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docs: update and reorganize documentation (#806)

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docs/tools/index.md
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@@ -43,7 +43,9 @@ The built-in tools can be broadly categorized as follows:
- **[File System Tools](./file-system.md):** For interacting with files and directories (reading, writing, listing, searching, etc.).
- **[Shell Tool](./shell.md):** For executing shell commands.
- **[Web Fetch Tool](./web.md):** For retrieving content from URLs.
- **[Web Fetch Tool](./web-fetch.md):** For retrieving content from URLs.
- **[Web Search Tool](./web-search.md):** For searching the web.
- **[Multi-File Read Tool](./multi-file.md):** A specialized tool for reading content from multiple files or directories, often used by the `@` command.
- **[Memory Tool](./memory.md):** For saving and recalling information across sessions.
Understanding the available tools and how they work will help you make the most effective use of the Gemini CLI.