kiri-mcp-server 0.16.0 → 0.17.0

package/README.md

@@ -2,7 +2,7 @@
 
 > Intelligent code context extraction for LLMs via Model Context Protocol
 
-[![Version](https://img.shields.io/badge/version-0.16.0-blue.svg)](package.json)
+[![Version](https://img.shields.io/badge/version-0.17.0-blue.svg)](package.json)
 [![License](https://img.shields.io/badge/license-MIT-green.svg)](LICENSE)
 [![TypeScript](https://img.shields.io/badge/TypeScript-5.6-blue.svg)](https://www.typescriptlang.org/)
 [![MCP](https://img.shields.io/badge/MCP-Compatible-green.svg)](https://modelcontextprotocol.io/)
@@ -20,20 +20,22 @@
 - **📝 Phrase-Aware**: Recognizes compound terms (kebab-case, snake_case) for precise matching
 - **🔒 Concurrency-Safe** _(v0.9.7+)_: Per-database queues, canonicalized DuckDB paths, and bootstrap-safe locking prevent FTS rebuild conflicts and keep locks consistent across symlinks—even on first run
 
-## 🆕 What's New in v0.16.0
+## 🆕 What's New in v0.17.0
 
-### ✨ Improvements
+### ✨ New Features
 
-- **DuckDB client migration**: Migrated to `@duckdb/node-api` from deprecated `duckdb` package
-  - No more native binding compilation errors with npx
-  - Pre-built binaries for all platforms
-  - Improved type safety and debugging support
+- **`code` boost_profile**: New boost profile that strongly deprioritizes documentation and config files (95% penalty) to focus search results on actual implementation code
+  - Use `boost_profile: "code"` when you want to find implementation files only
 
-### Previous Release (v0.15.0)
+### 🐛 Bug Fixes
 
-- **`snippets_get` view parameter**: Explicit retrieval strategy control (auto/symbol/lines/full)
-- **Co-change scoring**: Dependency graph with PageRank-like importance scoring
-- **Stop words & IDF weighting**: Multi-language support (en/ja) with BM25-style ranking
+- **Graph metrics retry logic**: Added retry logic for transient DuckDB errors during graph metrics computation
+
+### Previous Releases
+
+- **v0.16.1**: Graceful degradation for graph layer tables
+- **v0.16.0**: DuckDB client migration to `@duckdb/node-api`
+- **v0.15.0**: `snippets_get` view parameter, co-change scoring, stop words & IDF weighting
 
 ## ⚙️ Prerequisites
 
@@ -260,12 +262,12 @@ Tip: Avoid leading command words like `find` or `show`; instead list concrete mo
 
 **Parameters:**
 
-| Parameter       | Type    | Required | Description                                                                                                                                                                                                             |
-| --------------- | ------- | -------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `goal`          | string  | Yes      | Task description or question about the code                                                                                                                                                                             |
-| `limit`         | number  | No       | Max snippets to return (default: 12, max: 20)                                                                                                                                                                           |
-| `compact`       | boolean | No       | Return only metadata without preview (default: **true** in v0.8.0+, false in v0.7)                                                                                                                                      |
-| `boost_profile` | string  | No       | File type boosting: `"default"` (prioritizes src/, blacklists docs/), `"docs"` (prioritizes .md/.yaml, includes docs/ directory), `"balanced"` (equal weight for docs and impl, NEW in v0.9.10), `"none"` (no boosting) |
+| Parameter       | Type    | Required | Description                                                                                                                                                                                                                                                         |
+| --------------- | ------- | -------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `goal`          | string  | Yes      | Task description or question about the code                                                                                                                                                                                                                         |
+| `limit`         | number  | No       | Max snippets to return (default: 12, max: 20)                                                                                                                                                                                                                       |
+| `compact`       | boolean | No       | Return only metadata without preview (default: **true** in v0.8.0+, false in v0.7)                                                                                                                                                                                  |
+| `boost_profile` | string  | No       | File type boosting: `"default"` (prioritizes src/, blacklists docs/), `"code"` (strongly deprioritizes docs/config, 95% penalty), `"docs"` (prioritizes .md/.yaml, includes docs/ directory), `"balanced"` (equal weight for docs and impl), `"none"` (no boosting) |
 
 ### 2. files_search
 
@@ -302,14 +304,14 @@ Fast search across all indexed files. Supports multi-word queries, hyphenated te
 
 **Parameters:**
 
-| Parameter       | Type   | Required | Description                                                                                                                                                  |
-| --------------- | ------ | -------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| `query`         | string | Yes      | Search keywords or phrase                                                                                                                                    |
-| `limit`         | number | No       | Max results to return (default: 50, max: 200)                                                                                                                |
-| `lang`          | string | No       | Filter by language (e.g., "typescript", "python")                                                                                                            |
-| `ext`           | string | No       | Filter by extension (e.g., ".ts", ".md")                                                                                                                     |
-| `path_prefix`   | string | No       | Filter by path prefix (e.g., "src/auth/")                                                                                                                    |
-| `boost_profile` | string | No       | File type boosting: `"default"` (prioritizes src/, blacklists docs/), `"docs"` **(prioritizes .md/.yaml, includes docs/ directory)**, `"none"` (no boosting) |
+| Parameter       | Type   | Required | Description                                                                                                                                                                                                                                           |
+| --------------- | ------ | -------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `query`         | string | Yes      | Search keywords or phrase                                                                                                                                                                                                                             |
+| `limit`         | number | No       | Max results to return (default: 50, max: 200)                                                                                                                                                                                                         |
+| `lang`          | string | No       | Filter by language (e.g., "typescript", "python")                                                                                                                                                                                                     |
+| `ext`           | string | No       | Filter by extension (e.g., ".ts", ".md")                                                                                                                                                                                                              |
+| `path_prefix`   | string | No       | Filter by path prefix (e.g., "src/auth/")                                                                                                                                                                                                             |
+| `boost_profile` | string | No       | File type boosting: `"default"` (prioritizes src/, blacklists docs/), `"code"` (strongly deprioritizes docs/config, 95% penalty), `"docs"` **(prioritizes .md/.yaml, includes docs/ directory)**, `"balanced"` (equal weight), `"none"` (no boosting) |
 
 ### 3. snippets_get
 
@@ -550,6 +552,10 @@ Control search ranking behavior with the `boost_profile` parameter:
   - Implementation files get 30% boost, documentation files get 50% penalty
   - Config files heavily penalized (95% reduction)
   - `docs/` directory is blacklisted
+- **`"code"`** (NEW in v0.17.0): Strongly prioritizes implementation code only
+  - Documentation and config files get 95% penalty
+  - Best for finding actual implementation when you don't want docs in results
+  - `docs/` directory is blacklisted
 - **`"docs"`**: Prioritizes documentation files (`*.md`) over implementation
   - Documentation files get 50% boost, implementation files get 50% penalty
   - `docs/` directory is included in search results
@@ -564,6 +570,9 @@ Control search ranking behavior with the `boost_profile` parameter:
 // Find implementation files (default behavior)
 files_search({ query: "authentication", boost_profile: "default" });
 
+// Find only implementation code (no docs/config in results)
+files_search({ query: "authentication", boost_profile: "code" });
+
 // Find documentation
 files_search({ query: "setup guide", boost_profile: "docs" });
 
@@ -715,6 +724,71 @@ KIRI automatically filters sensitive files and masks sensitive values:
    pnpm unlink --global kiri-mcp-server
    ```
 
+#### Stale Lock File
+
+**Problem**: Daemon fails to start with error `Lock file already exists. Another process is indexing.`
+
+**Root Cause**: A previous daemon process crashed or was killed without proper cleanup, leaving a stale lock file.
+
+**Solution**:
+
+```bash
+# Remove the stale lock file
+rm -f .kiri/index.duckdb.sock.lock
+
+# Optionally, also remove the socket file
+rm -f .kiri/index.duckdb.sock
+
+# Restart the MCP server
+```
+
+#### Version Mismatch After Upgrade
+
+**Problem**: After upgrading KIRI, connection fails with `Version mismatch: client X.Y.Z is incompatible with daemon A.B.C`
+
+**Root Cause**: An old daemon process is still running after upgrading to a new version.
+
+**Solutions**:
+
+1. **Kill old daemon processes**:
+
+   ```bash
+   pkill -f "kiri.*daemon"
+   ```
+
+2. **Clear npx cache** (if using npx):
+
+   ```bash
+   npx clear-npx-cache
+   ```
+
+3. **Restart the MCP connection**
+
+#### Schema Mismatch After Upgrade (Degrade Mode)
+
+**Problem**: After upgrading KIRI, server shows `Server is running in degrade mode` and logs show errors like `Table with name graph_metrics does not exist`
+
+**Root Cause**: The existing index was created with an older schema version that doesn't include new tables (e.g., `graph_metrics`, `cochange`).
+
+**Solution**:
+
+1. **Stop the daemon**:
+
+   ```bash
+   pkill -f "kiri.*daemon"
+   rm -f .kiri/index.duckdb.sock.lock .kiri/index.duckdb.sock
+   ```
+
+2. **Rebuild index with full schema**:
+
+   ```bash
+   kiri --repo . --db .kiri/index.duckdb --full
+   ```
+
+3. **Restart your MCP client**
+
+> **Note**: The `--full` flag ensures all tables including `graph_metrics` and `cochange` are created. This is required when upgrading from versions prior to v0.15.0.
+
 ### Getting Help
 
 If you encounter issues not covered here:
@@ -914,8 +988,8 @@ Built with:
 
 ---
 
-**Status**: v0.15.0 (Beta) - Production-ready for MCP clients
+**Status**: v0.17.0 (Beta) - Production-ready for MCP clients
 
-**New in v0.15.0**: Co-change scoring, stop words/IDF weighting, and `snippets_get` view parameter for explicit retrieval control. See [CHANGELOG.md](CHANGELOG.md) for details.
+**New in v0.17.0**: `code` boost_profile for implementation-focused search. See [CHANGELOG.md](CHANGELOG.md) for details.
 
 For questions or support, please open a [GitHub issue](https://github.com/CAPHTECH/kiri/issues).

package/dist/package.json

@@ -1,6 +1,6 @@
 {
     "name": "kiri-mcp-server",
-    "version": "0.16.0",
+    "version": "0.16.1",
     "description": "KIRI context extraction platform",
     "type": "module",
     "packageManager": "pnpm@9.0.0",

package/dist/src/client/model-cli.d.ts

@@ -0,0 +1,12 @@
+#!/usr/bin/env node
+/**
+ * KIRI Model CLI
+ *
+ * Manages VSS models for semantic code search.
+ * Usage: kiri model <command> [options]
+ */
+/**
+ * Main entry point
+ */
+export declare function runModelCli(args: string[]): Promise<number>;
+//# sourceMappingURL=model-cli.d.ts.map

package/dist/src/client/model-cli.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"model-cli.d.ts","sourceRoot":"","sources":["../../../src/client/model-cli.ts"],"names":[],"mappings":";AACA;;;;;GAKG;AAsPH;;GAEG;AACH,wBAAsB,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,CAAC,CAgCjE"}

package/dist/src/client/model-cli.js

@@ -0,0 +1,247 @@
+#!/usr/bin/env node
+/**
+ * KIRI Model CLI
+ *
+ * Manages VSS models for semantic code search.
+ * Usage: kiri model <command> [options]
+ */
+import { createInterface } from "node:readline";
+import { getModelsDir, listInstalledModels } from "../shared/utils/global-dirs.js";
+import { SUPPORTED_MODELS } from "../vss/config.js";
+import { downloadModel, removeModel, getModelStatus, listAvailableModels, formatBytes, } from "../vss/model-downloader.js";
+/**
+ * Print usage information
+ */
+function printUsage() {
+    console.info(`
+KIRI Model Manager - Manage VSS models for semantic code search
+
+Usage: kiri model <command> [options]
+
+Commands:
+  download <model>    Download a model from HuggingFace
+  remove <model>      Remove an installed model
+  list                List available and installed models
+  status [model]      Show status of installed models
+
+Available models:
+  codebert-base       Microsoft CodeBERT (~500MB)
+  unixcoder-base      Microsoft UniXcoder (~500MB)
+
+Examples:
+  kiri model download codebert-base
+  kiri model list
+  kiri model status
+  kiri model remove codebert-base
+
+Environment variables:
+  KIRI_VSS_MODEL_DIR  Override model storage directory (default: ~/.kiri/models)
+`);
+}
+/**
+ * Create a progress bar string
+ */
+function progressBar(percentage, width = 30) {
+    const filled = Math.round((percentage / 100) * width);
+    const empty = width - filled;
+    return `[${"█".repeat(filled)}${"░".repeat(empty)}]`;
+}
+/**
+ * Progress callback for download
+ */
+function createProgressReporter() {
+    let lastFile = "";
+    return (progress) => {
+        if (progress.phase === "error") {
+            console.error(`\n❌ Error: ${progress.error}`);
+            return;
+        }
+        if (progress.phase === "complete" && progress.file !== lastFile) {
+            if (lastFile) {
+                process.stdout.write("\n");
+            }
+            console.info(`✅ ${progress.file}`);
+            lastFile = progress.file;
+            return;
+        }
+        if (progress.phase === "downloading") {
+            const bar = progressBar(progress.percentage);
+            const size = progress.total > 0
+                ? `${formatBytes(progress.downloaded)}/${formatBytes(progress.total)}`
+                : formatBytes(progress.downloaded);
+            process.stdout.write(`\r📥 ${progress.file} ${bar} ${progress.percentage}% ${size}`);
+            lastFile = progress.file;
+        }
+    };
+}
+/**
+ * Prompt user for confirmation
+ */
+async function confirm(message) {
+    const rl = createInterface({
+        input: process.stdin,
+        output: process.stdout,
+    });
+    return new Promise((resolve) => {
+        rl.question(`${message} [Y/n] `, (answer) => {
+            rl.close();
+            const normalized = answer.trim().toLowerCase();
+            resolve(normalized === "" || normalized === "y" || normalized === "yes");
+        });
+    });
+}
+/**
+ * Download command
+ */
+async function cmdDownload(modelName) {
+    if (!modelName) {
+        console.error("Error: Model name required");
+        console.info("Available models:", SUPPORTED_MODELS.join(", "));
+        return 1;
+    }
+    if (!SUPPORTED_MODELS.includes(modelName)) {
+        console.error(`Error: Unknown model "${modelName}"`);
+        console.info("Available models:", SUPPORTED_MODELS.join(", "));
+        return 1;
+    }
+    const model = modelName;
+    const status = getModelStatus(model);
+    if (status.installed) {
+        console.info(`Model "${model}" is already installed at ${status.path}`);
+        const reinstall = await confirm("Do you want to reinstall?");
+        if (!reinstall) {
+            return 0;
+        }
+        // Remove existing installation
+        await removeModel(model);
+    }
+    console.info(`\nDownloading ${model}...`);
+    console.info(`Target directory: ${getModelsDir()}\n`);
+    const result = await downloadModel(model, createProgressReporter());
+    if (result.success) {
+        console.info(`\n✅ Model "${model}" installed successfully`);
+        console.info(`   Location: ${result.modelPath}`);
+        return 0;
+    }
+    else {
+        console.error(`\n❌ Failed to download model: ${result.error}`);
+        return 1;
+    }
+}
+/**
+ * Remove command
+ */
+async function cmdRemove(modelName) {
+    if (!modelName) {
+        console.error("Error: Model name required");
+        return 1;
+    }
+    if (!SUPPORTED_MODELS.includes(modelName)) {
+        console.error(`Error: Unknown model "${modelName}"`);
+        return 1;
+    }
+    const model = modelName;
+    const status = getModelStatus(model);
+    if (!status.installed) {
+        console.info(`Model "${model}" is not installed`);
+        return 0;
+    }
+    const confirmed = await confirm(`Remove model "${model}" from ${status.path}?`);
+    if (!confirmed) {
+        console.info("Cancelled");
+        return 0;
+    }
+    const result = await removeModel(model);
+    if (result.success) {
+        console.info(`✅ Model "${model}" removed`);
+        return 0;
+    }
+    else {
+        console.error(`❌ Failed to remove model: ${result.error}`);
+        return 1;
+    }
+}
+/**
+ * List command
+ */
+function cmdList() {
+    console.info("\nAvailable VSS Models:\n");
+    const models = listAvailableModels();
+    const installed = listInstalledModels();
+    for (const { name, info, installed: isInstalled } of models) {
+        const status = isInstalled ? "✅ installed" : "⬜ not installed";
+        console.info(`  ${name}`);
+        console.info(`    ${info.description}`);
+        console.info(`    Size: ${info.sizeHuman}  Status: ${status}`);
+        console.info("");
+    }
+    console.info(`Models directory: ${getModelsDir()}`);
+    console.info(`Installed: ${installed.length}/${models.length}`);
+    return 0;
+}
+/**
+ * Status command
+ */
+function cmdStatus(modelName) {
+    if (modelName) {
+        if (!SUPPORTED_MODELS.includes(modelName)) {
+            console.error(`Error: Unknown model "${modelName}"`);
+            return 1;
+        }
+        const status = getModelStatus(modelName);
+        console.info(`\nModel: ${status.name}`);
+        console.info(`Installed: ${status.installed ? "Yes" : "No"}`);
+        console.info(`Path: ${status.path}`);
+        if (status.installed && status.sizeOnDisk !== undefined) {
+            console.info(`Size on disk: ${formatBytes(status.sizeOnDisk)}`);
+            console.info(`Files: ${status.files?.join(", ")}`);
+        }
+        return 0;
+    }
+    // Show status for all models
+    console.info("\nModel Status:\n");
+    for (const model of SUPPORTED_MODELS) {
+        const status = getModelStatus(model);
+        const icon = status.installed ? "✅" : "⬜";
+        const size = status.sizeOnDisk !== undefined ? formatBytes(status.sizeOnDisk) : "-";
+        console.info(`  ${icon} ${model.padEnd(20)} ${size.padStart(10)}`);
+    }
+    console.info(`\nModels directory: ${getModelsDir()}`);
+    return 0;
+}
+/**
+ * Main entry point
+ */
+export async function runModelCli(args) {
+    const command = args[0];
+    const arg1 = args[1];
+    switch (command) {
+        case "download":
+            return cmdDownload(arg1);
+        case "remove":
+        case "rm":
+        case "delete":
+            return cmdRemove(arg1);
+        case "list":
+        case "ls":
+            return cmdList();
+        case "status":
+            return cmdStatus(arg1);
+        case "help":
+        case "--help":
+        case "-h":
+        case undefined:
+            printUsage();
+            return 0;
+        default:
+            console.error(`Unknown command: ${command}`);
+            printUsage();
+            return 1;
+    }
+}
+// Run if executed directly
+if (import.meta.url === `file://${process.argv[1]}`) {
+    const args = process.argv.slice(2);
+    runModelCli(args).then((code) => process.exit(code));
+}
+//# sourceMappingURL=model-cli.js.map

package/dist/src/client/model-cli.js.map

@@ -0,0 +1 @@
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package/dist/src/indexer/graph-metrics.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"graph-metrics.d.ts","sourceRoot":"","sources":["../../../src/indexer/graph-metrics.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAExD;;GAEG;AACH,MAAM,WAAW,kBAAkB;IACjC,yDAAyD;IACzD,QAAQ,EAAE,MAAM,CAAC;IACjB,8CAA8C;IAC9C,aAAa,EAAE,MAAM,CAAC;IACtB,kDAAkD;IAClD,UAAU,EAAE,MAAM,CAAC;CACpB;AAWD;;;;;;;GAOG;AACH,wBAAsB,mBAAmB,CACvC,EAAE,EAAE,YAAY,EAChB,MAAM,EAAE,MAAM,EACd,MAAM,GAAE,OAAO,CAAC,kBAAkB,CAAM,GACvC,OAAO,CAAC,IAAI,CAAC,CAef;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAAC,EAAE,EAAE,YAAY,EAAE,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA0D7F;AAED;;;;GAIG;AACH,wBAAsB,wBAAwB,CAC5C,EAAE,EAAE,YAAY,EAChB,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,IAAI,CAAC,CAyCf;AAED;;;;;;;GAOG;AACH,wBAAsB,uBAAuB,CAC3C,EAAE,EAAE,YAAY,EAChB,MAAM,EAAE,MAAM,EACd,aAAa,EAAE,MAAM,EACrB,UAAU,EAAE,MAAM,GACjB,OAAO,CAAC,IAAI,CAAC,CAgFf;AAED;;;;;;;GAOG;AACH,wBAAsB,sBAAsB,CAC1C,EAAE,EAAE,YAAY,EAChB,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,MAAM,EAAE,GACrB,OAAO,CAAC,IAAI,CAAC,CAyCf"}
+{"version":3,"file":"graph-metrics.d.ts","sourceRoot":"","sources":["../../../src/indexer/graph-metrics.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAGxD;;GAEG;AACH,MAAM,WAAW,kBAAkB;IACjC,yDAAyD;IACzD,QAAQ,EAAE,MAAM,CAAC;IACjB,8CAA8C;IAC9C,aAAa,EAAE,MAAM,CAAC;IACtB,kDAAkD;IAClD,UAAU,EAAE,MAAM,CAAC;CACpB;AAuBD;;;;;;;GAOG;AACH,wBAAsB,mBAAmB,CACvC,EAAE,EAAE,YAAY,EAChB,MAAM,EAAE,MAAM,EACd,MAAM,GAAE,OAAO,CAAC,kBAAkB,CAAM,GACvC,OAAO,CAAC,IAAI,CAAC,CAef;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAAC,EAAE,EAAE,YAAY,EAAE,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA6D7F;AAED;;;;GAIG;AACH,wBAAsB,wBAAwB,CAC5C,EAAE,EAAE,YAAY,EAChB,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,IAAI,CAAC,CA4Cf;AAED;;;;;;;GAOG;AACH,wBAAsB,uBAAuB,CAC3C,EAAE,EAAE,YAAY,EAChB,MAAM,EAAE,MAAM,EACd,aAAa,EAAE,MAAM,EACrB,UAAU,EAAE,MAAM,GACjB,OAAO,CAAC,IAAI,CAAC,CAgFf;AAED;;;;;;;GAOG;AACH,wBAAsB,sBAAsB,CAC1C,EAAE,EAAE,YAAY,EAChB,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,MAAM,EAAE,GACrB,OAAO,CAAC,IAAI,CAAC,CAyCf"}

package/dist/src/indexer/graph-metrics.js

@@ -14,6 +14,7 @@
  * - Importance score (PageRank-like)
  * - Inbound closure (BFS up to depth 3)
  */
+import { withRetry } from "../shared/utils/retry.js";
 const DEFAULT_CONFIG = {
     maxDepth: 3,
     dampingFactor: 0.85,
@@ -21,6 +22,17 @@ const DEFAULT_CONFIG = {
 };
 /** Minimum score floor to prevent division by zero during PageRank normalization */
 const MIN_PAGERANK_SCORE = 0.001;
+/** Retry configuration for transient DuckDB errors (e.g., concurrent access) */
+const DB_RETRY_OPTIONS = {
+    maxAttempts: 3,
+    delayMs: 100,
+    jitterMs: 50,
+    isRetriable: (error) => {
+        const msg = error instanceof Error ? error.message : String(error);
+        // Retry on prepared statement failures (transient lock issues)
+        return msg.includes("Failed to execute prepared statement");
+    },
+};
 /**
  * Compute all graph metrics for a repository.
  * Called after dependency extraction during indexing.
@@ -47,8 +59,8 @@ export async function computeGraphMetrics(db, repoId, config = {}) {
  * Uses SQL aggregation for efficiency.
  */
 export async function computeDegreeCentrality(db, repoId) {
-    // Clear existing metrics for this repo
-    await db.run(`DELETE FROM graph_metrics WHERE repo_id = ?`, [repoId]);
+    // Clear existing metrics for this repo (with retry for transient lock issues)
+    await withRetry(() => db.run(`DELETE FROM graph_metrics WHERE repo_id = ?`, [repoId]), DB_RETRY_OPTIONS);
     // Compute outbound counts (files this file imports)
     await db.run(`
     INSERT INTO graph_metrics (repo_id, path, outbound_count, inbound_count, importance_score, computed_at)
@@ -99,8 +111,8 @@ export async function computeDegreeCentrality(db, repoId) {
  * Uses recursive CTE for efficient computation.
  */
 export async function precomputeInboundClosure(db, repoId, maxDepth) {
-    // Clear existing closure for this repo
-    await db.run(`DELETE FROM inbound_edges WHERE repo_id = ?`, [repoId]);
+    // Clear existing closure for this repo (with retry for transient lock issues)
+    await withRetry(() => db.run(`DELETE FROM inbound_edges WHERE repo_id = ?`, [repoId]), DB_RETRY_OPTIONS);
     // Use recursive CTE to compute transitive closure
     // This computes: for each file, which files import it (directly or transitively)
     await db.run(`

package/dist/src/indexer/graph-metrics.js.map

@@ -1 +1 @@
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package/dist/src/server/boost-profiles.d.ts

@@ -46,7 +46,7 @@ export interface BoostProfileConfig {
      */
     skipConfigAdditivePenalty?: boolean;
 }
-export type BoostProfileName = "default" | "docs" | "none" | "balanced" | "feature" | "bugfix" | "debug" | "api" | "editor" | "testfail" | "typeerror" | "vscode";
+export type BoostProfileName = "default" | "docs" | "none" | "balanced" | "code" | "feature" | "bugfix" | "debug" | "api" | "editor" | "testfail" | "typeerror" | "vscode";
 /**
  * Boost profile definitions
  * Centralized configuration for all boost profiles

package/dist/src/server/boost-profiles.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"boost-profiles.d.ts","sourceRoot":"","sources":["../../../src/server/boost-profiles.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,MAAM,WAAW,cAAc;IAC7B,MAAM,EAAE,MAAM,CAAC;IACf,UAAU,EAAE,MAAM,CAAC;CACpB;AAED;;;GAGG;AACH,MAAM,WAAW,kBAAkB;IACjC;;;;OAIG;IACH,iBAAiB,EAAE,MAAM,EAAE,CAAC;IAE5B,sDAAsD;IACtD,mBAAmB,EAAE;QACnB,mDAAmD;QACnD,GAAG,EAAE,MAAM,CAAC;QACZ,oCAAoC;QACpC,IAAI,EAAE,MAAM,CAAC;QACb,8DAA8D;QAC9D,MAAM,EAAE,MAAM,CAAC;KAChB,CAAC;IAEF;;;OAGG;IACH,eAAe,EAAE,cAAc,EAAE,CAAC;IAElC;;;;OAIG;IACH,yBAAyB,CAAC,EAAE,OAAO,CAAC;CACrC;AAED,MAAM,MAAM,gBAAgB,GACxB,SAAS,GACT,MAAM,GACN,MAAM,GACN,UAAU,GACV,MAAM,GACN,SAAS,GACT,QAAQ,GACR,OAAO,GACP,KAAK,GACL,QAAQ,GACR,UAAU,GACV,WAAW,GACX,QAAQ,CAAC;AAuDb;;;GAGG;AACH,eAAO,MAAM,cAAc,EAAE,MAAM,CAAC,gBAAgB,EAAE,kBAAkB,CAyQvE,CAAC;AAEF;;;GAGG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,gBAAgB,GAAG,kBAAkB,CAS1E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,IAAI,gBAAgB,CAE1E"}

package/dist/src/server/boost-profiles.js

@@ -124,6 +124,28 @@ export const BOOST_PROFILES = {
         },
         pathMultipliers: [],
     },
+    code: {
+        denylistOverrides: [],
+        fileTypeMultipliers: {
+            doc: 0.05, // 95% penalty for docs (stronger than default's 0.5)
+            impl: 1.4, // 40% boost for implementation
+            config: 0.05, // 95% penalty for config files
+        },
+        // Note: Order of pathMultipliers doesn't affect matching (longest prefix wins in applyPathMultipliers)
+        pathMultipliers: [
+            // Strongly suppress common root documentation files (×0.01 = 99% penalty)
+            { prefix: "CLAUDE.md", multiplier: 0.01 },
+            { prefix: "README.md", multiplier: 0.01 },
+            { prefix: "CHANGELOG.md", multiplier: 0.01 },
+            { prefix: "CONTRIBUTING.md", multiplier: 0.01 },
+            { prefix: "AGENTS.md", multiplier: 0.01 },
+            // Implementation file boosts (same as default)
+            { prefix: "src/components/", multiplier: 1.3 },
+            { prefix: "src/app/", multiplier: 1.4 },
+            { prefix: "src/lib/", multiplier: 1.2 },
+            { prefix: "src/", multiplier: 1.0 },
+        ],
+    },
     feature: {
         denylistOverrides: [],
         fileTypeMultipliers: {