@zabaca/lattice 1.0.2 → 1.0.3

package/commands/entity-extract.md

@@ -83,7 +83,7 @@ The goal is to ensure entities reflect the document's CURRENT state, not preserv
    - Preserve existing fields like `created`, `status`, `topic` (but update `updated` date)
    - **Replace** the `summary`, `entities` and `relationships` sections entirely
    - If no topic field exists, derive it from the directory name
-     (e.g., `docs/claude-code/file.md` -> `topic: claude-code`)
+     (e.g., `~/.lattice/docs/claude-code/file.md` -> `topic: claude-code`)
 
    Frontmatter template:
    ```yaml

package/commands/graph-sync.md

@@ -38,16 +38,16 @@ For each new or updated document identified:
 Task(
   subagent_type="general-purpose",
   model="haiku",
-  prompt="Use /entity-extract docs/topic/document.md to extract entities. Follow all instructions and report completion."
+  prompt="Use /entity-extract ~/.lattice/docs/topic/document.md to extract entities. Follow all instructions and report completion."
 )
 ```
 
 **For multiple documents, launch agents in parallel:**
 ```
 // In a single message, launch multiple Task tool calls:
-Task(subagent_type="general-purpose", model="haiku", prompt="/entity-extract docs/topic-a/README.md ...")
-Task(subagent_type="general-purpose", model="haiku", prompt="/entity-extract docs/topic-b/notes.md ...")
-Task(subagent_type="general-purpose", model="haiku", prompt="/entity-extract docs/topic-c/README.md ...")
+Task(subagent_type="general-purpose", model="haiku", prompt="/entity-extract ~/.lattice/docs/topic-a/README.md ...")
+Task(subagent_type="general-purpose", model="haiku", prompt="/entity-extract ~/.lattice/docs/topic-b/notes.md ...")
+Task(subagent_type="general-purpose", model="haiku", prompt="/entity-extract ~/.lattice/docs/topic-c/README.md ...")
 ```
 
 This is much faster than sequential execution for multiple documents.
@@ -87,15 +87,15 @@ Summarize what was processed:
 
 Processed 3 documents:
 
-1. docs/american-holidays/README.md
+1. ~/.lattice/docs/american-holidays/README.md
    - 4 entities extracted
    - 3 relationships defined
 
-2. docs/american-holidays/thanksgiving-vs-christmas.md
+2. ~/.lattice/docs/american-holidays/thanksgiving-vs-christmas.md
    - 8 entities extracted
    - 5 relationships defined
 
-3. docs/bun-nestjs/notes.md
+3. ~/.lattice/docs/bun-nestjs/notes.md
    - 5 entities extracted
    - 4 relationships defined
 

package/commands/research.md

@@ -65,7 +65,7 @@ If user wants new research:
 ### Step 6: Determine Topic and Filename
 
 **Identify the topic directory:**
-- Check if a relevant `docs/{topic-name}/` directory already exists
+- Check if a relevant `~/.lattice/docs/{topic-name}/` directory already exists
 - If not, derive a new topic name from the query (kebab-case)
 
 **Derive the research filename:**
@@ -89,7 +89,7 @@ Auto-derive from the specific focus of the query:
 
 Create TWO files:
 
-**1. `docs/{topic-name}/README.md`** (index):
+**1. `~/.lattice/docs/{topic-name}/README.md`** (index):
 ```markdown
 ---
 created: [TODAY'S DATE]
@@ -115,7 +115,7 @@ Brief description of what this topic covers.
 - [Related Topic](../related-topic/)
 ```
 
-**2. `docs/{topic-name}/{research-filename}.md`** (content):
+**2. `~/.lattice/docs/{topic-name}/{research-filename}.md`** (content):
 ```markdown
 ---
 created: [TODAY'S DATE]
@@ -146,9 +146,9 @@ What this research addresses.
 
 #### For EXISTING Topics (directory exists)
 
-**1. Create** `docs/{topic-name}/{research-filename}.md` with content template above
+**1. Create** `~/.lattice/docs/{topic-name}/{research-filename}.md` with content template above
 
-**2. Update** `docs/{topic-name}/README.md`:
+**2. Update** `~/.lattice/docs/{topic-name}/README.md`:
 - Add new row to the Documents table
 - Update the `updated` date in frontmatter
 
@@ -173,7 +173,7 @@ After creating files, confirm:
 ## File Structure Standard
 
 ```
-docs/{topic-name}/
+~/.lattice/docs/{topic-name}/
 ├── README.md              # Index: links to docs, brief overview
 ├── {research-1}.md        # Specific research
 ├── {research-2}.md        # Additional research

package/dist/main.js

@@ -832,6 +832,7 @@ EmbeddingService = __legacyDecorateClassTS([
 ], EmbeddingService);
 
 // src/graph/graph.service.ts
+import { existsSync as existsSync3, unlinkSync } from "fs";
 import { DuckDBInstance } from "@duckdb/node-api";
 import { Injectable as Injectable6, Logger as Logger3 } from "@nestjs/common";
 import { ConfigService as ConfigService2 } from "@nestjs/config";
@@ -874,6 +875,11 @@ class GraphService {
   }
   async connect() {
     try {
+      const walPath = `${this.dbPath}.wal`;
+      if (existsSync3(walPath)) {
+        this.logger.warn(`Removing WAL file to prevent HNSW index replay failure`);
+        unlinkSync(walPath);
+      }
       this.instance = await DuckDBInstance.create(this.dbPath, {
         allow_unsigned_extensions: "true"
       });
@@ -899,6 +905,11 @@ class GraphService {
   }
   async disconnect() {
     if (this.connection) {
+      try {
+        await this.connection.run("CHECKPOINT;");
+      } catch {
+        this.logger.debug("Checkpoint failed during disconnect");
+      }
       this.connection.closeSync();
       this.connection = null;
       this.logger.log("Disconnected from DuckDB");
@@ -1373,7 +1384,7 @@ import { Command as Command4, CommandRunner as CommandRunner4, Option as Option3
 
 // src/sync/manifest.service.ts
 import { createHash as createHash2 } from "crypto";
-import { existsSync as existsSync3 } from "fs";
+import { existsSync as existsSync4 } from "fs";
 import { readFile as readFile3, writeFile } from "fs/promises";
 import { Injectable as Injectable8 } from "@nestjs/common";
 
@@ -1401,7 +1412,7 @@ class ManifestService {
   }
   async load() {
     try {
-      if (existsSync3(this.manifestPath)) {
+      if (existsSync4(this.manifestPath)) {
         const content = await readFile3(this.manifestPath, "utf-8");
         this.manifest = SyncManifestSchema.parse(JSON.parse(content));
       } else {
@@ -1887,7 +1898,7 @@ CascadeService = __legacyDecorateClassTS([
 ], CascadeService);
 
 // src/sync/path-resolver.service.ts
-import { existsSync as existsSync4 } from "fs";
+import { existsSync as existsSync5 } from "fs";
 import { isAbsolute, resolve as resolve2 } from "path";
 import { Injectable as Injectable10 } from "@nestjs/common";
 class PathResolverService {
@@ -1909,7 +1920,7 @@ class PathResolverService {
     if (requireInDocs && !this.isUnderDocs(resolvedPath)) {
       throw new Error(`Path "${userPath}" resolves to "${resolvedPath}" which is outside the docs directory (${this.docsPath})`);
     }
-    if (requireExists && !existsSync4(resolvedPath)) {
+    if (requireExists && !existsSync5(resolvedPath)) {
       throw new Error(`Path "${userPath}" does not exist (resolved to: ${resolvedPath})`);
     }
     return resolvedPath;

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "@zabaca/lattice",
-	"version": "1.0.2",
+	"version": "1.0.3",
 	"description": "Human-initiated, AI-powered knowledge graph for markdown documentation",
 	"type": "module",
 	"bin": {