ability to override core system prompt (via .gemini/system.md) and specify core tools via coreTools setting (e.g. coreTools:["ls", "GrepTool", ...]) ; added tests, but did not update docs for now (#413)

2 files changed, 16 insertions, 10 deletions

diff --git a/packages/server/src/core/__snapshots__/prompts.test.ts.snap b/packages/server/src/core/__snapshots__/prompts.test.ts.snap
index b824d4f7..066bade7 100644
--- a/packages/server/src/core/__snapshots__/prompts.test.ts.snap
+++ b/packages/server/src/core/__snapshots__/prompts.test.ts.snap
@@ -65,7 +65,7 @@ Rigorously adhere to existing project conventions when reading or modifying code
 -   **Command Execution:** Use the 'execute_bash_command' 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 cancelled by the user.
--   **Remembering Facts:** Use the 'saveMemory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
+-   **Remembering Facts:** Use the 'save_memory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
 
 ## Interaction Details
 -   **Help Command:** The user can use '/help' to display help information.
@@ -219,7 +219,7 @@ Rigorously adhere to existing project conventions when reading or modifying code
 -   **Command Execution:** Use the 'execute_bash_command' 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 cancelled by the user.
--   **Remembering Facts:** Use the 'saveMemory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
+-   **Remembering Facts:** Use the 'save_memory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
 
 ## Interaction Details
 -   **Help Command:** The user can use '/help' to display help information.
@@ -368,7 +368,7 @@ Rigorously adhere to existing project conventions when reading or modifying code
 -   **Command Execution:** Use the 'execute_bash_command' 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 cancelled by the user.
--   **Remembering Facts:** Use the 'saveMemory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
+-   **Remembering Facts:** Use the 'save_memory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
 
 ## Interaction Details
 -   **Help Command:** The user can use '/help' to display help information.
@@ -517,7 +517,7 @@ Rigorously adhere to existing project conventions when reading or modifying code
 -   **Command Execution:** Use the 'execute_bash_command' 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 cancelled by the user.
--   **Remembering Facts:** Use the 'saveMemory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
+-   **Remembering Facts:** Use the 'save_memory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
 
 ## Interaction Details
 -   **Help Command:** The user can use '/help' to display help information.
@@ -666,7 +666,7 @@ Rigorously adhere to existing project conventions when reading or modifying code
 -   **Command Execution:** Use the 'execute_bash_command' 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 cancelled by the user.
--   **Remembering Facts:** Use the 'saveMemory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
+-   **Remembering Facts:** Use the 'save_memory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
 
 ## Interaction Details
 -   **Help Command:** The user can use '/help' to display help information.
@@ -815,7 +815,7 @@ Rigorously adhere to existing project conventions when reading or modifying code
 -   **Command Execution:** Use the 'execute_bash_command' 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 cancelled by the user.
--   **Remembering Facts:** Use the 'saveMemory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
+-   **Remembering Facts:** Use the 'save_memory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
 
 ## Interaction Details
 -   **Help Command:** The user can use '/help' to display help information.
@@ -964,7 +964,7 @@ Rigorously adhere to existing project conventions when reading or modifying code
 -   **Command Execution:** Use the 'execute_bash_command' 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 cancelled by the user.
--   **Remembering Facts:** Use the 'saveMemory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
+-   **Remembering Facts:** Use the 'save_memory' 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 that belongs in project-specific \`GEMINI.md\` files. If unsure whether to save something, you can ask the user, "Should I remember that for you?"
 
 ## Interaction Details
 -   **Help Command:** The user can use '/help' to display help information.
diff --git a/packages/server/src/core/prompts.ts b/packages/server/src/core/prompts.ts
index d21c78fe..dabd77a1 100644
--- a/packages/server/src/core/prompts.ts
+++ b/packages/server/src/core/prompts.ts
@@ -4,6 +4,8 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
+import path from 'node:path';
+import fs from 'node:fs';
 import { LSTool } from '../tools/ls.js';
 import { EditTool } from '../tools/edit.js';
 import { GlobTool } from '../tools/glob.js';
@@ -12,14 +14,18 @@ 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 process from 'node:process'; // Import process
+import process from 'node:process';
 import { execSync } from 'node:child_process';
-import { MemoryTool } from '../tools/memoryTool.js';
+import { MemoryTool, GEMINI_CONFIG_DIR } from '../tools/memoryTool.js';
 
 const contactEmail = '[email protected]';
 
 export function getCoreSystemPrompt(userMemory?: string): string {
-  const basePrompt = `
+  // replace base prompt with system.md if it exists under GEMINI_CONFIG_DIR
+  const systemMdPath = path.join(GEMINI_CONFIG_DIR, 'system.md');
+  const basePrompt = fs.existsSync(systemMdPath)
+    ? 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.
 
 # Primary Workflows