@grafema/cli 0.2.4-beta → 0.2.5-beta

package/README.md

@@ -0,0 +1,73 @@
+# @grafema/cli
+
+> Grafema command-line interface for building and querying the code graph.
+
+## Quick Start
+
+```bash
+npx @grafema/cli init
+npx @grafema/cli analyze
+npx @grafema/cli overview
+```
+
+## Commands
+
+### Project setup
+
+```bash
+npx @grafema/cli init           # Create .grafema/config.yaml
+npx @grafema/cli analyze         # Build the graph
+npx @grafema/cli overview        # Summary of nodes/edges found
+npx @grafema/cli schema          # List node and edge types
+npx @grafema/cli types           # List available node types
+```
+
+### Querying the graph
+
+```bash
+npx @grafema/cli query "auth"                    # Name search (partial match)
+npx @grafema/cli query "function login"          # Type + name
+npx @grafema/cli query "route /api"              # Route search
+npx @grafema/cli query "token in authenticate"   # Scope filtering
+npx @grafema/cli query --type http:request "/api" # Exact type
+npx @grafema/cli query --raw 'type(X, "FUNCTION")'
+```
+
+### Data flow tracing
+
+```bash
+npx @grafema/cli trace "userId"                   # Trace variable sources/sinks
+npx @grafema/cli trace "userId from authenticate" # Scoped trace
+npx @grafema/cli trace --to "addNode#0.type"       # Sink-based trace
+npx @grafema/cli trace --from-route "GET /status"  # Route response trace
+```
+
+### Navigation helpers
+
+```bash
+npx @grafema/cli ls --type FUNCTION        # List nodes by type
+npx @grafema/cli get <semantic-id>         # Get a single node by ID
+npx @grafema/cli explain <node-id>         # Explain a node (summary)
+```
+
+### Checks & diagnostics
+
+```bash
+npx @grafema/cli check                 # Run all guarantees
+npx @grafema/cli check dataflow        # Run a diagnostic category
+npx @grafema/cli check --list-categories
+npx @grafema/cli doctor                # Validate local setup
+```
+
+### Misc
+
+```bash
+npx @grafema/cli coverage               # Coverage stats
+npx @grafema/cli impact                 # Impact analysis
+npx @grafema/cli explore                # Interactive explorer (TUI)
+```
+
+## Notes
+
+- All commands accept `--project <path>` to point at a specific repo.
+- `npx @grafema/cli` works without global install and is preferred for docs/examples.

package/dist/cli.js

@@ -50,3 +50,4 @@ program.addCommand(doctorCommand);
 program.addCommand(schemaCommand);
 program.addCommand(explainCommand);
 program.parse();
+//# sourceMappingURL=cli.js.map

package/dist/cli.js.map

@@ -0,0 +1 @@
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package/dist/commands/analyze.d.ts

@@ -2,5 +2,14 @@
  * Analyze command - Run project analysis via Orchestrator
  */
 import { Command } from 'commander';
+export interface NodeEdgeCountBackend {
+    nodeCount: () => Promise<number>;
+    edgeCount: () => Promise<number>;
+}
+export declare function fetchNodeEdgeCounts(backend: NodeEdgeCountBackend): Promise<{
+    nodeCount: number;
+    edgeCount: number;
+}>;
+export declare function exitWithCode(code: number, exitFn?: (code: number) => void): void;
 export declare const analyzeCommand: Command;
 //# sourceMappingURL=analyze.d.ts.map

package/dist/commands/analyze.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"analyze.d.ts","sourceRoot":"","sources":["../../src/commands/analyze.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AA2DpC,MAAM,WAAW,oBAAoB;IACnC,SAAS,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,CAAC;IACjC,SAAS,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,CAAC;CAClC;AAED,wBAAsB,mBAAmB,CAAC,OAAO,EAAE,oBAAoB,GAAG,OAAO,CAAC;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,SAAS,EAAE,MAAM,CAAA;CAAE,CAAC,CAG1H;AAED,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,GAAE,CAAC,IAAI,EAAE,MAAM,KAAK,IAAmB,GAAG,IAAI,CAE9F;AAyID,eAAO,MAAM,cAAc,SA+PvB,CAAC"}

package/dist/commands/analyze.js

@@ -5,7 +5,7 @@ import { Command } from 'commander';
 import { resolve, join } from 'path';
 import { existsSync, mkdirSync, readdirSync } from 'fs';
 import { pathToFileURL } from 'url';
-import { Orchestrator, RFDBServerBackend, DiagnosticReporter, DiagnosticWriter, createLogger, loadConfig, 
+import { Orchestrator, RFDBServerBackend, DiagnosticReporter, DiagnosticWriter, createLogger, loadConfig, StrictModeFailure, 
 // Discovery
 SimpleProjectDiscovery, MonorepoServiceDiscovery, WorkspaceDiscovery, 
 // Indexing
@@ -13,9 +13,17 @@ JSModuleIndexer, RustModuleIndexer,
 // Analysis
 JSASTAnalyzer, ExpressRouteAnalyzer, ExpressResponseAnalyzer, SocketIOAnalyzer, DatabaseAnalyzer, FetchAnalyzer, ServiceLayerAnalyzer, ReactAnalyzer, RustAnalyzer, 
 // Enrichment
-MethodCallResolver, ArgumentParameterLinker, AliasTracker, ValueDomainAnalyzer, MountPointResolver, PrefixEvaluator, InstanceOfResolver, ImportExportLinker, FunctionCallResolver, HTTPConnectionEnricher, RustFFIEnricher, 
+MethodCallResolver, ArgumentParameterLinker, AliasTracker, ValueDomainAnalyzer, MountPointResolver, ExpressHandlerLinker, PrefixEvaluator, InstanceOfResolver, ImportExportLinker, FunctionCallResolver, HTTPConnectionEnricher, RustFFIEnricher, RejectionPropagationEnricher, 
 // Validation
 CallResolverValidator, EvalBanValidator, SQLInjectionValidator, ShadowingDetector, GraphConnectivityValidator, DataFlowValidator, TypeScriptDeadCodeValidator, BrokenImportValidator, } from '@grafema/core';
+import { ProgressRenderer } from '../utils/progressRenderer.js';
+export async function fetchNodeEdgeCounts(backend) {
+    const [nodeCount, edgeCount] = await Promise.all([backend.nodeCount(), backend.edgeCount()]);
+    return { nodeCount, edgeCount };
+}
+export function exitWithCode(code, exitFn = process.exit) {
+    exitFn(code);
+}
 const BUILTIN_PLUGINS = {
     // Discovery
     SimpleProjectDiscovery: () => new SimpleProjectDiscovery(),
@@ -40,12 +48,14 @@ const BUILTIN_PLUGINS = {
     AliasTracker: () => new AliasTracker(),
     ValueDomainAnalyzer: () => new ValueDomainAnalyzer(),
     MountPointResolver: () => new MountPointResolver(),
+    ExpressHandlerLinker: () => new ExpressHandlerLinker(),
     PrefixEvaluator: () => new PrefixEvaluator(),
     InstanceOfResolver: () => new InstanceOfResolver(),
     ImportExportLinker: () => new ImportExportLinker(),
     FunctionCallResolver: () => new FunctionCallResolver(),
     HTTPConnectionEnricher: () => new HTTPConnectionEnricher(),
     RustFFIEnricher: () => new RustFFIEnricher(),
+    RejectionPropagationEnricher: () => new RejectionPropagationEnricher(),
     // Validation
     CallResolverValidator: () => new CallResolverValidator(),
     EvalBanValidator: () => new EvalBanValidator(),
@@ -66,30 +76,36 @@ async function loadCustomPlugins(projectPath, log) {
     }
     const customPlugins = {};
     try {
-        const files = readdirSync(pluginsDir).filter((f) => f.endsWith('.js') || f.endsWith('.mjs'));
+        const files = readdirSync(pluginsDir).filter((f) => f.endsWith('.js') || f.endsWith('.mjs') || f.endsWith('.cjs'));
         for (const file of files) {
             try {
                 const pluginPath = join(pluginsDir, file);
                 const pluginUrl = pathToFileURL(pluginPath).href;
                 const module = await import(pluginUrl);
-                const PluginClass = module.default || module[file.replace(/\.(m?js)$/, '')];
+                const PluginClass = module.default || module[file.replace(/\.[cm]?js$/, '')];
                 if (PluginClass && typeof PluginClass === 'function') {
-                    const pluginName = PluginClass.name || file.replace(/\.(m?js)$/, '');
-                    customPlugins[pluginName] = () => new PluginClass();
+                    const pluginName = PluginClass.name || file.replace(/\.[cm]?js$/, '');
+                    customPlugins[pluginName] = () => {
+                        const instance = new PluginClass();
+                        instance.config.sourceFile = pluginPath;
+                        return instance;
+                    };
                     log(`Loaded custom plugin: ${pluginName}`);
                 }
             }
             catch (err) {
-                console.warn(`Failed to load plugin ${file}: ${err.message}`);
+                const message = err instanceof Error ? err.message : String(err);
+                console.warn(`Failed to load plugin ${file}: ${message}`);
             }
         }
     }
     catch (err) {
-        console.warn(`Error loading custom plugins: ${err.message}`);
+        const message = err instanceof Error ? err.message : String(err);
+        console.warn(`Error loading custom plugins: ${message}`);
     }
     return customPlugins;
 }
-function createPlugins(config, customPlugins = {}) {
+function createPlugins(config, customPlugins = {}, verbose = false) {
     const plugins = [];
     const phases = ['discovery', 'indexing', 'analysis', 'enrichment', 'validation'];
     for (const phase of phases) {
@@ -100,8 +116,9 @@ function createPlugins(config, customPlugins = {}) {
             if (factory) {
                 plugins.push(factory());
             }
-            else {
-                console.warn(`Unknown plugin: ${name}`);
+            else if (verbose) {
+                // Only show plugin warning in verbose mode
+                console.warn(`Plugin not found: ${name} (skipping). Check .grafema/config.yaml or add to .grafema/plugins/`);
             }
         }
     }
@@ -109,7 +126,10 @@ function createPlugins(config, customPlugins = {}) {
 }
 /**
  * Determine log level from CLI options.
- * Priority: --log-level > --quiet > --verbose > default ('info')
+ * Priority: --log-level > --quiet > --verbose > default ('silent')
+ *
+ * By default, logs are silent to allow clean progress UI.
+ * Use --verbose to see detailed logs (disables interactive progress).
  */
 function getLogLevel(options) {
     if (options.logLevel) {
@@ -121,8 +141,8 @@ function getLogLevel(options) {
     if (options.quiet)
         return 'silent';
     if (options.verbose)
-        return 'debug';
-    return 'info';
+        return 'info'; // --verbose shows logs instead of progress UI
+    return 'silent'; // Default: silent logs, clean progress UI
 }
 export const analyzeCommand = new Command('analyze')
     .description('Run project analysis')
@@ -134,6 +154,7 @@ export const analyzeCommand = new Command('analyze')
     .option('-v, --verbose', 'Show verbose logging')
     .option('--debug', 'Enable debug mode (writes diagnostics.log)')
     .option('--log-level <level>', 'Set log level (silent, errors, warnings, info, debug)')
+    .option('--log-file <path>', 'Write all log output to a file')
     .option('--strict', 'Enable strict mode (fail on unresolved references)')
     .option('--auto-start', 'Auto-start RFDB server if not running')
     .addHelpText('after', `
@@ -144,6 +165,7 @@ Examples:
   grafema analyze -s api         Analyze only "api" service (monorepo)
   grafema analyze -v             Verbose output with progress details
   grafema analyze --debug        Write diagnostics.log for debugging
+  grafema analyze --log-file out.log  Write all logs to a file
   grafema analyze --strict       Fail on unresolved references (debugging)
   grafema analyze --auto-start   Auto-start server (useful for CI)
 
@@ -156,17 +178,27 @@ Note: Start the server first with: grafema server start
     if (!existsSync(grafemaDir)) {
         mkdirSync(grafemaDir, { recursive: true });
     }
-    const log = options.quiet ? () => { } : console.log;
+    // Two log levels for CLI output:
+    // - info: important results (shows unless --quiet)
+    // - debug: verbose details (shows only with --verbose)
+    const info = options.quiet ? () => { } : console.log;
+    const debug = options.verbose ? console.log : () => { };
     // Create logger based on CLI flags
     const logLevel = getLogLevel(options);
-    const logger = createLogger(logLevel);
-    log(`Analyzing project: ${projectPath}`);
+    const logFile = options.logFile ? resolve(options.logFile) : undefined;
+    const logger = createLogger(logLevel, logFile ? { logFile } : undefined);
+    if (logFile) {
+        debug(`Log file: ${logFile}`);
+    }
+    debug(`Analyzing project: ${projectPath}`);
     // Connect to RFDB server
     // Default: require explicit `grafema server start`
     // Use --auto-start for CI or backwards compatibility
+    // In normal mode (not verbose), suppress backend logs for clean progress UI
     const backend = new RFDBServerBackend({
         dbPath,
-        autoStart: options.autoStart ?? false
+        autoStart: options.autoStart ?? false,
+        silent: !options.verbose // Silent in normal mode (show progress), verbose shows logs
     });
     try {
         await backend.connect();
@@ -187,28 +219,51 @@ Note: Start the server first with: grafema server start
         throw err;
     }
     if (options.clear) {
-        log('Clearing existing database...');
+        debug('Clearing existing database...');
         await backend.clear();
     }
     const config = loadConfig(projectPath, logger);
     // Extract services from config (REG-174)
     if (config.services.length > 0) {
-        log(`Loaded ${config.services.length} service(s) from config`);
+        debug(`Loaded ${config.services.length} service(s) from config`);
         for (const svc of config.services) {
             const entry = svc.entryPoint ? ` (entry: ${svc.entryPoint})` : '';
-            log(`  - ${svc.name}: ${svc.path}${entry}`);
+            debug(`  - ${svc.name}: ${svc.path}${entry}`);
         }
     }
     // Load custom plugins from .grafema/plugins/
-    const customPlugins = await loadCustomPlugins(projectPath, log);
-    const plugins = createPlugins(config.plugins, customPlugins);
-    log(`Loaded ${plugins.length} plugins`);
+    const customPlugins = await loadCustomPlugins(projectPath, debug);
+    const plugins = createPlugins(config.plugins, customPlugins, options.verbose);
+    debug(`Loaded ${plugins.length} plugins`);
     // Resolve strict mode: CLI flag overrides config
     const strictMode = options.strict ?? config.strict ?? false;
     if (strictMode) {
-        log('Strict mode enabled - analysis will fail on unresolved references');
+        debug('Strict mode enabled - analysis will fail on unresolved references');
     }
     const startTime = Date.now();
+    // Create progress renderer for CLI output
+    // In quiet mode, use a no-op renderer (skip rendering)
+    // In verbose mode, use non-interactive (newlines per update)
+    // In normal mode, use interactive (spinner with line overwrite)
+    const renderer = options.quiet
+        ? null
+        : new ProgressRenderer({
+            isInteractive: !options.verbose && process.stdout.isTTY,
+        });
+    // Poll graph stats periodically to show node/edge counts in progress
+    let statsInterval = null;
+    if (renderer && !options.quiet) {
+        statsInterval = setInterval(async () => {
+            try {
+                const stats = await fetchNodeEdgeCounts(backend);
+                renderer.setStats(stats.nodeCount, stats.edgeCount);
+            }
+            catch {
+                // Ignore stats errors during analysis
+            }
+        }, 500); // Poll every 500ms
+        statsInterval.unref?.();
+    }
     const orchestrator = new Orchestrator({
         graph: backend,
         plugins,
@@ -219,39 +274,41 @@ Note: Start the server first with: grafema server start
         services: config.services.length > 0 ? config.services : undefined, // Pass config services (REG-174)
         strictMode, // REG-330: Pass strict mode flag
         onProgress: (progress) => {
-            if (options.verbose) {
-                log(`[${progress.phase}] ${progress.message}`);
-            }
+            renderer?.update(progress);
         },
     });
     let exitCode = 0;
     try {
         await orchestrator.run(projectPath);
         await backend.flush();
-        const elapsed = ((Date.now() - startTime) / 1000).toFixed(2);
-        const stats = await backend.getStats();
-        log('');
-        log(`Analysis complete in ${elapsed}s`);
-        log(`  Nodes: ${stats.nodeCount}`);
-        log(`  Edges: ${stats.edgeCount}`);
+        const elapsedSeconds = (Date.now() - startTime) / 1000;
+        const stats = await fetchNodeEdgeCounts(backend);
+        // Clear progress line in interactive mode, then show results
+        if (renderer && process.stdout.isTTY) {
+            process.stdout.write('\r\x1b[K'); // Clear line
+        }
+        info('');
+        info(renderer ? renderer.finish(elapsedSeconds) : `Analysis complete in ${elapsedSeconds.toFixed(2)}s`);
+        info(`  Nodes: ${stats.nodeCount}`);
+        info(`  Edges: ${stats.edgeCount}`);
         // Get diagnostics and report summary
         const diagnostics = orchestrator.getDiagnostics();
         const reporter = new DiagnosticReporter(diagnostics);
         // Print summary if there are any issues
         if (diagnostics.count() > 0) {
-            log('');
-            log(reporter.categorizedSummary());
+            info('');
+            info(reporter.categorizedSummary());
             // In verbose mode, print full report
             if (options.verbose) {
-                log('');
-                log(reporter.report({ format: 'text', includeSummary: false }));
+                debug('');
+                debug(reporter.report({ format: 'text', includeSummary: false }));
             }
         }
         // Always write diagnostics.log (required for `grafema check` command)
         const writer = new DiagnosticWriter();
         await writer.write(diagnostics, grafemaDir);
         if (options.debug) {
-            log(`Diagnostics written to ${writer.getLogPath(grafemaDir)}`);
+            debug(`Diagnostics written to ${writer.getLogPath(grafemaDir)}`);
         }
         // Determine exit code based on severity
         if (diagnostics.hasFatal()) {
@@ -265,17 +322,36 @@ Note: Start the server first with: grafema server start
         }
     }
     catch (e) {
-        // Orchestrator threw (fatal error stopped analysis)
-        const error = e instanceof Error ? e : new Error(String(e));
         const diagnostics = orchestrator.getDiagnostics();
         const reporter = new DiagnosticReporter(diagnostics);
-        console.error('');
-        console.error(`✗ Analysis failed: ${error.message}`);
-        console.error('');
-        console.error('→ Run with --debug for detailed diagnostics');
-        if (diagnostics.count() > 0) {
+        // Clear progress line in interactive mode
+        if (renderer && process.stdout.isTTY) {
+            process.stdout.write('\r\x1b[K');
+        }
+        // Check if this is a strict mode failure (REG-332: structured output)
+        if (e instanceof StrictModeFailure) {
+            // Format ONLY from diagnostics, not from error.message
+            console.error('');
+            console.error(`✗ Strict mode: ${e.count} unresolved reference(s) found during ENRICHMENT.`);
+            console.error('');
+            console.error(reporter.formatStrict(e.diagnostics, {
+                verbose: options.verbose,
+                suppressedCount: e.suppressedCount, // REG-332
+            }));
+            console.error('');
+            console.error('Run without --strict for graceful degradation, or fix the underlying issues.');
+        }
+        else {
+            // Generic error handling (non-strict)
+            const error = e instanceof Error ? e : new Error(String(e));
+            console.error('');
+            console.error(`✗ Analysis failed: ${error.message}`);
             console.error('');
-            console.error(reporter.report({ format: 'text', includeSummary: true }));
+            console.error('→ Run with --debug for detailed diagnostics');
+            if (diagnostics.count() > 0) {
+                console.error('');
+                console.error(reporter.report({ format: 'text', includeSummary: true }));
+            }
         }
         // Write diagnostics.log in debug mode even on failure
         if (options.debug) {
@@ -285,10 +361,18 @@ Note: Start the server first with: grafema server start
         }
         exitCode = 1;
     }
-    await backend.close();
-    // Exit with appropriate code
-    // 0 = success, 1 = fatal, 2 = errors
-    if (exitCode !== 0) {
-        process.exit(exitCode);
+    finally {
+        // Stop stats polling
+        if (statsInterval) {
+            clearInterval(statsInterval);
+            statsInterval = null;
+        }
+        if (backend.connected) {
+            await backend.close();
+        }
+        // Exit with appropriate code
+        // 0 = success, 1 = fatal, 2 = errors
+        exitWithCode(exitCode);
     }
 });
+//# sourceMappingURL=analyze.js.map

package/dist/commands/analyze.js.map

@@ -0,0 +1 @@
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package/dist/commands/check.d.ts

@@ -6,11 +6,7 @@
  * 2. Built-in validators: --guarantee=<name> (e.g., --guarantee=node-creation)
  */
 import { Command } from 'commander';
-export interface DiagnosticCheckCategory {
-    name: string;
-    description: string;
-    codes: string[];
-}
-export declare const CHECK_CATEGORIES: Record<string, DiagnosticCheckCategory>;
+import { DIAGNOSTIC_CATEGORIES } from '@grafema/core';
+export { DIAGNOSTIC_CATEGORIES as CHECK_CATEGORIES };
 export declare const checkCommand: Command;
 //# sourceMappingURL=check.d.ts.map

package/dist/commands/check.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../src/commands/check.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAiCpC,MAAM,WAAW,uBAAuB;IACtC,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,KAAK,EAAE,MAAM,EAAE,CAAC;CACjB;AAGD,eAAO,MAAM,gBAAgB,EAAE,MAAM,CAAC,MAAM,EAAE,uBAAuB,CAqBpE,CAAC;AAEF,eAAO,MAAM,YAAY,SA2OtB,CAAC"}
+{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../src/commands/check.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAGpC,OAAO,EAKL,qBAAqB,EACtB,MAAM,eAAe,CAAC;AAiBvB,OAAO,EAAE,qBAAqB,IAAI,gBAAgB,EAAE,CAAC;AAErD,eAAO,MAAM,YAAY,SA2OtB,CAAC"}