Docs: Refresh docs to organize and standardize reference materials. (#18403)

docs/core/concepts.md

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+# Core concepts
+
+This guide explains the fundamental concepts and terminology used throughout the
+Gemini CLI ecosystem. Understanding these terms will help you make the most of
+the tool's capabilities.
+
+## Approval mode
+
+**Approval mode** determines the level of autonomy you grant to the agent when
+executing tools.
+
+- **Default:** The agent asks for confirmation before performing any potentially
+  impactful action (like writing files or running shell commands).
+- **Auto-edit:** File modifications are applied automatically, but shell
+  commands still require confirmation.
+- **YOLO (You Only Look Once):** The agent runs all tools without asking for
+  permission. High risk, high speed.
+
+## Checkpointing
+
+**Checkpointing** is a safety feature that automatically snapshots your
+project's file state before the agent performs any destructive action (like
+writing a file).
+
+- **Snapshots:** Stored in a hidden Git repository (separate from your project's
+  Git history).
+- **Restore:** Allows you to instantly revert changes if the agent makes a
+  mistake, using the `/restore` command.
+
+## Context
+
+**Context** refers to the information the agent has about your current task and
+environment. Gemini CLI provides context through several mechanisms:
+
+- **Conversation history:** The chat log of the current session.
+- **Project context (`GEMINI.md`):** Persistent instructions and rules defined
+  in your project's root or subdirectories.
+- **File content:** Files you explicitly reference (e.g., `@src/app.ts`) or that
+  the agent reads using tools.
+- **Environment:** Information about your operating system, shell, and working
+  directory.
+
+Effective context management is key to getting accurate and relevant responses.
+
+## Extension
+
+An **Extension** is a pluggable package that adds new capabilities to Gemini
+CLI. Extensions can bundle:
+
+- **Skills:** Specialized procedural knowledge.
+- **MCP Servers:** Connections to external tools and data.
+- **Commands:** Custom slash commands.
+
+## Headless mode
+
+**Headless mode** refers to running Gemini CLI without the interactive terminal
+UI (TUI). This is used for scripting, automation, and piping data into or out of
+the agent.
+
+- **Interactive:** `gemini` (starts the REPL).
+- **Headless:** `gemini "Fix this file"` (runs once and exits).
+
+## Hook
+
+A **Hook** is a script or function that intercepts specific lifecycle events in
+the CLI.
+
+- **Use cases:** Logging tool usage, validating user input, or modifying the
+  agent's system prompt dynamically.
+- **Lifecycle:** Hooks can run before or after the agent starts, before tools
+  are executed, or after the session ends.
+
+## Model Context Protocol (MCP)
+
+The **Model Context Protocol (MCP)** is an open standard that allows Gemini CLI
+to connect to external data sources and tools.
+
+- **MCP Server:** A lightweight application that exposes resources (data) and
+  tools (functions) to the CLI.
+- **Use case:** Connecting Gemini to a PostgreSQL database, a GitHub repository,
+  or a Slack workspace without building custom integration logic into the CLI
+  core.
+
+## Policy engine
+
+The **Policy Engine** is the security subsystem that enforces rules on tool
+execution. It evaluates every tool call against your configuration (e.g.,
+[Trusted folders](#trusted-folders), allowed commands) to decide whether to:
+
+- Allow the action immediately.
+- Require user confirmation.
+- Block the action entirely.
+
+## Sandboxing
+
+**Sandboxing** is an optional security mode that isolates the agent's execution
+environment. When enabled, the agent runs inside a secure container (e.g.,
+Docker), preventing it from accessing sensitive files or system resources
+outside of the designated workspace.
+
+## Session
+
+A **Session** is a single continuous interaction thread with the agent.
+
+- **State:** Sessions maintain conversation history and short-term memory.
+- **Persistence:** Sessions are automatically saved, allowing you to pause,
+  resume, or rewind them later.
+
+## Skill
+
+A **Skill** (or **Agent Skill**) is a package of specialized expertise that the
+agent can load on demand. Unlike general context, a skill provides specific
+procedural knowledge for a distinct task.
+
+- **Example:** A "Code Reviewer" skill might contain a checklist of security
+  vulnerabilities to look for and a specific format for reporting findings.
+- **Activation:** Skills are typically activated dynamically when the agent
+  recognizes a matching request.
+
+## Tool
+
+A **Tool** is a specific function or capability that the agent can execute.
+Tools allow the AI to interact with the outside world.
+
+- **Built-in tools:** Core capabilities like `read_file`, `run_shell_command`,
+  and `google_web_search`.
+- **MCP tools:** External tools provided by
+  [MCP servers](#model-context-protocol-mcp).
+
+When the agent uses a tool, it pauses generation, executes the code, and feeds
+the output back into its context window.
+
+## Trusted folders
+
+**Trusted folders** are specific directories you have explicitly authorized the
+agent to access without repeated confirmation prompts. This is a key component
+of the [Policy engine](#policy-engine) to balance security and usability.