pupt 1.2.1 → 1.3.1

package/dist/cli.js

@@ -228,6 +228,8 @@ program
     .description('Execute a prompt with an external tool')
     .usage('[tool] [args...] [-- tool-specific-args]')
     .option('-h, --history <number>', 'Use prompt from history by number')
+    .option('-p, --prompt <name>', 'Use specified prompt by title or filename')
+    .option('--no-interactive', 'Use default values for all prompt inputs')
     .helpOption('--help', 'Display help for run command')
     .addHelpText('after', `
 Examples:
@@ -239,13 +241,17 @@ Examples:
   pt run npm test -- --coverage  # Complex command with args
   pt run -h 3                # Re-run prompt from history #3
   pt run -h 1 claude         # Send history #1 to claude
+  pt run -p api-client       # Run specific prompt by name
+  pt run -p api-client --no-interactive  # Run with defaults only
 `)
     .action(async (tool, args, options) => {
     try {
         // Combine tool and args into single array
         const allArgs = tool ? [tool, ...args] : args;
         await runCommand(allArgs, {
-            historyIndex: options.history ? parseInt(options.history) : undefined
+            historyIndex: options.history ? parseInt(options.history) : undefined,
+            promptName: options.prompt,
+            noInteractive: options.interactive === false
         });
     }
     catch (error) {

package/dist/cli.js.map

@@ -1 +1 @@
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package/dist/commands/init-refactored.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"init-refactored.d.ts","sourceRoot":"","sources":["../../src/commands/init-refactored.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAC;AAKhF,UAAU,SAAS;IACjB,SAAS,EAAE,OAAO,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;IAClB,aAAa,EAAE,OAAO,CAAC;IACvB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,aAAa,CAAC,EAAE,MAAM,CAAC;CACxB;AAED,qBAAa,WAAY,SAAQ,WAAW,CAAC,SAAS,EAAE,IAAI,CAAC;IAC3D,OAAO,CAAC,UAAU,CAAS;gBAEf,OAAO,EAAE,cAAc,EAAE,OAAO,GAAE,cAAmB;IAKjE,SAAS,KAAK,IAAI,IAAI,MAAM,CAE3B;cAEe,qBAAqB,IAAI,OAAO,CAAC,IAAI,CAAC;cAStC,YAAY,IAAI,OAAO,CAAC,SAAS,CAAC;cA2DlC,aAAa,CAAC,KAAK,EAAE,SAAS,GAAG,OAAO,CAAC,IAAI,CAAC;CAwD/D;AAGD,wBAAsB,WAAW,CAAC,OAAO,CAAC,EAAE,cAAc,EAAE,OAAO,CAAC,EAAE,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,CAgBnG"}

package/dist/commands/init-refactored.js

@@ -130,9 +130,10 @@ export async function initCommand(context, options) {
         promptDirs: ['./.prompts'],
         ...DEFAULT_CONFIG
     };
+    const ConsoleUI = (await import('../ui/console-ui.js')).ConsoleUI;
     const defaultContext = context || {
         config: defaultConfig,
-        ui: (await import('../ui/console-ui.js')).ui,
+        ui: new ConsoleUI(),
         logger: (await import('../services/logging-service.js')).createLogger(defaultConfig)
     };
     const command = new InitCommand(defaultContext, options);

package/dist/commands/init-refactored.js.map

@@ -1 +1 @@
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+{"version":3,"file":"init-refactored.js","sourceRoot":"","sources":["../../src/commands/init-refactored.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,MAAM,mBAAmB,CAAC;AACnD,OAAO,EAAE,MAAM,UAAU,CAAC;AAC1B,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,WAAW,EAAkC,MAAM,mBAAmB,CAAC;AAChF,OAAO,EAAU,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAC5D,OAAO,EAAE,eAAe,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AACxE,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAU5C,MAAM,OAAO,WAAY,SAAQ,WAA4B;IACnD,UAAU,CAAS;IAE3B,YAAY,OAAuB,EAAE,UAA0B,EAAE;QAC/D,KAAK,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;QACxB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,iBAAiB,CAAC,CAAC;IAChE,CAAC;IAED,IAAc,IAAI;QAChB,OAAO,MAAM,CAAC;IAChB,CAAC;IAES,KAAK,CAAC,qBAAqB;QACnC,+CAA+C;QAC/C,IAAI,CAAC;YACH,MAAM,EAAE,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC;QACpD,CAAC;QAAC,MAAM,CAAC;YACP,MAAM,MAAM,CAAC,gBAAgB,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC;QAC/C,CAAC;IACH,CAAC;IAES,KAAK,CAAC,YAAY;QAC1B,4BAA4B;QAC5B,IAAI,SAAS,GAAG,IAAI,CAAC;QACrB,IAAI,MAAM,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE,CAAC;YACzC,SAAS,GAAG,MAAM,OAAO,CAAC;gBACxB,OAAO,EAAE,wCAAwC;gBACjD,OAAO,EAAE,KAAK;aACf,CAAC,CAAC;YACH,IAAI,CAAC,SAAS,EAAE,CAAC;gBACf,OAAO;oBACL,SAAS,EAAE,KAAK;oBAChB,SAAS,EAAE,EAAE;oBACb,aAAa,EAAE,KAAK;iBACrB,CAAC;YACJ,CAAC;QACH,CAAC;QAED,2BAA2B;QAC3B,MAAM,SAAS,GAAG,MAAM,KAAK,CAAC;YAC5B,OAAO,EAAE,iCAAiC;YAC1C,OAAO,EAAE,YAAY;SACtB,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,MAAM,OAAO,CAAC;YAClC,OAAO,EAAE,wBAAwB;YACjC,OAAO,EAAE,IAAI;SACd,CAAC,CAAC;QAEH,IAAI,UAA8B,CAAC;QACnC,IAAI,aAAiC,CAAC;QAEtC,IAAI,aAAa,EAAE,CAAC;YAClB,UAAU,GAAG,MAAM,KAAK,CAAC;gBACvB,OAAO,EAAE,iCAAiC;gBAC1C,OAAO,EAAE,cAAc;aACxB,CAAC,CAAC;YAEH,MAAM,iBAAiB,GAAG,MAAM,OAAO,CAAC;gBACtC,OAAO,EAAE,6BAA6B;gBACtC,OAAO,EAAE,IAAI;aACd,CAAC,CAAC;YAEH,IAAI,iBAAiB,EAAE,CAAC;gBACtB,aAAa,GAAG,MAAM,KAAK,CAAC;oBAC1B,OAAO,EAAE,qCAAqC;oBAC9C,OAAO,EAAE,cAAc;iBACxB,CAAC,CAAC;YACL,CAAC;QACH,CAAC;QAED,OAAO;YACL,SAAS;YACT,SAAS;YACT,aAAa;YACb,UAAU;YACV,aAAa;SACd,CAAC;IACJ,CAAC;IAES,KAAK,CAAC,aAAa,CAAC,KAAgB;QAC5C,IAAI,CAAC,KAAK,CAAC,SAAS,EAAE,CAAC;YACrB,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC,IAAI,CAAC,0BAA0B,CAAC,CAAC;YACjD,OAAO;QACT,CAAC;QAED,qBAAqB;QACrB,MAAM,YAAY,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC;QACvC,IAAI,KAAK,CAAC,UAAU;YAAE,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;QAC1D,IAAI,KAAK,CAAC,aAAa,IAAI,KAAK,CAAC,aAAa,KAAK,KAAK,CAAC,UAAU,EAAE,CAAC;YACpE,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC;QACzC,CAAC;QAED,KAAK,MAAM,GAAG,IAAI,YAAY,EAAE,CAAC;YAC/B,IAAI,CAAC,GAAG;gBAAE,SAAS;YACnB,MAAM,WAAW,GAAG,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC;gBACrC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,IAAI,EAAE,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;gBACjD,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;YACtB,MAAM,EAAE,CAAC,SAAS,CAAC,WAAW,CAAC,CAAC;QAClC,CAAC;QAED,kBAAkB;QAClB,MAAM,MAAM,GAAG;YACb,UAAU,EAAE,CAAC,KAAK,CAAC,SAAS,CAAC;YAC7B,GAAG,CAAC,KAAK,CAAC,UAAU,IAAI,EAAE,UAAU,EAAE,KAAK,CAAC,UAAU,EAAE,CAAC;YACzD,GAAG,CAAC,KAAK,CAAC,aAAa,IAAI,EAAE,aAAa,EAAE,KAAK,CAAC,aAAa,EAAE,CAAC;YAClE,GAAG,cAAc;SAClB,CAAC;QAEF,cAAc;QACd,MAAM,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,UAAU,EAAE,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC;QAE3D,yCAAyC;QACzC,IAAI,MAAM,eAAe,EAAE,EAAE,CAAC;YAC5B,MAAM,eAAe,GAAa,EAAE,CAAC;YAErC,yBAAyB;YACzB,eAAe,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAC;YAE/C,kDAAkD;YAClD,IAAI,KAAK,CAAC,UAAU,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;gBAChG,eAAe,CAAC,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;YACzC,CAAC;YAED,4BAA4B;YAC5B,MAAM,YAAY,GAAG,MAAM,CAAC,YAAY,IAAI,cAAc,CAAC,YAAY,IAAI,cAAc,CAAC;YAC1F,eAAe,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;YAEnC,gCAAgC;YAChC,KAAK,MAAM,KAAK,IAAI,eAAe,EAAE,CAAC;gBACpC,MAAM,cAAc,CAAC,KAAK,CAAC,CAAC;YAC9B,CAAC;QACH,CAAC;QAED,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,qCAAqC,CAAC,CAAC;IACjE,CAAC;CACF;AAED,qDAAqD;AACrD,MAAM,CAAC,KAAK,UAAU,WAAW,CAAC,OAAwB,EAAE,OAAwB;IAClF,+CAA+C;IAC/C,MAAM,aAAa,GAAW;QAC5B,UAAU,EAAE,CAAC,YAAY,CAAC;QAC1B,GAAG,cAAc;KAClB,CAAC;IAEF,MAAM,SAAS,GAAG,CAAC,MAAM,MAAM,CAAC,qBAAqB,CAAC,CAAC,CAAC,SAAS,CAAC;IAClE,MAAM,cAAc,GAAG,OAAO,IAAI;QAChC,MAAM,EAAE,aAAa;QACrB,EAAE,EAAE,IAAI,SAAS,EAAE;QACnB,MAAM,EAAE,CAAC,MAAM,MAAM,CAAC,gCAAgC,CAAC,CAAC,CAAC,YAAY,CAAC,aAAa,CAAC;KACrF,CAAC;IAEF,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,cAAc,EAAE,OAAO,CAAC,CAAC;IACzD,OAAO,OAAO,CAAC,OAAO,EAAE,CAAC;AAC3B,CAAC"}

package/dist/commands/run.d.ts

@@ -16,6 +16,8 @@ export interface RunOptions {
         timestamp?: Date;
     };
     isAutoRun?: boolean;
+    promptName?: string;
+    noInteractive?: boolean;
 }
 interface ParsedArgs {
     tool: string | undefined;

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

@@ -1 +1 @@
-{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/commands/run.ts"],"names":[],"mappings":"AAoBA,MAAM,WAAW,UAAU;IACzB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,YAAY,CAAC,EAAE;QACb,YAAY,EAAE,MAAM,CAAC;QACrB,eAAe,EAAE,MAAM,CAAC;QACxB,SAAS,EAAE,GAAG,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;QAChC,WAAW,EAAE,MAAM,CAAC;QACpB,KAAK,CAAC,EAAE,MAAM,CAAC;QACf,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,WAAW,CAAC,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,KAAK,EAAE,OAAO,CAAA;SAAE,CAAC,CAAC;QACtD,SAAS,CAAC,EAAE,IAAI,CAAC;KAClB,CAAC;IACF,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAED,UAAU,UAAU;IAClB,IAAI,EAAE,MAAM,GAAG,SAAS,CAAC;IACzB,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,SAAS,EAAE,MAAM,EAAE,CAAC;CACrB;AAED,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,UAAU,CAqBvD;AAED,wBAAsB,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,CAiPnF"}
+{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/commands/run.ts"],"names":[],"mappings":"AAoBA,MAAM,WAAW,UAAU;IACzB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,YAAY,CAAC,EAAE;QACb,YAAY,EAAE,MAAM,CAAC;QACrB,eAAe,EAAE,MAAM,CAAC;QACxB,SAAS,EAAE,GAAG,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;QAChC,WAAW,EAAE,MAAM,CAAC;QACpB,KAAK,CAAC,EAAE,MAAM,CAAC;QACf,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,WAAW,CAAC,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,KAAK,EAAE,OAAO,CAAA;SAAE,CAAC,CAAC;QACtD,SAAS,CAAC,EAAE,IAAI,CAAC;KAClB,CAAC;IACF,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,aAAa,CAAC,EAAE,OAAO,CAAC;CACzB;AAED,UAAU,UAAU;IAClB,IAAI,EAAE,MAAM,GAAG,SAAS,CAAC;IACzB,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,SAAS,EAAE,MAAM,EAAE,CAAC;CACrB;AAED,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,UAAU,CAqBvD;AAED,wBAAsB,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,CAmQnF"}

package/dist/commands/run.js

@@ -113,17 +113,30 @@ export async function runCommand(args, options) {
     else {
         // Normal flow - discover and process prompts
         const promptManager = new PromptManager(config.promptDirs);
-        const prompts = await promptManager.discoverPrompts();
-        if (prompts.length === 0) {
-            throw errors.noPromptsFound(config.promptDirs);
+        let selected;
+        if (options.promptName) {
+            // Find specific prompt by name
+            const prompt = await promptManager.findPrompt(options.promptName);
+            if (!prompt) {
+                throw errors.promptNotFound(options.promptName);
+            }
+            selected = prompt;
+            logger.log(chalk.blue(`\nUsing prompt: ${selected.title}`));
+            logger.log(chalk.dim(`Location: ${selected.path}\n`));
+        }
+        else {
+            // Interactive search
+            const prompts = await promptManager.discoverPrompts();
+            if (prompts.length === 0) {
+                throw errors.noPromptsFound(config.promptDirs);
+            }
+            const search = new InteractiveSearch();
+            selected = await search.selectPrompt(prompts);
+            logger.log(chalk.blue(`\nProcessing: ${selected.title}`));
+            logger.log(chalk.dim(`Location: ${selected.path}\n`));
         }
-        // Interactive search
-        const search = new InteractiveSearch();
-        const selected = await search.selectPrompt(prompts);
-        logger.log(chalk.blue(`\nProcessing: ${selected.title}`));
-        logger.log(chalk.dim(`Location: ${selected.path}\n`));
         // Process template
-        const engine = new TemplateEngine(config, configDir);
+        const engine = new TemplateEngine(config, configDir, options.noInteractive);
         promptResult = await engine.processTemplate(selected.content, selected);
         // Store template info for history saving after successful execution
         templateInfo = {
@@ -141,13 +154,19 @@ export async function runCommand(args, options) {
     if (!tool && ((config.defaultCmd && config.defaultCmd.trim() !== '') || (config.codingTool && config.codingTool.trim() !== '')) && (config.defaultCmdOptions || config.codingToolOptions)) {
         // Prompt for each option
         const selectedOptions = [];
-        for (const [question, arg] of Object.entries(config.defaultCmdOptions || config.codingToolOptions || {})) {
-            const answer = await confirm({
-                message: question,
-                default: false
-            });
-            if (answer) {
-                selectedOptions.push(arg);
+        if (options.noInteractive) {
+            // In no-interactive mode, don't add any optional flags
+            logger.log(chalk.dim('Skipping tool options in non-interactive mode'));
+        }
+        else {
+            for (const [question, arg] of Object.entries(config.defaultCmdOptions || config.codingToolOptions || {})) {
+                const answer = await confirm({
+                    message: question,
+                    default: false
+                });
+                if (answer) {
+                    selectedOptions.push(arg);
+                }
             }
         }
         // Insert options before extra args
@@ -170,13 +189,13 @@ export async function runCommand(args, options) {
                 dateStr,
                 timeStr,
                 randomSuffix
-            });
+            }, tool === 'claude' || (tool === undefined && finalTool === 'claude'));
             exitCode = result.exitCode;
             outputFile = result.outputFile;
             outputSize = result.outputSize;
         }
         else {
-            exitCode = await executeTool(finalTool, finalArgs, promptResult);
+            exitCode = await executeTool(finalTool, finalArgs, promptResult, tool === 'claude' || (tool === undefined && finalTool === 'claude'));
         }
     }
     finally {
@@ -232,7 +251,7 @@ export async function runCommand(args, options) {
         }
         // Handle post-run file reviews
         if (templateInfo?.reviewFiles && templateInfo.reviewFiles.length > 0) {
-            await handlePostRunReviews(templateInfo.reviewFiles, config, options.isAutoRun);
+            await handlePostRunReviews(templateInfo.reviewFiles, config, options.isAutoRun || options.noInteractive);
         }
     }
     // Exit with the same code as the tool
@@ -240,26 +259,42 @@ export async function runCommand(args, options) {
         process.exit(exitCode);
     }
 }
-async function executeToolWithCapture(tool, args, prompt, config, filenameComponents) {
+async function executeToolWithCapture(tool, args, prompt, config, filenameComponents, isClaudeCode = false) {
     const outputCapture = new OutputCaptureService({
         outputDirectory: config.outputCapture?.directory || config.historyDir,
         maxOutputSize: (config.outputCapture?.maxSizeMB || 10) * 1024 * 1024
     });
     // Use provided filename components for synchronized naming
     const { dateStr, timeStr, randomSuffix } = filenameComponents;
-    const outputFilename = `${dateStr}-${timeStr}-${randomSuffix}-output.txt`;
+    const outputFilename = `${dateStr}-${timeStr}-${randomSuffix}-output.json`;
     const outputPath = path.join(config.outputCapture?.directory || config.historyDir, outputFilename);
-    const result = await outputCapture.captureCommand(tool, args, prompt, outputPath);
+    // For Claude Code, pass prompt as argument; for others, use stdin
+    let finalArgs = args;
+    let finalPrompt = prompt;
+    if (isClaudeCode) {
+        finalArgs = [...args, prompt];
+        finalPrompt = ''; // Don't send via stdin
+    }
+    const result = await outputCapture.captureCommand(tool, finalArgs, finalPrompt, outputPath);
     return {
         exitCode: result.exitCode,
         outputFile: outputPath,
         outputSize: result.outputSize
     };
 }
-async function executeTool(tool, args, prompt) {
+async function executeTool(tool, args, prompt, isClaudeCode = false) {
+    // For Claude Code, pass prompt as argument; for others, use stdin
+    let finalArgs = args;
+    let finalPrompt = prompt;
+    if (isClaudeCode) {
+        finalArgs = [...args, prompt];
+        finalPrompt = ''; // Don't send via stdin
+    }
     return new Promise((resolve, reject) => {
-        const child = spawn(tool, args, {
-            stdio: ['pipe', 'inherit', tool === 'claude' ? 'pipe' : 'inherit']
+        // When running Claude Code, inherit stdin so Ink can use the TTY
+        // For other tools, pipe stdin to send the prompt
+        const child = spawn(tool, finalArgs, {
+            stdio: [isClaudeCode ? 'inherit' : 'pipe', 'inherit', tool === 'claude' ? 'pipe' : 'inherit']
         });
         let _stderrData = '';
         let errorDetected = false;
@@ -290,7 +325,8 @@ async function executeTool(tool, args, prompt) {
         });
         child.on('close', (code) => {
             // Handle Claude raw mode error specifically
-            if (tool === 'claude' && errorDetected) {
+            // Only show error if Claude actually failed (non-zero exit code)
+            if (tool === 'claude' && errorDetected && code !== 0) {
                 logger.error(chalk.red('\nError: Claude cannot run in interactive mode when launched from pt.'));
                 logger.log(chalk.yellow('\nThis typically happens when Claude needs to ask for directory trust permissions.'));
                 logger.log(chalk.blue('\nTo fix this:'));
@@ -303,30 +339,36 @@ async function executeTool(tool, args, prompt) {
             }
             resolve(code);
         });
-        // Write prompt to stdin
-        try {
-            if (child.stdin) {
-                // Only add error handler if stdin has on method (not mocked in tests)
-                if (typeof child.stdin.on === 'function') {
-                    child.stdin.on('error', (error) => {
-                        // Ignore EPIPE errors which happen when the tool closes stdin early
-                        const errorCode = error.code;
-                        if (errorCode !== 'EPIPE') {
-                            logger.error(`stdin error: ${error}`);
-                        }
-                    });
+        // Write prompt to stdin (only if not Claude Code)
+        if (finalPrompt) {
+            try {
+                if (child.stdin) {
+                    // Only add error handler if stdin has on method (not mocked in tests)
+                    if (typeof child.stdin.on === 'function') {
+                        child.stdin.on('error', (error) => {
+                            // Ignore EPIPE errors which happen when the tool closes stdin early
+                            const errorCode = error.code;
+                            if (errorCode !== 'EPIPE') {
+                                logger.error(`stdin error: ${error}`);
+                            }
+                        });
+                    }
+                    child.stdin.write(finalPrompt);
+                    child.stdin.end();
                 }
-                child.stdin.write(prompt);
-                child.stdin.end();
             }
-        }
-        catch (error) {
-            // Ignore EPIPE errors which happen when the tool closes stdin early
-            const errorCode = error.code;
-            if (errorCode !== 'EPIPE') {
-                reject(new Error(`Failed to write prompt to tool: ${error instanceof Error ? error.message : String(error)}`));
+            catch (error) {
+                // Ignore EPIPE errors which happen when the tool closes stdin early
+                const errorCode = error.code;
+                if (errorCode !== 'EPIPE') {
+                    reject(new Error(`Failed to write prompt to tool: ${error instanceof Error ? error.message : String(error)}`));
+                }
             }
         }
+        else if (child.stdin) {
+            // Close stdin even if we're not writing to it
+            child.stdin.end();
+        }
     });
 }
 async function handlePostRunReviews(reviewFiles, config, isAutoRun) {

package/dist/commands/run.js.map

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package/dist/config/config-manager.d.ts

@@ -1,5 +1,5 @@
 import { Config } from '../types/config.js';
-export interface ConfigResult {
+interface ConfigResult {
     config: Config;
     filepath?: string;
     configDir?: string;
@@ -16,4 +16,5 @@ export declare class ConfigManager {
     private static expandPaths;
     private static expandPath;
 }
+export {};
 //# sourceMappingURL=config-manager.d.ts.map

package/dist/config/config-manager.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"config-manager.d.ts","sourceRoot":"","sources":["../../src/config/config-manager.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,MAAM,EAAkB,MAAM,oBAAoB,CAAC;AAY5D,MAAM,WAAW,YAAY;IAC3B,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,qBAAa,aAAa;IACxB,OAAO,CAAC,MAAM,CAAC,WAAW;WAeb,sBAAsB,CAAC,GAAG,GAAE,MAAsB,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;WActE,mBAAmB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;WAgCrD,IAAI,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;WAKxC,YAAY,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,CAAC;IA+FnE,OAAO,CAAC,MAAM,CAAC,cAAc;mBAyCR,aAAa;IA+DlC,OAAO,CAAC,MAAM,CAAC,YAAY;IAmH3B,OAAO,CAAC,MAAM,CAAC,WAAW;IAuD1B,OAAO,CAAC,MAAM,CAAC,UAAU;CAkB1B"}
+{"version":3,"file":"config-manager.d.ts","sourceRoot":"","sources":["../../src/config/config-manager.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,MAAM,EAAkB,MAAM,oBAAoB,CAAC;AAY5D,UAAU,YAAY;IACpB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,qBAAa,aAAa;IACxB,OAAO,CAAC,MAAM,CAAC,WAAW;WAeb,sBAAsB,CAAC,GAAG,GAAE,MAAsB,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;WActE,mBAAmB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;WAgCrD,IAAI,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;WAKxC,YAAY,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,CAAC;IA+FnE,OAAO,CAAC,MAAM,CAAC,cAAc;mBAyCR,aAAa;IA+DlC,OAAO,CAAC,MAAM,CAAC,YAAY;IAmH3B,OAAO,CAAC,MAAM,CAAC,WAAW;IAuD1B,OAAO,CAAC,MAAM,CAAC,UAAU;CAkB1B"}

package/dist/config/migration.d.ts

@@ -1,5 +1,5 @@
 import { Config } from '../types/config.js';
-export interface ConfigMigration {
+interface ConfigMigration {
     version: string;
     migrate: (config: Record<string, unknown>) => Record<string, unknown>;
 }
@@ -8,4 +8,5 @@ export declare const migrateConfig: ((config: Record<string, unknown>) => Config
     needsMigration(config: Record<string, unknown>): boolean;
     createBackup(configPath: string): Promise<void>;
 };
+export {};
 //# sourceMappingURL=migration.d.ts.map

package/dist/config/migration.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"migration.d.ts","sourceRoot":"","sources":["../../src/config/migration.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAG5C,UAAU,eAAe;IACvB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,CAAC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,KAAK,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;CACvE;AAED,eAAO,MAAM,UAAU,EAAE,eAAe,EAkGvC,CAAC;AAEF,eAAO,MAAM,aAAa,YACP,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,KAAG,MAAM;2BAsBxB,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,OAAO;6BA0BzB,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;CAkBxD,CAAC"}

package/dist/config/migration.js

@@ -94,7 +94,9 @@ export const migrateConfig = Object.assign(function (config) {
         // Apply v3 migration first
         migrated = migrations[0].migrate(migrated);
     }
-    if (!migrated.version || migrated.version < '4.0.0') {
+    // Apply v4 migration if version is old OR if required v4 fields are missing
+    if (!migrated.version || migrated.version < '4.0.0' ||
+        (migrated.version === '4.0.0' && (!migrated.outputCapture || !migrated.autoAnnotate))) {
         // Apply v4 migration
         migrated = migrations[1].migrate(migrated);
     }
@@ -113,6 +115,12 @@ export const migrateConfig = Object.assign(function (config) {
         if (!config.version || config.version !== '4.0.0') {
             return true;
         }
+        // Check if v4.0.0 config is missing required v4 fields
+        // This handles cases where a config was manually edited or created
+        // before these fields were added to the v4 migration
+        if (config.version === '4.0.0' && (!config.outputCapture || !config.autoAnnotate)) {
+            return true;
+        }
         return false;
     },
     async createBackup(configPath) {

package/dist/config/migration.js.map

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package/dist/history/enhanced-history-manager.d.ts

@@ -1,6 +1,6 @@
 import { HistoryManager } from './history-manager.js';
 import { EnhancedHistoryEntry } from '../types/history.js';
-export interface EnhancedHistorySaveOptions {
+interface EnhancedHistorySaveOptions {
     templatePath: string;
     templateContent: string;
     variables: Map<string, unknown>;
@@ -14,6 +14,7 @@ export interface EnhancedHistorySaveOptions {
     exitCode?: number | null;
     outputFile?: string;
     outputSize?: number;
+    executionTime?: number;
 }
 export declare class EnhancedHistoryManager extends HistoryManager {
     private enhancedHistoryDir;
@@ -22,4 +23,5 @@ export declare class EnhancedHistoryManager extends HistoryManager {
     getHistoryEntry(index: number): Promise<EnhancedHistoryEntry | null>;
     savePrompt(options: EnhancedHistorySaveOptions): Promise<string>;
 }
+export {};
 //# sourceMappingURL=enhanced-history-manager.d.ts.map

package/dist/history/enhanced-history-manager.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"enhanced-history-manager.d.ts","sourceRoot":"","sources":["../../src/history/enhanced-history-manager.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AACtD,OAAO,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAC;AAS3D,UAAU,0BAA0B;IAClC,YAAY,EAAE,MAAM,CAAC;IACrB,eAAe,EAAE,MAAM,CAAC;IACxB,SAAS,EAAE,GAAG,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAChC,WAAW,EAAE,MAAM,CAAC;IACpB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,CAAC,EAAE,IAAI,CAAC;IACf,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,aAAa,CAAC,EAAE,MAAM,CAAC;CACxB;AAED,qBAAa,sBAAuB,SAAQ,cAAc;IAC5C,OAAO,CAAC,kBAAkB;gBAAlB,kBAAkB,EAAE,MAAM;IAIxC,WAAW,CAAC,KAAK,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,oBAAoB,EAAE,CAAC;IAO5D,eAAe,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,oBAAoB,GAAG,IAAI,CAAC;IAIpE,UAAU,CAAC,OAAO,EAAE,0BAA0B,GAAG,OAAO,CAAC,MAAM,CAAC;CAoGvE"}

package/dist/history/enhanced-history-manager.js

@@ -2,6 +2,7 @@ import { HistoryManager } from './history-manager.js';
 import { getGitInfo, formatDuration } from '../utils/git-info.js';
 import fs from 'fs-extra';
 import path from 'node:path';
+import { calculateActiveExecutionTime, extractUserInputLines } from '../services/output-capture-service.js';
 import crypto from 'node:crypto';
 import { sanitizeObject } from '../utils/security.js';
 import { DateFormats } from '../utils/date-formatter.js';
@@ -53,14 +54,40 @@ export class EnhancedHistoryManager extends HistoryManager {
             let execution;
             if (options.startTime) {
                 const endTime = options.endTime || new Date();
+                let duration = formatDuration(options.startTime, endTime);
+                let activeTime;
+                let userInputCount;
+                // If we have a JSON output file, calculate active execution time
+                if (options.outputFile && options.outputFile.endsWith('.json')) {
+                    try {
+                        const activeNanos = await calculateActiveExecutionTime(options.outputFile);
+                        const activeMs = Number(activeNanos / 1000000n);
+                        activeTime = `${activeMs}ms`;
+                        // Also get user input count
+                        const userInputs = await extractUserInputLines(options.outputFile);
+                        userInputCount = userInputs.length;
+                    }
+                    catch {
+                        // If calculation fails, just use the provided execution time
+                        if (options.executionTime) {
+                            activeTime = `${options.executionTime}ms`;
+                        }
+                    }
+                }
+                else if (options.executionTime) {
+                    // Use the execution time from run.ts if no JSON file
+                    duration = `${options.executionTime}ms`;
+                }
                 execution = {
                     start_time: options.startTime.toISOString(),
                     end_time: endTime.toISOString(),
-                    duration: formatDuration(options.startTime, endTime),
+                    duration,
                     exit_code: options.exitCode ?? null,
                     command: options.command || 'unknown',
                     ...(options.outputFile && { output_file: options.outputFile }),
-                    ...(options.outputSize !== undefined && { output_size: options.outputSize })
+                    ...(options.outputSize !== undefined && { output_size: options.outputSize }),
+                    ...(activeTime && { active_time: activeTime }),
+                    ...(userInputCount !== undefined && { user_input_count: userInputCount })
                 };
             }
             // Create enhanced history entry

package/dist/history/enhanced-history-manager.js.map

@@ -1 +1 @@
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