = fullSourceReindex ||
+                settingsChanged ||
                 previous == null ||
                 previous.mtimeMs !== summary.updatedAt.getTime() ||
                 previous.size !== summary.size ||
@@ -148,7 +153,8 @@ export const indexVaultWithOptions = async (vaultPath, options) => {
         if (changedPaths.size === 0 &&
             !hasDeletes &&
             existingIndexedDocuments.length === summaries.length &&
-            previousState != null) {
+            previousState != null &&
+            !fullReindex) {
             const result = {
                 ...toIndexResult(existingIndexedDocuments),
                 elapsedMs: elapsedMs(),
@@ -205,7 +211,6 @@ export const indexVaultWithOptions = async (vaultPath, options) => {
             return needsRelink ? relinkIndexedDocument(existing, titleMaps) : existing;
         });
         emit('persist', 'start', 'Persisting index');
-        await index.reset();
         await index.saveDocuments(indexedDocuments);
         emit('persist', 'finish', 'Index persisted', {
             indexedDocuments: indexedDocuments.length
@@ -217,6 +222,8 @@ export const indexVaultWithOptions = async (vaultPath, options) => {
         const previousPendingPackChanges = previousState?.pendingPackChanges ?? 0;
         const pendingPackChanges = previousPendingPackChanges + changedCount;
         const shouldRebuildPacks = !existingPackManifest ||
+            fullReindex ||
+            graphLinkModelChanged ||
             settingsChanged ||
             packSettingsChanged ||
             hasDeletes ||
@@ -226,21 +233,25 @@ export const indexVaultWithOptions = async (vaultPath, options) => {
         let packResult;
         const packReason = !existingPackManifest
             ? 'Missing pack manifest'
-            : manifestRecovery.repaired
-                ? 'Pack manifest repaired from existing packs'
-                : settingsChanged
-                    ? 'Index settings changed'
-                    : packSettingsChanged
-                        ? 'Search pack settings changed'
-                        : hasDeletes
-                            ? 'Document deletions detected'
-                            : changedCount >= 400
-                                ? 'Changed file count threshold reached'
-                                : changeRatio >= 0.04
-                                    ? 'Change ratio threshold reached'
-                                    : pendingPackChanges >= 1200
-                                        ? 'Pending pack changes threshold reached'
-                                        : 'Pack rebuild skipped';
+            : fullReindex
+                ? 'Full reindex requested'
+                : graphLinkModelChanged
+                    ? 'Graph link model changed'
+                    : manifestRecovery.repaired
+                        ? 'Pack manifest repaired from existing packs'
+                        : settingsChanged
+                            ? 'Index settings changed'
+                            : packSettingsChanged
+                                ? 'Search pack settings changed'
+                                : hasDeletes
+                                    ? 'Document deletions detected'
+                                    : changedCount >= 400
+                                        ? 'Changed file count threshold reached'
+                                        : changeRatio >= 0.04
+                                            ? 'Change ratio threshold reached'
+                                            : pendingPackChanges >= 1200
+                                                ? 'Pending pack changes threshold reached'
+                                                : 'Pack rebuild skipped';
         if (shouldRebuildPacks) {
             emit('packs', 'start', 'Rebuilding compressed search packs', {
                 reason: packReason

package/dist/cli/commands/write-commands.js

@@ -860,12 +860,17 @@ export const registerWriteCommands = (program) => {
     program
         .command('index')
         .option('-v, --vault <vault>', 'vault directory')
+        .option('--full', 'force a complete reindex from Markdown source without reusing unchanged index entries')
         .option('--json', 'print machine-readable JSON')
         .description('index markdown notes, links, tags and chunks')
         .action(async (options) => {
         const resolved = await resolveOptions(options);
-        const result = await indexVault(resolved.vault);
-        print(options.json, result, () => `Indexed ${result.documentCount} documents, ${result.chunkCount} chunks and ${result.linkCount} links`);
+        const result = await indexVault(resolved.vault, {
+            full: options.full === true
+        });
+        print(options.json, result, () => options.full === true
+            ? `Fully reindexed ${result.documentCount} documents, ${result.chunkCount} chunks and ${result.linkCount} links`
+            : `Indexed ${result.documentCount} documents, ${result.chunkCount} chunks and ${result.linkCount} links`);
     });
     program
         .command('bench')

package/dist/domain/markdown.js

@@ -18,9 +18,7 @@ const priorityBoosts = {
     high: 3,
     critical: 6
 };
-const graphLinkLimit = 4;
-export const graphLinkModelVersion = 2;
-const hubLinkTitlePattern = /\b(?:memory\s*hub|knowledge\s*root|moc|map)\b/i;
+export const graphLinkModelVersion = 3;
 const priorityPatterns = [
     ['critical', /\b(?:priority|prioridade|importance|importancia|importância)\s*[:=]\s*(?:critical|critica|crítica|urgent|urgente|p0)\b/i],
     ['critical', /#(?:critical|critica|crítica|urgent|urgente|p0)\b/i],
@@ -34,7 +32,6 @@ const priorityPatterns = [
 const normalizeTitle = (title) => title.trim().replace(/\.md$/i, '');
 const unique = (values) => Array.from(new Set(values.map((value) => value.trim()).filter(Boolean)));
 const maxPriority = (left, right) => priorityRanks[left] >= priorityRanks[right] ? left : right;
-const isHubLinkTitle = (title) => hubLinkTitlePattern.test(title);
 const parseFrontmatter = (content) => {
     const match = content.match(frontmatterPattern);
     if (!match) {
@@ -114,11 +111,7 @@ const compareGraphLinks = (left, right) => {
     return left.title.localeCompare(right.title);
 };
 export const selectGraphWikiLinkWeights = (links) => {
-    const sorted = [...links].sort(compareGraphLinks);
-    const structuralLinks = sorted.filter((link) => isHubLinkTitle(link.title) && !['high', 'critical'].includes(link.priority));
-    const directLinks = sorted.filter((link) => !structuralLinks.includes(link));
-    const selected = (directLinks.length > 0 ? directLinks : sorted).slice(0, graphLinkLimit);
-    return selected.length > 0 ? selected : structuralLinks.slice(0, graphLinkLimit);
+    return [...links].sort(compareGraphLinks);
 };
 const extractTitle = (filePath, content, frontmatter) => {
     if (frontmatter.title) {

package/dist/mcp/server.js

@@ -70,7 +70,7 @@ export const createBrainlinkMcpServer = () => {
     }, addFileTool);
     server.registerTool('brainlink_index', {
         title: 'Index Brainlink Vault',
-        description: 'Rebuild the local Brainlink index from Markdown notes.',
+        description: 'Rebuild the local Brainlink index from Markdown notes. Pass full=true to force a complete source rebuild.',
         inputSchema: indexInputSchema
     }, indexTool);
     server.registerTool('brainlink_stats', {

package/dist/mcp/tools.js

@@ -262,7 +262,12 @@ export const addFileInputSchema = {
     allowSensitive: z.boolean().optional().default(false).describe('Allow content that looks like a secret.')
 };
 export const indexInputSchema = {
-    ...vaultInput
+    ...vaultInput,
+    full: z
+        .boolean()
+        .optional()
+        .default(false)
+        .describe('Force a complete reindex from Markdown source without reusing unchanged index entries.')
 };
 export const validateInputSchema = {
     ...vaultInput,
@@ -469,7 +474,9 @@ export const addFileTool = async (input) => {
 };
 export const indexTool = async (input) => {
     const context = await resolveExecutionContext(input);
-    const result = await indexVault(context.vault);
+    const result = await indexVault(context.vault, {
+        full: input.full === true
+    });
     return jsonResult({
         vault: context.vault,
         ...result

package/docs/AGENT_USAGE.md

@@ -161,7 +161,7 @@ Brainlink only builds graph edges from Markdown `[[wiki links]]`.
 
 The `context` command is read-only. It retrieves indexed notes and returns a compact package for the model, but it does not write memory, create backlinks, infer relationships or modify the graph. If an agent reads context and then learns something durable, the agent must write a note with explicit links before that knowledge becomes connected memory.
 
-Graph edges are weighted during indexing. Repeated links increase weight. Links inside headings or task-list lines receive a small boost. Priority markers on the same line as a link raise its priority. The graph relationship model promotes only representative links per note: high-priority and high-weight links win, structural hub links such as `Memory Hub`, `Knowledge Root`, `MOC` and map notes are not promoted when stronger direct links exist, and each note emits a small bounded set of graph edges. Older indexes without the current graph link model version are automatically rebuilt on the next index run.
+Graph edges are weighted during indexing. Repeated links increase weight. Links inside headings or task-list lines receive a small boost. Priority markers on the same line as a link raise its priority. The graph relationship model indexes every non-self Markdown `[[wiki link]]` as an edge, including structural hub links such as `Memory Hub`, `Knowledge Root`, `MOC` and map notes. Older indexes without the current graph link model version are automatically rebuilt on the next index run.
 
 ```md
 - [ ] Review [[Architecture]] priority: high
@@ -292,6 +292,8 @@ blink add "Implementation Boundary" \
 blink index
 ```
 
+Use `blink index --full` when you need to rebuild every note from Markdown source. Full reindexing builds the replacement index before persisting it, preserving the previous context until the new index is ready. Brainlink also runs this complete source reindex automatically when it detects an older stored graph link model.
+
 ### Claude Code-Style Agent
 
 Use Brainlink as a preflight memory read before editing files:

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@andespindola/brainlink",
-  "version": "0.1.0-beta.150",
+  "version": "0.1.0-beta.151",
   "description": "Local-first knowledge memory for agents with Markdown, backlinks, indexing and context retrieval.",
   "type": "module",
   "license": "MIT",