@zabaca/lattice 1.0.2 → 1.0.4

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

@@ -844,11 +844,35 @@ class GraphService {
   connecting = null;
   vectorIndexes = new Set;
   embeddingDimensions;
+  signalHandlersRegistered = false;
   constructor(configService) {
     this.configService = configService;
     ensureLatticeHome();
     this.dbPath = getDatabasePath();
     this.embeddingDimensions = this.configService.get("EMBEDDING_DIMENSIONS") || 512;
+    this.registerSignalHandlers();
+  }
+  registerSignalHandlers() {
+    if (this.signalHandlersRegistered)
+      return;
+    this.signalHandlersRegistered = true;
+    const gracefulShutdown = async (signal) => {
+      this.logger.log(`Received ${signal}, checkpointing before exit...`);
+      try {
+        await this.checkpoint();
+        await this.disconnect();
+      } catch (error) {
+        this.logger.error(`Error during graceful shutdown: ${error instanceof Error ? error.message : String(error)}`);
+      }
+      process.exit(0);
+    };
+    process.on("SIGINT", () => gracefulShutdown("SIGINT"));
+    process.on("SIGTERM", () => gracefulShutdown("SIGTERM"));
+    process.on("beforeExit", async () => {
+      if (this.connection) {
+        await this.checkpoint();
+      }
+    });
   }
   async onModuleDestroy() {
     await this.disconnect();
@@ -874,7 +898,7 @@ class GraphService {
   }
   async connect() {
     try {
-      this.instance = await DuckDBInstance.create(this.dbPath, {
+      this.instance = await DuckDBInstance.create(":memory:", {
         allow_unsigned_extensions: "true"
       });
       this.connection = await this.instance.connect();
@@ -888,8 +912,10 @@ class GraphService {
       } catch (e) {
         this.logger.warn(`DuckPGQ extension not available: ${e instanceof Error ? e.message : String(e)}`);
       }
+      await this.connection.run(`ATTACH '${this.dbPath}' AS lattice (READ_WRITE);`);
+      await this.connection.run("USE lattice;");
       await this.initializeSchema();
-      this.logger.log(`Connected to DuckDB at ${this.dbPath}`);
+      this.logger.log(`Connected to DuckDB (in-memory + ATTACH) at ${this.dbPath}`);
     } catch (error) {
       this.connection = null;
       this.instance = null;
@@ -899,6 +925,7 @@ class GraphService {
   }
   async disconnect() {
     if (this.connection) {
+      await this.checkpoint();
       this.connection.closeSync();
       this.connection = null;
       this.logger.log("Disconnected from DuckDB");
@@ -907,6 +934,17 @@ class GraphService {
       this.instance = null;
     }
   }
+  async checkpoint() {
+    if (!this.connection) {
+      return;
+    }
+    try {
+      await this.connection.run("CHECKPOINT;");
+      this.logger.debug("Checkpoint completed");
+    } catch (error) {
+      this.logger.warn(`Checkpoint failed: ${error instanceof Error ? error.message : String(error)}`);
+    }
+  }
   async initializeSchema() {
     if (!this.connection) {
       throw new Error("Cannot initialize schema: not connected");
@@ -2037,10 +2075,13 @@ class SyncService {
       }
       if (!options.dryRun) {
         result.entityEmbeddingsGenerated = await this.syncEntities(uniqueEntities, options);
+        await this.graph.checkpoint();
         if (options.verbose) {
           this.logger.log(`Synced ${uniqueEntities.size} entities, generated ${result.entityEmbeddingsGenerated} embeddings`);
         }
       }
+      const CHECKPOINT_BATCH_SIZE = 10;
+      let processedCount = 0;
       for (const change of changes) {
         try {
           const doc = docsByPath.get(change.path);
@@ -2063,12 +2104,19 @@ class SyncService {
           if (change.embeddingGenerated) {
             result.embeddingsGenerated++;
           }
+          processedCount++;
+          if (!options.dryRun && processedCount % CHECKPOINT_BATCH_SIZE === 0) {
+            await this.graph.checkpoint();
+          }
         } catch (error) {
           const errorMessage = error instanceof Error ? error.message : String(error);
           result.errors.push({ path: change.path, error: errorMessage });
           this.logger.warn(`Error processing ${change.path}: ${errorMessage}`);
         }
       }
+      if (!options.dryRun && processedCount > 0) {
+        await this.graph.checkpoint();
+      }
       if (!options.dryRun) {
         await this.manifest.save();
       }

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "@zabaca/lattice",
-	"version": "1.0.2",
+	"version": "1.0.4",
 	"description": "Human-initiated, AI-powered knowledge graph for markdown documentation",
 	"type": "module",
 	"bin": {