@machina.ai/cell-cli-core 1.6.1-rc2 → 1.10.0-rc1

package/dist/src/core/prompts.d.ts

@@ -3,12 +3,13 @@
  * Copyright 2025 Google LLC
  * SPDX-License-Identifier: Apache-2.0
  */
+import type { Config } from '../config/config.js';
 export declare function resolvePathFromEnv(envVar?: string): {
     isSwitch: boolean;
     value: string | null;
     isDisabled: boolean;
 };
-export declare function getCoreSystemPrompt(userMemory?: string): string;
+export declare function getCoreSystemPrompt(config: Config, userMemory?: string): string;
 /**
  * Provides the system prompt for the history compression process.
  * This prompt instructs the model to act as a specialized state manager,

package/dist/src/core/prompts.js

@@ -6,17 +6,18 @@
 import path from 'node:path';
 import fs from 'node:fs';
 import os from 'node:os';
-import { LSTool } from '../tools/ls.js';
 import { EditTool } from '../tools/edit.js';
 import { GlobTool } from '../tools/glob.js';
 import { GrepTool } from '../tools/grep.js';
 import { ReadFileTool } from '../tools/read-file.js';
 import { ReadManyFilesTool } from '../tools/read-many-files.js';
 import { ShellTool } from '../tools/shell.js';
-import { WriteFileTool } from '../tools/write-file.js';
+import { WRITE_FILE_TOOL_NAME } from '../tools/tool-names.js';
 import process from 'node:process';
 import { isGitRepository } from '../utils/gitUtils.js';
-import { MemoryTool, CELL_CONFIG_DIR } from '../tools/memoryTool.js';
+import { MemoryTool } from '../tools/memoryTool.js';
+import { CodebaseInvestigatorAgent } from '../agents/codebase-investigator.js';
+import { CELL_DIR } from '../utils/paths.js';
 export function resolvePathFromEnv(envVar) {
     // Handle the case where the environment variable is not set, empty, or just whitespace.
     const trimmedEnvVar = envVar?.trim();
@@ -57,11 +58,11 @@ export function resolvePathFromEnv(envVar) {
         isDisabled: false,
     };
 }
-export function getCoreSystemPrompt(userMemory) {
+export function getCoreSystemPrompt(config, userMemory) {
     // A flag to indicate whether the system prompt override is active.
     let systemMdEnabled = false;
     // The default path for the system prompt file. This can be overridden.
-    let systemMdPath = path.resolve(path.join(CELL_CONFIG_DIR, 'system.md'));
+    let systemMdPath = path.resolve(path.join(CELL_DIR, 'system.md'));
     // Resolve the environment variable to get either a path or a switch value.
     const systemMdResolution = resolvePathFromEnv(process.env['CELL_SYSTEM_MD']);
     // Proceed only if the environment variable is set and is not disabled.
@@ -76,10 +77,13 @@ export function getCoreSystemPrompt(userMemory) {
             throw new Error(`missing system prompt file '${systemMdPath}'`);
         }
     }
+    const enableCodebaseInvestigator = config
+        .getToolRegistry()
+        .getAllToolNames()
+        .includes(CodebaseInvestigatorAgent.name);
     const basePrompt = systemMdEnabled
         ? fs.readFileSync(systemMdPath, 'utf8')
-        : `
-You are an interactive CLI agent specializing in software engineering tasks. Your primary goal is to help users safely and efficiently, adhering strictly to the following instructions and utilizing your available tools.
+        : `You are an interactive CLI agent specializing in software engineering tasks. Your primary goal is to help users safely and efficiently, adhering strictly to the following instructions and utilizing your available tools.
 
 # Core Mandates
 
@@ -88,25 +92,35 @@ You are an interactive CLI agent specializing in software engineering tasks. You
 - **Style & Structure:** Mimic the style (formatting, naming), structure, framework choices, typing, and architectural patterns of existing code in the project.
 - **Idiomatic Changes:** When editing, understand the local context (imports, functions/classes) to ensure your changes integrate naturally and idiomatically.
 - **Comments:** Add code comments sparingly. Focus on *why* something is done, especially for complex logic, rather than *what* is done. Only add high-value comments if necessary for clarity or if requested by the user. Do not edit comments that are separate from the code you are changing. *NEVER* talk to the user or describe your changes through comments.
-- **Proactiveness:** Fulfill the user's request thoroughly, including reasonable, directly implied follow-up actions.
+- **Proactiveness:** Fulfill the user's request thoroughly. When adding features or fixing bugs, this includes adding tests to ensure quality. Consider all created files, especially tests, to be permanent artifacts unless the user says otherwise.
 - **Confirm Ambiguity/Expansion:** Do not take significant actions beyond the clear scope of the request without confirming with the user. If asked *how* to do something, explain first, don't just do it.
 - **Explaining Changes:** After completing a code modification or file operation *do not* provide summaries unless asked.
-- **Path Construction:** Before using any file system tool (e.g., ${ReadFileTool.Name}' or '${WriteFileTool.Name}'), you must construct the full absolute path for the file_path argument. Always combine the absolute path of the project's root directory with the file's path relative to the root. For example, if the project root is /path/to/project/ and the file is foo/bar/baz.txt, the final path you must use is /path/to/project/foo/bar/baz.txt. If the user provides a relative path, you must resolve it against the root directory to create an absolute path.
+- **Path Construction:** Before using any file system tool (e.g., ${ReadFileTool.Name}' or '${WRITE_FILE_TOOL_NAME}'), you must construct the full absolute path for the file_path argument. Always combine the absolute path of the project's root directory with the file's path relative to the root. For example, if the project root is /path/to/project/ and the file is foo/bar/baz.txt, the final path you must use is /path/to/project/foo/bar/baz.txt. If the user provides a relative path, you must resolve it against the root directory to create an absolute path.
 - **Do Not revert changes:** Do not revert changes to the codebase unless asked to do so by the user. Only revert changes made by you if they have resulted in an error or if the user has explicitly asked you to revert the changes.
 
+
 # Primary Workflows
 
 ## Software Engineering Tasks
 When requested to perform tasks like fixing bugs, adding features, refactoring, or explaining code, follow this sequence:
+${(function () {
+            if (enableCodebaseInvestigator) {
+                return `
+1. **Understand & Strategize:** Think about the user's request and the relevant codebase context. When the task involves **complex refactoring, codebase exploration or system-wide analysis**, your **first and primary tool** must be '${CodebaseInvestigatorAgent.name}'. Use it to build a comprehensive understanding of the code, its structure, and dependencies. For **simple, targeted searches** (like finding a specific function name, file path, or variable declaration), you should use '${GrepTool.Name}' or '${GlobTool.Name}' directly.
+2. **Plan:** Build a coherent and grounded (based on the understanding in step 1) plan for how you intend to resolve the user's task. If '${CodebaseInvestigatorAgent.name}' was used, do not ignore the output of '${CodebaseInvestigatorAgent.name}', you must use it as the foundation of your plan. Share an extremely concise yet clear plan with the user if it would help the user understand your thought process. As part of the plan, you should use an iterative development process that includes writing unit tests to verify your changes. Use output logs or debug statements as part of this process to arrive at a solution.`;
+            }
+            return `
 1. **Understand:** Think about the user's request and the relevant codebase context. Use '${GrepTool.Name}' and '${GlobTool.Name}' search tools extensively (in parallel if independent) to understand file structures, existing code patterns, and conventions. Use '${ReadFileTool.Name}' and '${ReadManyFilesTool.Name}' to understand context and validate any assumptions you may have.
-2. **Plan:** Build a coherent and grounded (based on the understanding in step 1) plan for how you intend to resolve the user's task. Share an extremely concise yet clear plan with the user if it would help the user understand your thought process. As part of the plan, you should try to use a self-verification loop by writing unit tests if relevant to the task. Use output logs or debug statements as part of this self verification loop to arrive at a solution.
-3. **Implement:** Use the available tools (e.g., '${EditTool.Name}', '${WriteFileTool.Name}' '${ShellTool.Name}' ...) to act on the plan, strictly adhering to the project's established conventions (detailed under 'Core Mandates').
+2. **Plan:** Build a coherent and grounded (based on the understanding in step 1) plan for how you intend to resolve the user's task. Share an extremely concise yet clear plan with the user if it would help the user understand your thought process. As part of the plan, you should use an iterative development process that includes writing unit tests to verify your changes. Use output logs or debug statements as part of this process to arrive at a solution.`;
+        })()}
+3. **Implement:** Use the available tools (e.g., '${EditTool.Name}', '${WRITE_FILE_TOOL_NAME}' '${ShellTool.Name}' ...) to act on the plan, strictly adhering to the project's established conventions (detailed under 'Core Mandates').
 4. **Verify (Tests):** If applicable and feasible, verify the changes using the project's testing procedures. Identify the correct test commands and frameworks by examining 'README' files, build/package configuration (e.g., 'package.json'), or existing test execution patterns. NEVER assume standard test commands.
 5. **Verify (Standards):** VERY IMPORTANT: After making code changes, execute the project-specific build, linting and type-checking commands (e.g., 'tsc', 'npm run lint', 'ruff check .') that you have identified for this project (or obtained from the user). This ensures code quality and adherence to standards. If unsure about these commands, you can ask the user if they'd like you to run them and if so how to.
+6. **Finalize:** After all verification passes, consider the task complete. Do not remove or revert any changes or created files (like tests). Await the user's next instruction.
 
 ## New Applications
 
-**Goal:** Autonomously implement and deliver a visually appealing, substantially complete, and functional prototype. Utilize all tools at your disposal to implement the application. Some tools you may especially find useful are '${WriteFileTool.Name}', '${EditTool.Name}' and '${ShellTool.Name}'.
+**Goal:** Autonomously implement and deliver a visually appealing, substantially complete, and functional prototype. Utilize all tools at your disposal to implement the application. Some tools you may especially find useful are '${WRITE_FILE_TOOL_NAME}', '${EditTool.Name}' and '${ShellTool.Name}'.
 
 1. **Understand Requirements:** Analyze the user's request to identify core features, desired user experience (UX), visual aesthetic, application type/platform (web, mobile, desktop, CLI, library, 2D or 3D game), and explicit constraints. If critical information for initial planning is missing or ambiguous, ask concise, targeted clarification questions.
 2. **Propose Plan:** Formulate an internal development plan. Present a clear, concise, high-level summary to the user. This summary must effectively convey the application's type and core purpose, key technologies to be used, main features and how users will interact with them, and the general approach to the visual design and user experience (UX) with the intention of delivering something beautiful, modern, and polished, especially for UI-based applications. For applications requiring visual assets (like games or rich UIs), briefly describe the strategy for sourcing or generating placeholders (e.g., simple geometric shapes, procedurally generated patterns, or open-source assets if feasible and licenses permit) to ensure a visually complete initial prototype. Ensure this information is presented in a structured and easily digestible manner.
@@ -124,6 +138,24 @@ When requested to perform tasks like fixing bugs, adding features, refactoring,
 6. **Solicit Feedback:** If still applicable, provide instructions on how to start the application and request user feedback on the prototype.
 
 # Operational Guidelines
+${(function () {
+            if (config.getEnableShellOutputEfficiency()) {
+                const tempDir = config.storage.getProjectTempDir();
+                return `
+## Shell tool output token efficiency:
+
+IT IS CRITICAL TO FOLLOW THESE GUIDELINES TO AVOID EXCESSIVE TOKEN CONSUMPTION.
+
+- Always prefer command flags that reduce output verbosity when using '${ShellTool.Name}'.
+- Aim to minimize tool output tokens while still capturing necessary information.
+- If a command is expected to produce a lot of output, use quiet or silent flags where available and appropriate.
+- Always consider the trade-off between output verbosity and the need for information. If a command's full output is essential for understanding the result, avoid overly aggressive quieting that might obscure important details.
+- If a command does not have quiet/silent flags or for commands with potentially long output that may not be useful, redirect stdout and stderr to temp files in the project's temporary directory: ${tempDir}. For example: 'command > ${path.posix.join(tempDir, 'out.log')} 2> ${path.posix.join(tempDir, 'err.log')}'.
+- After the command runs, inspect the temp files (e.g. '${path.posix.join(tempDir, 'out.log')}' and '${path.posix.join(tempDir, 'err.log')}') using commands like 'grep', 'tail', 'head', ... (or platform equivalents). Remove the temp files when done.
+`;
+            }
+            return '';
+        })()}
 
 ## Tone and Style (CLI Interaction)
 - **Concise & Direct:** Adopt a professional, direct, and concise tone suitable for a CLI environment.
@@ -140,11 +172,18 @@ When requested to perform tasks like fixing bugs, adding features, refactoring,
 - **Security First:** Always apply security best practices. Never introduce code that exposes, logs, or commits secrets, API keys, or other sensitive information.
 
 ## Tool Usage
-- **File Paths:** Always use absolute paths when referring to files with tools like '${ReadFileTool.Name}' or '${WriteFileTool.Name}'. Relative paths are not supported. You must provide an absolute path.
+- **File Paths:** Always use absolute paths when referring to files with tools like '${ReadFileTool.Name}' or '${WRITE_FILE_TOOL_NAME}'. Relative paths are not supported. You must provide an absolute path.
 - **Parallelism:** Execute multiple independent tool calls in parallel when feasible (i.e. searching the codebase).
 - **Command Execution:** Use the '${ShellTool.Name}' tool for running shell commands, remembering the safety rule to explain modifying commands first.
 - **Background Processes:** Use background processes (via \`&\`) for commands that are unlikely to stop on their own, e.g. \`node server.js &\`. If unsure, ask the user.
-- **Interactive Commands:** Try to avoid shell commands that are likely to require user interaction (e.g. \`git rebase -i\`). Use non-interactive versions of commands (e.g. \`npm init -y\` instead of \`npm init\`) when available, and otherwise remind the user that interactive shell commands are not supported and may cause hangs until canceled by the user.
+${(function () {
+            if (!config.isInteractiveShellEnabled()) {
+                return `- **Interactive Commands:** Some commands are interactive, meaning they can accept user input during their execution (e.g. ssh, vim). Only execute non-interactive commands. Use non-interactive versions of commands (e.g. \`npm init -y\` instead of \`npm init\`) when available. Interactive shell commands are not supported and may cause hangs until canceled by the user.`;
+            }
+            else {
+                return `- **Interactive Commands:** Prefer non-interactive commands when it makes sense; however, some commands are only interactive and expect user input during their execution (e.g. ssh, vim). If you choose to execute an interactive command consider letting the user know they can press \`ctrl + f\` to focus into the shell to provide input.`;
+            }
+        })()}
 - **Remembering Facts:** Use the '${MemoryTool.Name}' tool to remember specific, *user-related* facts or preferences when the user explicitly asks, or when they state a clear, concise piece of information that would help personalize or streamline *your future interactions with them* (e.g., preferred coding style, common project paths they use, personal tool aliases). This tool is for user-specific information that should persist across sessions. Do *not* use it for general project context or information. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
 - **Respect User Confirmations:** Most tool calls (also denoted as 'function calls') will first require confirmation from the user, where they will either approve or cancel the function call. If a user cancels a function call, respect their choice and do _not_ try to make the function call again. It is okay to request the tool call again _only_ if the user requests that same tool call on a subsequent prompt. When a user cancels a function call, assume best intentions from the user and consider inquiring if they prefer any alternative paths forward.
 
@@ -198,103 +237,6 @@ ${(function () {
             return '';
         })()}
 
-# Examples (Illustrating Tone and Workflow)
-<example>
-user: 1 + 2
-model: 3
-</example>
-
-<example>
-user: is 13 a prime number?
-model: true
-</example>
-
-<example>
-user: list files here.
-model: [tool_call: ${LSTool.Name} for path '/path/to/project']
-</example>
-
-<example>
-user: start the server implemented in server.js
-model: [tool_call: ${ShellTool.Name} for 'node server.js &' because it must run in the background]
-</example>
-
-<example>
-user: Refactor the auth logic in src/auth.py to use the requests library instead of urllib.
-model: Okay, I can refactor 'src/auth.py'.
-First, I'll analyze the code and check for a test safety net before planning any changes.
-[tool_call: ${GlobTool.Name} for path 'tests/test_auth.py']
-[tool_call: ${ReadFileTool.Name} for absolute_path '/path/to/tests/test_auth.py']
-(After analysis)
-Great, 'tests/test_auth.py' exists and covers the core authentication logic. With this safety net in place, I can safely plan the refactoring.
-I'll also confirm 'requests' is a dependency.
-[tool_call: ${ReadFileTool.Name} for absolute_path '/path/to/requirements.txt']
-(After analysis)
-Looks good, 'requests' is available.
-
-Here's the plan:
-1.  Replace the 'urllib' calls with 'requests'.
-2.  Add proper 'try...except' error handling for the new network calls.
-3.  Remove the old 'urllib' import.
-4.  Run the project's linter and tests to verify the changes.
-
-Should I proceed?
-user: Yes
-model:
-[tool_call: ${WriteFileTool.Name} or ${EditTool.Name} to apply the refactoring to 'src/auth.py']
-Refactoring complete. Running verification...
-[tool_call: ${ShellTool.Name} for 'ruff check src/auth.py && pytest']
-(After verification passes)
-All checks passed. This is a stable checkpoint.
-${(function () {
-            if (isGitRepository(process.cwd())) {
-                return `Would you like me to write a commit message and commit these changes?`;
-            }
-            return '';
-        })()}
-</example>
-
-<example>
-user: Delete the temp directory.
-model: I can run \`rm -rf /path/to/project/temp\`. This will permanently delete the directory and all its contents.
-</example>
-
-<example>
-user: Write tests for someFile.ts
-model:
-Okay, I can write those tests. First, I'll read \`someFile.ts\` to understand its functionality.
-[tool_call: ${ReadFileTool.Name} for absolute_path '/path/to/someFile.ts' or use ${GlobTool.Name} to find \`someFile.ts\` if its location is unknown]
-Now I'll look for existing or related test files to understand current testing conventions and dependencies.
-[tool_call: ${ReadManyFilesTool.Name} for paths ['**/*.test.ts', 'src/**/*.spec.ts'] assuming someFile.ts is in the src directory]
-(After reviewing existing tests and the file content)
-[tool_call: ${WriteFileTool.Name} to create /path/to/someFile.test.ts with the test code]
-I've written the tests. Now I'll run the project's test command to verify them.
-[tool_call: ${ShellTool.Name} for 'npm run test']
-</example>
-
-<example>
-user: How do I update the user's profile information in this system?
-model:
-I'm not immediately sure how user profile information is updated. I'll search the codebase for terms like 'UserProfile', 'updateProfile', or 'editUser' to find relevant files or API endpoints.
-[tool_call: ${GrepTool.Name} for pattern 'UserProfile|updateProfile|editUser']
-(After reviewing search results, assuming a relevant file like '/path/to/UserProfileService.java' was found)
-Okay, \`/path/to/UserProfileService.java\` seems like the most relevant file. I'll read its content to understand how updates are handled.
-[tool_call: ${ReadFileTool.Name} for absolute_path '/path/to/UserProfileService.java']
-(After reading the file)
-It appears the \`updateUserProfile\` method in \`UserProfileService.java\` is responsible for this. It expects a user ID and a \`UserProfileDTO\` object...
-</example>
-
-<example>
-user: Where are all the 'app.config' files in this project? I need to check their settings.
-model:
-[tool_call: ${GlobTool.Name} for pattern '**/app.config']
-(Assuming GlobTool returns a list of paths like ['/path/to/moduleA/app.config', '/path/to/moduleB/app.config'])
-I found the following 'app.config' files:
-- /path/to/moduleA/app.config
-- /path/to/moduleB/app.config
-To help you check their settings, I can read their contents. Which one would you like to start with, or should I read all of them?
-</example>
-
 # Final Reminder
 Your core function is efficient and safe assistance. Balance extreme conciseness with the crucial need for clarity, especially regarding safety and potential system modifications. Always prioritize user control and project conventions. Never make assumptions about the contents of files; instead use '${ReadFileTool.Name}' or '${ReadManyFilesTool.Name}' to ensure you aren't making broad assumptions. Finally, you are an agent - please keep going until the user's query is completely resolved.
 `.trim();

package/dist/src/core/prompts.js.map

@@ -1 +1 @@
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+{"version":3,"file":"prompts.js","sourceRoot":"","sources":["../../../src/core/prompts.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAC5C,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAC5C,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAC5C,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAC;AACrD,OAAO,EAAE,iBAAiB,EAAE,MAAM,6BAA6B,CAAC;AAChE,OAAO,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAC9C,OAAO,EAAE,oBAAoB,EAAE,MAAM,wBAAwB,CAAC;AAC9D,OAAO,OAAO,MAAM,cAAc,CAAC;AACnC,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAC;AACvD,OAAO,EAAE,UAAU,EAAE,MAAM,wBAAwB,CAAC;AACpD,OAAO,EAAE,yBAAyB,EAAE,MAAM,oCAAoC,CAAC;AAE/E,OAAO,EAAE,QAAQ,EAAE,MAAM,mBAAmB,CAAC;AAE7C,MAAM,UAAU,kBAAkB,CAAC,MAAe;IAKhD,wFAAwF;IACxF,MAAM,aAAa,GAAG,MAAM,EAAE,IAAI,EAAE,CAAC;IACrC,IAAI,CAAC,aAAa,EAAE,CAAC;QACnB,OAAO,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,UAAU,EAAE,KAAK,EAAE,CAAC;IAC7D,CAAC;IAED,MAAM,WAAW,GAAG,aAAa,CAAC,WAAW,EAAE,CAAC;IAChD,sDAAsD;IACtD,IAAI,CAAC,GAAG,EAAE,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE,CAAC;QACtD,yDAAyD;QACzD,MAAM,UAAU,GAAG,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC;QACxD,OAAO,EAAE,QAAQ,EAAE,IAAI,EAAE,KAAK,EAAE,WAAW,EAAE,UAAU,EAAE,CAAC;IAC5D,CAAC;IAED,2DAA2D;IAC3D,IAAI,UAAU,GAAG,aAAa,CAAC;IAE/B,sEAAsE;IACtE,IAAI,UAAU,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,UAAU,KAAK,GAAG,EAAE,CAAC;QACtD,IAAI,CAAC;YACH,MAAM,IAAI,GAAG,EAAE,CAAC,OAAO,EAAE,CAAC,CAAC,4CAA4C;YACvE,IAAI,UAAU,KAAK,GAAG,EAAE,CAAC;gBACvB,UAAU,GAAG,IAAI,CAAC;YACpB,CAAC;iBAAM,CAAC;gBACN,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC;YACpD,CAAC;QACH,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,iEAAiE;YACjE,OAAO,CAAC,IAAI,CACV,8CAA8C,aAAa,EAAE,EAC7D,KAAK,CACN,CAAC;YACF,sDAAsD;YACtD,OAAO,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,UAAU,EAAE,KAAK,EAAE,CAAC;QAC7D,CAAC;IACH,CAAC;IAED,mEAAmE;IACnE,OAAO;QACL,QAAQ,EAAE,KAAK;QACf,KAAK,EAAE,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC;QAC/B,UAAU,EAAE,KAAK;KAClB,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,mBAAmB,CACjC,MAAc,EACd,UAAmB;IAEnB,mEAAmE;IACnE,IAAI,eAAe,GAAG,KAAK,CAAC;IAC5B,uEAAuE;IACvE,IAAI,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,WAAW,CAAC,CAAC,CAAC;IAClE,2EAA2E;IAC3E,MAAM,kBAAkB,GAAG,kBAAkB,CAAC,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,CAAC,CAAC;IAE7E,uEAAuE;IACvE,IAAI,kBAAkB,CAAC,KAAK,IAAI,CAAC,kBAAkB,CAAC,UAAU,EAAE,CAAC;QAC/D,eAAe,GAAG,IAAI,CAAC;QAEvB,kDAAkD;QAClD,IAAI,CAAC,kBAAkB,CAAC,QAAQ,EAAE,CAAC;YACjC,YAAY,GAAG,kBAAkB,CAAC,KAAK,CAAC;QAC1C,CAAC;QAED,iDAAiD;QACjD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;YACjC,MAAM,IAAI,KAAK,CAAC,+BAA+B,YAAY,GAAG,CAAC,CAAC;QAClE,CAAC;IACH,CAAC;IAED,MAAM,0BAA0B,GAAG,MAAM;SACtC,eAAe,EAAE;SACjB,eAAe,EAAE;SACjB,QAAQ,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAC;IAE5C,MAAM,UAAU,GAAG,eAAe;QAChC,CAAC,CAAC,EAAE,CAAC,YAAY,CAAC,YAAY,EAAE,MAAM,CAAC;QACvC,CAAC,CAAC;;;;;;;;;;;;oEAY8D,YAAY,CAAC,IAAI,SAAS,oBAAoB;;;;;;;;EAQhH,CAAC;YACD,IAAI,0BAA0B,EAAE,CAAC;gBAC/B,OAAO;2OACgO,yBAAyB,CAAC,IAAI,iOAAiO,QAAQ,CAAC,IAAI,SAAS,QAAQ,CAAC,IAAI;4IACjY,yBAAyB,CAAC,IAAI,4CAA4C,yBAAyB,CAAC,IAAI,0XAA0X,CAAC;YAC7mB,CAAC;YACD,OAAO;4FACmF,QAAQ,CAAC,IAAI,UAAU,QAAQ,CAAC,IAAI,wIAAwI,YAAY,CAAC,IAAI,UAAU,iBAAiB,CAAC,IAAI;4cACmJ,CAAC;QAC7c,CAAC,CAAC,EAAE;oDACgD,QAAQ,CAAC,IAAI,OAAO,oBAAoB,MAAM,SAAS,CAAC,IAAI;;;;;;;uOAOuH,oBAAoB,OAAO,QAAQ,CAAC,IAAI,UAAU,SAAS,CAAC,IAAI;;;;;;;;;;;;;8LAazG,SAAS,CAAC,IAAI;;;;;EAK1M,CAAC;YACD,IAAI,MAAM,CAAC,8BAA8B,EAAE,EAAE,CAAC;gBAC5C,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,iBAAiB,EAAE,CAAC;gBACnD,OAAO;;;;;yEAK8D,SAAS,CAAC,IAAI;;;;sMAI+G,OAAO,6BAA6B,IAAI,CAAC,KAAK,CAAC,IAAI,CACnP,OAAO,EACP,SAAS,CACV,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,OAAO,EAAE,SAAS,CAAC;0DACW,IAAI,CAAC,KAAK,CAAC,IAAI,CACnE,OAAO,EACP,SAAS,CACV,UAAU,IAAI,CAAC,KAAK,CAAC,IAAI,CACxB,OAAO,EACP,SAAS,CACV;CACJ,CAAC;YACA,CAAC;YACD,OAAO,EAAE,CAAC;QACZ,CAAC,CAAC,EAAE;;;;;;;;;;;;;mEAa+D,SAAS,CAAC,IAAI;;;;uFAIM,YAAY,CAAC,IAAI,SAAS,oBAAoB;;oCAEjG,SAAS,CAAC,IAAI;;EAEhD,CAAC;YACD,IAAI,CAAC,MAAM,CAAC,yBAAyB,EAAE,EAAE,CAAC;gBACxC,OAAO,mXAAmX,CAAC;YAC7X,CAAC;iBAAM,CAAC;gBACN,OAAO,iVAAiV,CAAC;YAC3V,CAAC;QACH,CAAC,CAAC,EAAE;oCACgC,UAAU,CAAC,IAAI;;;;;;;EAOjD,CAAC;YACD,0DAA0D;YAC1D,MAAM,aAAa,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,KAAK,cAAc,CAAC;YAChE,MAAM,gBAAgB,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,iDAAiD;YAEpG,IAAI,aAAa,EAAE,CAAC;gBAClB,OAAO;;;CAGV,CAAC;YACA,CAAC;iBAAM,IAAI,gBAAgB,EAAE,CAAC;gBAC5B,OAAO;;;CAGV,CAAC;YACA,CAAC;iBAAM,CAAC;gBACN,OAAO;;;CAGV,CAAC;YACA,CAAC;QACH,CAAC,CAAC,EAAE;;EAEF,CAAC;YACD,IAAI,eAAe,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,EAAE,CAAC;gBACnC,OAAO;;;;;;;;;;;;;;;CAeV,CAAC;YACA,CAAC;YACD,OAAO,EAAE,CAAC;QACZ,CAAC,CAAC,EAAE;;;+SAG2S,YAAY,CAAC,IAAI,SAAS,iBAAiB,CAAC,IAAI;CAC9V,CAAC,IAAI,EAAE,CAAC;IAEP,qFAAqF;IACrF,MAAM,uBAAuB,GAAG,kBAAkB,CAChD,OAAO,CAAC,GAAG,CAAC,sBAAsB,CAAC,CACpC,CAAC;IAEF,yEAAyE;IACzE,wDAAwD;IACxD,IAAI,uBAAuB,CAAC,KAAK,IAAI,CAAC,uBAAuB,CAAC,UAAU,EAAE,CAAC;QACzE,MAAM,SAAS,GAAG,uBAAuB,CAAC,QAAQ;YAChD,CAAC,CAAC,YAAY;YACd,CAAC,CAAC,uBAAuB,CAAC,KAAK,CAAC;QAElC,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,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package/dist/src/core/prompts.test.js

@@ -9,7 +9,8 @@ import { isGitRepository } from '../utils/gitUtils.js';
 import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
-import { CELL_CONFIG_DIR } from '../tools/memoryTool.js';
+import { CodebaseInvestigatorAgent } from '../agents/codebase-investigator.js';
+import { CELL_DIR } from '../utils/paths.js';
 // Mock tool names if they are dynamically generated or complex
 vi.mock('../tools/ls', () => ({ LSTool: { Name: 'list_directory' } }));
 vi.mock('../tools/edit', () => ({ EditTool: { Name: 'replace' } }));
@@ -25,33 +26,48 @@ vi.mock('../tools/shell', () => ({
 vi.mock('../tools/write-file', () => ({
     WriteFileTool: { Name: 'write_file' },
 }));
+vi.mock('../agents/codebase-investigator.js', () => ({
+    CodebaseInvestigatorAgent: { name: 'codebase_investigator' },
+}));
 vi.mock('../utils/gitUtils', () => ({
     isGitRepository: vi.fn(),
 }));
 vi.mock('node:fs');
 describe('Core System Prompt (prompts.ts)', () => {
+    let mockConfig;
     beforeEach(() => {
         vi.resetAllMocks();
         vi.stubEnv('CELL_SYSTEM_MD', undefined);
         vi.stubEnv('CELL_WRITE_SYSTEM_MD', undefined);
+        mockConfig = {
+            getToolRegistry: vi.fn().mockReturnValue({
+                getAllToolNames: vi.fn().mockReturnValue([]),
+            }),
+            getEnableShellOutputEfficiency: vi.fn().mockReturnValue(true),
+            storage: {
+                getProjectTempDir: vi.fn().mockReturnValue('/tmp/project-temp'),
+            },
+            isInteractive: vi.fn().mockReturnValue(true),
+            isInteractiveShellEnabled: vi.fn().mockReturnValue(true),
+        };
     });
     it('should return the base prompt when no userMemory is provided', () => {
         vi.stubEnv('SANDBOX', undefined);
-        const prompt = getCoreSystemPrompt();
+        const prompt = getCoreSystemPrompt(mockConfig, '');
         expect(prompt).not.toContain('---\n\n'); // Separator should not be present
         expect(prompt).toContain('You are an interactive CLI agent'); // Check for core content
         expect(prompt).toMatchSnapshot(); // Use snapshot for base prompt structure
     });
     it('should return the base prompt when userMemory is empty string', () => {
         vi.stubEnv('SANDBOX', undefined);
-        const prompt = getCoreSystemPrompt('');
+        const prompt = getCoreSystemPrompt(mockConfig, '');
         expect(prompt).not.toContain('---\n\n');
         expect(prompt).toContain('You are an interactive CLI agent');
         expect(prompt).toMatchSnapshot();
     });
     it('should return the base prompt when userMemory is whitespace only', () => {
         vi.stubEnv('SANDBOX', undefined);
-        const prompt = getCoreSystemPrompt('   \n  \t ');
+        const prompt = getCoreSystemPrompt(mockConfig, '   \n  \t ');
         expect(prompt).not.toContain('---\n\n');
         expect(prompt).toContain('You are an interactive CLI agent');
         expect(prompt).toMatchSnapshot();
@@ -60,14 +76,14 @@ describe('Core System Prompt (prompts.ts)', () => {
         vi.stubEnv('SANDBOX', undefined);
         const memory = 'This is custom user memory.\nBe extra polite.';
         const expectedSuffix = `\n\n---\n\n${memory}`;
-        const prompt = getCoreSystemPrompt(memory);
+        const prompt = getCoreSystemPrompt(mockConfig, memory);
         expect(prompt.endsWith(expectedSuffix)).toBe(true);
         expect(prompt).toContain('You are an interactive CLI agent'); // Ensure base prompt follows
         expect(prompt).toMatchSnapshot(); // Snapshot the combined prompt
     });
     it('should include sandbox-specific instructions when SANDBOX env var is set', () => {
         vi.stubEnv('SANDBOX', 'true'); // Generic sandbox value
-        const prompt = getCoreSystemPrompt();
+        const prompt = getCoreSystemPrompt(mockConfig);
         expect(prompt).toContain('# Sandbox');
         expect(prompt).not.toContain('# macOS Seatbelt');
         expect(prompt).not.toContain('# Outside of Sandbox');
@@ -75,15 +91,15 @@ describe('Core System Prompt (prompts.ts)', () => {
     });
     it('should include seatbelt-specific instructions when SANDBOX env var is "sandbox-exec"', () => {
         vi.stubEnv('SANDBOX', 'sandbox-exec');
-        const prompt = getCoreSystemPrompt();
+        const prompt = getCoreSystemPrompt(mockConfig);
         expect(prompt).toContain('# macOS Seatbelt');
         expect(prompt).not.toContain('# Sandbox');
         expect(prompt).not.toContain('# Outside of Sandbox');
         expect(prompt).toMatchSnapshot();
     });
     it('should include non-sandbox instructions when SANDBOX env var is not set', () => {
-        vi.stubEnv('SANDBOX', undefined); // Ensure it's not set
-        const prompt = getCoreSystemPrompt();
+        vi.stubEnv('SANDBOX', undefined); // Ensure it\'s not set
+        const prompt = getCoreSystemPrompt(mockConfig);
         expect(prompt).toContain('# Outside of Sandbox');
         expect(prompt).not.toContain('# Sandbox');
         expect(prompt).not.toContain('# macOS Seatbelt');
@@ -92,27 +108,65 @@ describe('Core System Prompt (prompts.ts)', () => {
     it('should include git instructions when in a git repo', () => {
         vi.stubEnv('SANDBOX', undefined);
         vi.mocked(isGitRepository).mockReturnValue(true);
-        const prompt = getCoreSystemPrompt();
+        const prompt = getCoreSystemPrompt(mockConfig);
         expect(prompt).toContain('# Git Repository');
         expect(prompt).toMatchSnapshot();
     });
     it('should not include git instructions when not in a git repo', () => {
         vi.stubEnv('SANDBOX', undefined);
         vi.mocked(isGitRepository).mockReturnValue(false);
-        const prompt = getCoreSystemPrompt();
+        const prompt = getCoreSystemPrompt(mockConfig);
         expect(prompt).not.toContain('# Git Repository');
         expect(prompt).toMatchSnapshot();
     });
+    it('should return the interactive avoidance prompt when in non-interactive mode', () => {
+        vi.stubEnv('SANDBOX', undefined);
+        mockConfig.isInteractive = vi.fn().mockReturnValue(false);
+        const prompt = getCoreSystemPrompt(mockConfig, '');
+        expect(prompt).toContain('**Interactive Commands:**'); // Check for interactive prompt
+        expect(prompt).toMatchSnapshot(); // Use snapshot for base prompt structure
+    });
+    describe('with CodebaseInvestigator enabled', () => {
+        beforeEach(() => {
+            mockConfig = {
+                getToolRegistry: vi.fn().mockReturnValue({
+                    getAllToolNames: vi
+                        .fn()
+                        .mockReturnValue([CodebaseInvestigatorAgent.name]),
+                }),
+                getEnableShellOutputEfficiency: vi.fn().mockReturnValue(true),
+                storage: {
+                    getProjectTempDir: vi.fn().mockReturnValue('/tmp/project-temp'),
+                },
+                isInteractive: vi.fn().mockReturnValue(false),
+                isInteractiveShellEnabled: vi.fn().mockReturnValue(false),
+            };
+        });
+        it('should include CodebaseInvestigator instructions in the prompt', () => {
+            const prompt = getCoreSystemPrompt(mockConfig);
+            expect(prompt).toContain(`your **first and primary tool** must be '${CodebaseInvestigatorAgent.name}'`);
+            expect(prompt).toContain(`do not ignore the output of '${CodebaseInvestigatorAgent.name}'`);
+            expect(prompt).not.toContain("Use 'search_file_content' and 'glob' search tools extensively");
+        });
+    });
+    describe('with CodebaseInvestigator disabled', () => {
+        // No beforeEach needed, will use the default from the parent describe
+        it('should include standard tool instructions in the prompt', () => {
+            const prompt = getCoreSystemPrompt(mockConfig);
+            expect(prompt).not.toContain(`your **first and primary tool** must be '${CodebaseInvestigatorAgent.name}'`);
+            expect(prompt).toContain("Use 'search_file_content' and 'glob' search tools extensively");
+        });
+    });
     describe('CELL_SYSTEM_MD environment variable', () => {
         it('should use default prompt when CELL_SYSTEM_MD is "false"', () => {
             vi.stubEnv('CELL_SYSTEM_MD', 'false');
-            const prompt = getCoreSystemPrompt();
+            const prompt = getCoreSystemPrompt(mockConfig);
             expect(fs.readFileSync).not.toHaveBeenCalled();
             expect(prompt).not.toContain('custom system prompt');
         });
         it('should use default prompt when CELL_SYSTEM_MD is "0"', () => {
             vi.stubEnv('CELL_SYSTEM_MD', '0');
-            const prompt = getCoreSystemPrompt();
+            const prompt = getCoreSystemPrompt(mockConfig);
             expect(fs.readFileSync).not.toHaveBeenCalled();
             expect(prompt).not.toContain('custom system prompt');
         });
@@ -120,23 +174,23 @@ describe('Core System Prompt (prompts.ts)', () => {
             const customPath = '/non/existent/path/system.md';
             vi.stubEnv('CELL_SYSTEM_MD', customPath);
             vi.mocked(fs.existsSync).mockReturnValue(false);
-            expect(() => getCoreSystemPrompt()).toThrow(`missing system prompt file '${path.resolve(customPath)}'`);
+            expect(() => getCoreSystemPrompt(mockConfig)).toThrow(`missing system prompt file '${path.resolve(customPath)}'`);
         });
         it('should read from default path when CELL_SYSTEM_MD is "true"', () => {
-            const defaultPath = path.resolve(path.join(CELL_CONFIG_DIR, 'system.md'));
+            const defaultPath = path.resolve(path.join(CELL_DIR, 'system.md'));
             vi.stubEnv('CELL_SYSTEM_MD', 'true');
             vi.mocked(fs.existsSync).mockReturnValue(true);
             vi.mocked(fs.readFileSync).mockReturnValue('custom system prompt');
-            const prompt = getCoreSystemPrompt();
+            const prompt = getCoreSystemPrompt(mockConfig);
             expect(fs.readFileSync).toHaveBeenCalledWith(defaultPath, 'utf8');
             expect(prompt).toBe('custom system prompt');
         });
         it('should read from default path when CELL_SYSTEM_MD is "1"', () => {
-            const defaultPath = path.resolve(path.join(CELL_CONFIG_DIR, 'system.md'));
+            const defaultPath = path.resolve(path.join(CELL_DIR, 'system.md'));
             vi.stubEnv('CELL_SYSTEM_MD', '1');
             vi.mocked(fs.existsSync).mockReturnValue(true);
             vi.mocked(fs.readFileSync).mockReturnValue('custom system prompt');
-            const prompt = getCoreSystemPrompt();
+            const prompt = getCoreSystemPrompt(mockConfig);
             expect(fs.readFileSync).toHaveBeenCalledWith(defaultPath, 'utf8');
             expect(prompt).toBe('custom system prompt');
         });
@@ -145,7 +199,7 @@ describe('Core System Prompt (prompts.ts)', () => {
             vi.stubEnv('CELL_SYSTEM_MD', customPath);
             vi.mocked(fs.existsSync).mockReturnValue(true);
             vi.mocked(fs.readFileSync).mockReturnValue('custom system prompt');
-            const prompt = getCoreSystemPrompt();
+            const prompt = getCoreSystemPrompt(mockConfig);
             expect(fs.readFileSync).toHaveBeenCalledWith(customPath, 'utf8');
             expect(prompt).toBe('custom system prompt');
         });
@@ -157,7 +211,7 @@ describe('Core System Prompt (prompts.ts)', () => {
             vi.stubEnv('CELL_SYSTEM_MD', customPath);
             vi.mocked(fs.existsSync).mockReturnValue(true);
             vi.mocked(fs.readFileSync).mockReturnValue('custom system prompt');
-            const prompt = getCoreSystemPrompt();
+            const prompt = getCoreSystemPrompt(mockConfig);
             expect(fs.readFileSync).toHaveBeenCalledWith(path.resolve(expectedPath), 'utf8');
             expect(prompt).toBe('custom system prompt');
         });
@@ -165,30 +219,30 @@ describe('Core System Prompt (prompts.ts)', () => {
     describe('CELL_WRITE_SYSTEM_MD environment variable', () => {
         it('should not write to file when CELL_WRITE_SYSTEM_MD is "false"', () => {
             vi.stubEnv('CELL_WRITE_SYSTEM_MD', 'false');
-            getCoreSystemPrompt();
+            getCoreSystemPrompt(mockConfig);
             expect(fs.writeFileSync).not.toHaveBeenCalled();
         });
         it('should not write to file when CELL_WRITE_SYSTEM_MD is "0"', () => {
             vi.stubEnv('CELL_WRITE_SYSTEM_MD', '0');
-            getCoreSystemPrompt();
+            getCoreSystemPrompt(mockConfig);
             expect(fs.writeFileSync).not.toHaveBeenCalled();
         });
         it('should write to default path when CELL_WRITE_SYSTEM_MD is "true"', () => {
-            const defaultPath = path.resolve(path.join(CELL_CONFIG_DIR, 'system.md'));
+            const defaultPath = path.resolve(path.join(CELL_DIR, 'system.md'));
             vi.stubEnv('CELL_WRITE_SYSTEM_MD', 'true');
-            getCoreSystemPrompt();
+            getCoreSystemPrompt(mockConfig);
             expect(fs.writeFileSync).toHaveBeenCalledWith(defaultPath, expect.any(String));
         });
         it('should write to default path when CELL_WRITE_SYSTEM_MD is "1"', () => {
-            const defaultPath = path.resolve(path.join(CELL_CONFIG_DIR, 'system.md'));
+            const defaultPath = path.resolve(path.join(CELL_DIR, 'system.md'));
             vi.stubEnv('CELL_WRITE_SYSTEM_MD', '1');
-            getCoreSystemPrompt();
+            getCoreSystemPrompt(mockConfig);
             expect(fs.writeFileSync).toHaveBeenCalledWith(defaultPath, expect.any(String));
         });
         it('should write to custom path when CELL_WRITE_SYSTEM_MD provides one', () => {
             const customPath = path.resolve('/custom/path/system.md');
             vi.stubEnv('CELL_WRITE_SYSTEM_MD', customPath);
-            getCoreSystemPrompt();
+            getCoreSystemPrompt(mockConfig);
             expect(fs.writeFileSync).toHaveBeenCalledWith(customPath, expect.any(String));
         });
         it('should expand tilde in custom path when CELL_WRITE_SYSTEM_MD is set', () => {
@@ -197,7 +251,7 @@ describe('Core System Prompt (prompts.ts)', () => {
             const customPath = '~/custom/system.md';
             const expectedPath = path.join(homeDir, 'custom/system.md');
             vi.stubEnv('CELL_WRITE_SYSTEM_MD', customPath);
-            getCoreSystemPrompt();
+            getCoreSystemPrompt(mockConfig);
             expect(fs.writeFileSync).toHaveBeenCalledWith(path.resolve(expectedPath), expect.any(String));
         });
         it('should expand tilde in custom path when CELL_WRITE_SYSTEM_MD is just ~', () => {
@@ -206,7 +260,7 @@ describe('Core System Prompt (prompts.ts)', () => {
             const customPath = '~';
             const expectedPath = homeDir;
             vi.stubEnv('CELL_WRITE_SYSTEM_MD', customPath);
-            getCoreSystemPrompt();
+            getCoreSystemPrompt(mockConfig);
             expect(fs.writeFileSync).toHaveBeenCalledWith(path.resolve(expectedPath), expect.any(String));
         });
     });