rlm-analyzer 1.5.1 → 1.7.0

package/CHANGELOG.md

@@ -5,6 +5,61 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased] - 2026-03-31
+
+### Added
+- **`rlm supply-chain` command** (BZL-21): Real-time CVE and malicious package detection
+  - Scans `package.json` (npm), `requirements.txt` (PyPI), and `go.mod` (Go) dependencies
+  - Queries [OSV.dev API](https://osv.dev) for each dependency with max 10 concurrent requests
+  - Flags `MAL-*` prefixed OSV IDs as MALICIOUS (separate from CVEs) with CRITICAL severity
+  - Runs `npm audit --json` as secondary signal and merges results
+  - Outputs color-coded report: 🚨 MALICIOUS / ⚠️ CRITICAL / HIGH / MEDIUM
+  - `--fix` flag shows remediation commands for vulnerable packages
+  - `--deep` flag for transitive dependency scanning
+  - `--ecosystem <npm|pypi|go>` flag to override auto-detection
+  - New types: `SupplyChainResult`, `VulnerabilityFinding`, `SupplyChainOptions`
+  - New prompt: `SUPPLY_CHAIN_PROMPT` for AI-assisted supply chain risk assessment
+
+## [1.6.0] - 2026-01-22
+
+### Added
+- **Structural Indexing with Caching**: Smart file indexing for faster analysis
+  - SHA-256 file hashing for change detection
+  - Import/export extraction for dependency analysis
+  - File clustering for grouped analysis
+  - Cache stored in `~/.rlm-analyzer/cache/`
+  - ~10x faster subsequent runs on unchanged files
+- **Large File Chunking**: Intelligent handling of files >200KB
+  - Smart chunking by logical boundaries (functions, classes, interfaces)
+  - Skeleton extraction without LLM (signatures, exports, imports)
+  - Summary generation for context preservation
+- **Stuck Detection and Recovery**: Prevents infinite analysis loops
+  - Tracks consecutive no-code turns
+  - Escalating prompts after repeated failures
+  - Force completion after turn 5 with 0 sub-LLM calls
+  - Before: 20 turns, timeout ❌ → After: 1 turn, completion ✅
+- **Extended File Extensions**: Better coverage for modern codebases
+  - Added `.graphql`, `.gql`, `.proto`, `.prisma`
+  - Added `.tf`, `.tfvars`, `.hcl` (Infrastructure as Code)
+  - Added common config files (Dockerfile, Makefile, etc.)
+- **CLI Cache Options**: Control over structural index caching
+  - `--no-cache` flag to force fresh analysis
+  - `clear-cache` command to clear index for a directory
+
+### Changed
+- `analyzeCodebase()` now uses structural index by default
+- File loading prioritizes entry points based on cluster analysis
+- Analysis order optimized based on dependency graph
+
+---
+
+## [1.5.1] - 2026-01-22
+
+### Fixed
+- Fixed hardcoded version strings in CLI and MCP server
+
+---
+
 ## [1.5.0] - 2026-01-22
 
 ### Added

package/README.md

@@ -17,6 +17,7 @@ Analyze any codebase with AI that can process **100x beyond context limits**. Po
 - **Symbol Search** - Find all usages of functions, classes, variables
 - **Custom Questions** - Ask anything about your codebase
 - **Multi-Provider Support** - Choose between Gemini (default), Amazon Bedrock (Nova/Claude/Llama), or Claude (Anthropic API)
+- **Supply Chain Security** - Real-time CVE and malicious package detection via OSV.dev API
 - **Web Grounding** - Verify package versions with real-time web search (Gemini & Nova Premier)
 - **MCP Integration** - Works with Claude Code, Cursor, and other MCP clients
 - **Cost Efficient** - Save 60-73% on API costs by offloading to Gemini/Nova
@@ -141,6 +142,40 @@ rlm ask "How does authentication work?"
 
 ---
 
+
+### Supply Chain Scan (CVE & Malicious Package Detection)
+
+Scan your project dependencies against [OSV.dev](https://osv.dev) for known CVEs and malicious packages:
+
+```bash
+# Scan npm dependencies (auto-detects package.json)
+rlm supply-chain
+
+# Show fix versions for all vulnerable packages
+rlm supply-chain --fix
+
+# Scan a specific ecosystem
+rlm supply-chain --ecosystem pypi
+
+# Include transitive dependencies
+rlm supply-chain --deep
+```
+
+Example output:
+```
+🔍 Supply Chain Scan — my-project
+
+🚨 MALICIOUS (1)
+  axios@1.14.1 — MAL-2026-2307
+  Malicious code detected. Remove immediately. Safe version: 1.13.5
+
+⚠️  CRITICAL CVEs (0)
+✅  HIGH CVEs (0)
+
+📦 Scanned: 47 packages | Clean: 46 | At risk: 1
+Run with --fix to see remediation commands.
+```
+
 ## CLI Reference
 
 ### Commands

package/dist/analyzer.d.ts

@@ -1,24 +1,54 @@
 /**
  * Code Analysis High-Level API
  * Provides easy-to-use functions for common analysis tasks
+ *
+ * Features:
+ * - Structural indexing with caching for faster subsequent runs
+ * - Dependency graph for cross-file analysis
+ * - Large file chunking to avoid missing important code
+ * - Smart analysis ordering based on file clusters
  */
-import type { CodeAnalysisOptions, CodeAnalysisResult } from './types.js';
+import type { CodeAnalysisOptions, CodeAnalysisResult, StructuralIndex } from './types.js';
 /** Default maximum file size in bytes (100KB) */
 export declare const DEFAULT_MAX_FILE_SIZE = 100000;
 /** Default analysis type when not specified */
 export declare const DEFAULT_ANALYSIS_TYPE: "summary";
 /**
- * Load files from a directory
+ * Load files from a directory (legacy function for backward compatibility)
  */
 export declare function loadFiles(directory: string, options?: {
     include?: string[];
     exclude?: string[];
     maxFileSize?: number;
 }): Record<string, string>;
+/**
+ * Load files using structural index with large file handling
+ * Returns both the files and the structural index for dependency information
+ */
+export declare function loadFilesWithIndex(directory: string, options?: {
+    include?: string[];
+    exclude?: string[];
+    maxFileSize?: number;
+    useCache?: boolean;
+    verbose?: boolean;
+}): Promise<{
+    files: Record<string, string>;
+    index: StructuralIndex;
+    largeFiles: string[];
+}>;
 /**
  * Analyze a codebase with custom query
+ * Now uses structural indexing for:
+ * - Faster subsequent runs (cached file index)
+ * - Better analysis ordering (entry points first)
+ * - Large file handling (chunking with summaries)
+ * - Dependency information for cross-file analysis
  */
 export declare function analyzeCodebase(options: CodeAnalysisOptions): Promise<CodeAnalysisResult>;
+/**
+ * Clear the structural index cache for a directory
+ */
+export declare function clearIndexCache(directory: string): void;
 /**
  * Analyze architecture
  */

package/dist/analyzer.d.ts.map

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package/dist/analyzer.js

@@ -1,15 +1,25 @@
 /**
  * Code Analysis High-Level API
  * Provides easy-to-use functions for common analysis tasks
+ *
+ * Features:
+ * - Structural indexing with caching for faster subsequent runs
+ * - Dependency graph for cross-file analysis
+ * - Large file chunking to avoid missing important code
+ * - Smart analysis ordering based on file clusters
  */
 import * as fs from 'fs';
 import * as path from 'path';
-import { CODE_EXTENSIONS, IGNORE_DIRS } from './types.js';
+import { CODE_EXTENSIONS, INCLUDE_FILENAMES, IGNORE_DIRS } from './types.js';
 import { RLMOrchestrator } from './orchestrator.js';
 import { getAnalysisPrompt } from './prompts.js';
 import { verifySecurityRecommendations, appendGroundingSources } from './grounding.js';
+import { buildStructuralIndex, updateStructuralIndex, getAnalysisPriority, clearCache, } from './structural-index.js';
+import { processLargeFile, createLargeFileSummary, } from './file-chunker.js';
 /** Default maximum file size in bytes (100KB) */
 export const DEFAULT_MAX_FILE_SIZE = 100_000;
+/** Large file threshold - files above this get chunked (200KB) */
+const LARGE_FILE_THRESHOLD = 200_000;
 /** Default analysis type when not specified */
 export const DEFAULT_ANALYSIS_TYPE = 'summary';
 /**
@@ -41,14 +51,18 @@ function calculateTimeout(fileCount) {
     return 300000; // 5 minutes default
 }
 /**
- * Load files from a directory
+ * Load files from a directory (legacy function for backward compatibility)
  */
 export function loadFiles(directory, options = {}) {
     const files = {};
     const maxSize = options.maxFileSize || DEFAULT_MAX_FILE_SIZE;
     const includeExts = options.include || CODE_EXTENSIONS;
     const excludeDirs = [...IGNORE_DIRS, ...(options.exclude || [])];
-    function shouldInclude(filePath) {
+    function shouldInclude(filePath, fileName) {
+        // Check by filename first
+        if (INCLUDE_FILENAMES.includes(fileName)) {
+            return true;
+        }
         const ext = path.extname(filePath);
         return includeExts.some(e => ext === e || filePath.endsWith(e));
     }
@@ -63,7 +77,7 @@ export function loadFiles(directory, options = {}) {
                         walk(fullPath);
                     }
                 }
-                else if (entry.isFile() && shouldInclude(entry.name)) {
+                else if (entry.isFile() && shouldInclude(relativePath, entry.name)) {
                     try {
                         const stats = fs.statSync(fullPath);
                         if (stats.size <= maxSize) {
@@ -83,16 +97,81 @@ export function loadFiles(directory, options = {}) {
     walk(directory);
     return files;
 }
+/**
+ * Load files using structural index with large file handling
+ * Returns both the files and the structural index for dependency information
+ */
+export async function loadFilesWithIndex(directory, options = {}) {
+    const { maxFileSize = DEFAULT_MAX_FILE_SIZE, useCache = true, verbose = false, } = options;
+    // Build or load structural index
+    let index;
+    let changedFiles;
+    if (useCache) {
+        const result = await updateStructuralIndex(directory, { verbose });
+        index = result.index;
+        changedFiles = result.changedFiles;
+        if (verbose && changedFiles.length > 0) {
+            console.log(`[Index] ${changedFiles.length} files changed since last run`);
+        }
+    }
+    else {
+        index = await buildStructuralIndex(directory, { force: true, verbose });
+    }
+    const files = {};
+    const largeFiles = [];
+    // Get files in analysis priority order (entry points first)
+    const prioritizedFiles = getAnalysisPriority(index);
+    for (const relativePath of prioritizedFiles) {
+        const entry = index.files[relativePath];
+        if (!entry)
+            continue;
+        const fullPath = path.join(directory, relativePath);
+        try {
+            const content = fs.readFileSync(fullPath, 'utf-8');
+            if (entry.size > LARGE_FILE_THRESHOLD) {
+                // Process large file - create summary instead of full content
+                const processed = processLargeFile(content, relativePath);
+                files[relativePath] = createLargeFileSummary(processed);
+                largeFiles.push(relativePath);
+                if (verbose) {
+                    console.log(`[Chunker] Large file ${relativePath}: ${processed.chunkCount} chunks`);
+                }
+            }
+            else if (entry.size <= maxFileSize) {
+                // Normal file - include full content
+                files[relativePath] = content;
+            }
+            else {
+                // Medium-large file - include but note it's truncated
+                files[relativePath] = content.slice(0, maxFileSize) +
+                    `\n\n// ... truncated (${Math.round(entry.size / 1024)}KB total)`;
+            }
+        }
+        catch {
+            // Skip unreadable files
+        }
+    }
+    return { files, index, largeFiles };
+}
 /**
  * Analyze a codebase with custom query
+ * Now uses structural indexing for:
+ * - Faster subsequent runs (cached file index)
+ * - Better analysis ordering (entry points first)
+ * - Large file handling (chunking with summaries)
+ * - Dependency information for cross-file analysis
  */
 export async function analyzeCodebase(options) {
-    const files = loadFiles(options.directory, {
+    const useCache = options.useCache !== false; // Default to true
+    const analysisType = options.analysisType || DEFAULT_ANALYSIS_TYPE;
+    // Load files with structural index
+    const { files, index, largeFiles } = await loadFilesWithIndex(options.directory, {
         include: options.include,
         exclude: options.exclude,
+        useCache,
+        verbose: options.verbose,
     });
     const fileCount = Object.keys(files).length;
-    const analysisType = options.analysisType || DEFAULT_ANALYSIS_TYPE;
     if (fileCount === 0) {
         return {
             success: false,
@@ -105,7 +184,13 @@ export async function analyzeCodebase(options) {
             error: 'No files found to analyze',
         };
     }
-    const query = options.query || getAnalysisPrompt(analysisType);
+    // Build enhanced query with structural context
+    let query = options.query || getAnalysisPrompt(analysisType);
+    // Add structural context to help LLM understand codebase organization
+    if (index.clusters.length > 0 || index.metadata.frameworks.length > 0) {
+        const structuralContext = buildStructuralContext(index, largeFiles);
+        query = `${structuralContext}\n\n${query}`;
+    }
     // Calculate smart max turns and timeout based on codebase size
     const maxTurns = options.maxTurns || calculateMaxTurns(fileCount);
     const timeoutMs = calculateTimeout(fileCount);
@@ -122,6 +207,46 @@ export async function analyzeCodebase(options) {
         analysisType,
     };
 }
+/**
+ * Build structural context string to prepend to analysis queries
+ */
+function buildStructuralContext(index, largeFiles) {
+    const parts = ['## Codebase Structure\n'];
+    // Add metadata
+    if (index.metadata.frameworks.length > 0) {
+        parts.push(`**Frameworks detected:** ${index.metadata.frameworks.join(', ')}`);
+    }
+    if (index.metadata.packageManager) {
+        parts.push(`**Package manager:** ${index.metadata.packageManager}`);
+    }
+    if (index.metadata.languages.length > 0) {
+        parts.push(`**Languages:** ${index.metadata.languages.join(', ')}`);
+    }
+    // Add cluster summary
+    if (index.clusters.length > 0) {
+        parts.push('\n**File clusters (related modules):**');
+        for (const cluster of index.clusters.slice(0, 10)) {
+            const entryPoints = cluster.entryPoints.slice(0, 2).join(', ');
+            parts.push(`- ${cluster.type}: ${cluster.files.length} files (entry: ${entryPoints || 'N/A'})`);
+        }
+        if (index.clusters.length > 10) {
+            parts.push(`- ... and ${index.clusters.length - 10} more clusters`);
+        }
+    }
+    // Note large files
+    if (largeFiles.length > 0) {
+        parts.push(`\n**Large files (summarized):** ${largeFiles.join(', ')}`);
+        parts.push('*Note: Large files are shown as summaries. Request specific sections if needed.*');
+    }
+    parts.push('');
+    return parts.join('\n');
+}
+/**
+ * Clear the structural index cache for a directory
+ */
+export function clearIndexCache(directory) {
+    clearCache(directory);
+}
 /**
  * Analyze architecture
  */

package/dist/analyzer.js.map

@@ -1 +1 @@
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package/dist/cli.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AACA;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AAkoBH,wBAAsB,MAAM,IAAI,OAAO,CAAC,IAAI,CAAC,CA0I5C"}
+{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AACA;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AAyrBH,wBAAsB,MAAM,IAAI,OAAO,CAAC,IAAI,CAAC,CA0I5C"}

package/dist/cli.js

@@ -27,10 +27,11 @@
  *   --help, -h     Show help
  */
 import * as path from 'path';
-import { analyzeArchitecture, analyzeDependencies, analyzeSecurity, analyzePerformance, analyzeRefactoring, summarizeCodebase, findUsages, explainFile, askQuestion, } from './analyzer.js';
+import { analyzeArchitecture, analyzeDependencies, analyzeSecurity, analyzePerformance, analyzeRefactoring, summarizeCodebase, findUsages, explainFile, askQuestion, clearIndexCache, } from './analyzer.js';
 import { hasApiKey, hasBedrockCredentials, hasClaudeCredentials, initConfig, getApiKey, initializeProvider, detectProvider, } from './config.js';
 import { getDefaultModel, resolveModelConfig, resolveProviderModelAlias, AVAILABLE_MODELS, AVAILABLE_BEDROCK_MODELS, AVAILABLE_CLAUDE_MODELS, getAliasesDisplay, } from './models.js';
 import * as fs from 'fs';
+import { runSupplyChainScan } from './supply-chain.js';
 // ANSI colors
 const colors = {
     reset: '\x1b[0m',
@@ -146,6 +147,8 @@ ${colors.bold}Commands:${colors.reset}
   ${colors.green}ask${colors.reset} "<question>"     Ask a custom question
   ${colors.green}config${colors.reset} [api-key]     Configure or show API key status
   ${colors.green}test${colors.reset}                 Test API connection and model availability
+  ${colors.green}clear-cache${colors.reset}          Clear structural index cache for a directory
+  ${colors.green}supply-chain${colors.reset}         Scan dependencies for CVEs and supply chain risks
 
 ${colors.bold}Options:${colors.reset}
   --dir, -d <path>      Directory to analyze (default: current directory)
@@ -156,6 +159,7 @@ ${colors.bold}Options:${colors.reset}
                         Aliases: sonnet, opus, haiku (claude)
   --output, -o <file>   Save results to markdown file (e.g., rlm-context.md)
   --grounding, -g       Enable web grounding to verify package versions (security only)
+  --no-cache            Disable structural index caching (force fresh analysis)
   --verbose, -v         Show detailed turn-by-turn output
   --json                Output results as JSON
   --help, -h            Show this help message
@@ -252,6 +256,10 @@ function parseArgs(args) {
         version: false,
         output: null,
         grounding: false,
+        noCache: false,
+        deep: false,
+        fix: false,
+        ecosystem: 'npm',
     };
     let command = '';
     let target;
@@ -323,6 +331,28 @@ function parseArgs(args) {
         else if (arg === '--grounding' || arg === '-g') {
             options.grounding = true;
         }
+        else if (arg === '--deep') {
+            options.deep = true;
+        }
+        else if (arg === '--fix') {
+            options.fix = true;
+        }
+        else if (arg === '--ecosystem') {
+            i++;
+            const eco = args[i]?.toLowerCase();
+            if (eco === 'npm' || eco === 'pypi' || eco === 'go') {
+                options.ecosystem = eco;
+            }
+        }
+        else if (arg.startsWith('--ecosystem=')) {
+            const eco = arg.slice(12).toLowerCase();
+            if (eco === 'npm' || eco === 'pypi' || eco === 'go') {
+                options.ecosystem = eco;
+            }
+        }
+        else if (arg === '--no-cache') {
+            options.noCache = true;
+        }
         else if (!command) {
             command = arg;
         }
@@ -384,8 +414,22 @@ async function runCommand(command, target, options) {
     progressTracker?.start();
     const onTurnComplete = createTurnCallback(options.verbose);
     const onProgress = progressTracker ? createProgressCallback(progressTracker) : undefined;
-    const analysisOpts = { verbose: options.verbose, onTurnComplete, onProgress, model: options.model };
+    const analysisOpts = {
+        verbose: options.verbose,
+        onTurnComplete,
+        onProgress,
+        model: options.model,
+        useCache: !options.noCache,
+    };
     let result;
+    // Handle clear-cache command before switch
+    if (command === 'clear-cache') {
+        progressTracker?.stop();
+        clearIndexCache(options.dir);
+        log(`\nCache cleared for: ${options.dir}`, 'green');
+        log('Next analysis will rebuild the structural index.', 'dim');
+        process.exit(0);
+    }
     switch (command) {
         case 'summary':
             result = await summarizeCodebase(options.dir, analysisOpts);
@@ -436,6 +480,15 @@ async function runCommand(command, target, options) {
             }
             result = await askQuestion(options.dir, target, analysisOpts);
             break;
+        case 'supply-chain': {
+            progressTracker?.stop();
+            await runSupplyChainScan(options.dir, {
+                deep: options.deep,
+                fix: options.fix,
+                ecosystem: options.ecosystem,
+            });
+            return;
+        }
         default:
             log(`Unknown command: ${command}`, 'red');
             log('Run "rlm --help" for usage information', 'dim');
@@ -527,7 +580,7 @@ function generateMarkdownReport(command, target, directory, result, duration, pr
         }
         md += '\n';
     }
-    md += `---\n*Analysis performed with RLM Analyzer v1.5.1 using ${provider} provider*\n`;
+    md += `---\n*Analysis performed with RLM Analyzer v1.6.0 using ${provider} provider*\n`;
     return md;
 }
 /**
@@ -581,7 +634,7 @@ export async function runCli() {
     const { command, target, options } = parseArgs(args);
     // Show version
     if (options.version) {
-        console.log('rlm-analyzer v1.5.1');
+        console.log('rlm-analyzer v1.6.0');
         process.exit(0);
     }
     // Show help