Update changed links. Delete cli/index as it's an

outdated clone of docs/index.

docs/reference/commands.md

@@ -217,7 +217,7 @@ Slash commands provide meta-level control over the CLI itself.
       model.
   - **Note:** For more details on how `GEMINI.md` files contribute to
     hierarchical memory, see the
-    [CLI Configuration documentation](../get-started/configuration.md).
+    [CLI Configuration documentation](../reference/configuration.md).
 
 ### `/model`
 
@@ -247,7 +247,7 @@ Slash commands provide meta-level control over the CLI itself.
   checkpoints to restore from.
 - **Usage:** `/restore [tool_call_id]`
 - **Note:** Only available if checkpointing is configured via
-  [settings](../get-started/configuration.md). See
+  [settings](../reference/configuration.md). See
   [Checkpointing documentation](../cli/checkpointing.md) for more details.
 
 ### `/rewind`
@@ -286,7 +286,8 @@ Slash commands provide meta-level control over the CLI itself.
   settings that control the behavior and appearance of Gemini CLI. It is
   equivalent to manually editing the `.gemini/settings.json` file, but with
   validation and guidance to prevent errors. See the
-  [settings documentation](./settings.md) for a full list of available settings.
+  [settings documentation](../cli/settings.md) for a full list of available
+  settings.
 - **Usage:** Simply run `/settings` and the editor will open. You can then
   browse or search for specific settings, view their current values, and modify
   them as desired. Changes to some settings are applied immediately, while
@@ -373,7 +374,8 @@ Slash commands provide meta-level control over the CLI itself.
 
 Custom commands allow you to create personalized shortcuts for your most-used
 prompts. For detailed instructions on how to create, manage, and use them,
-please see the dedicated [Custom Commands documentation](./custom-commands.md).
+please see the dedicated
+[Custom Commands documentation](../cli/custom-commands.md).
 
 ## Input prompt shortcuts
 

docs/reference/configuration.md

@@ -1199,8 +1199,8 @@ within your user's home folder.
 Environment variables are a common way to configure applications, especially for
 sensitive information like API keys or for settings that might change between
 environments. For authentication setup, see the
-[Authentication documentation](./authentication.md) which covers all available
-authentication methods.
+[Authentication documentation](../get-started/authentication.md) which covers
+all available authentication methods.
 
 The CLI automatically loads environment variables from an `.env` file. The
 loading order is:
@@ -1219,7 +1219,8 @@ the `advanced.excludedEnvVars` setting in your `settings.json` file.
 
 - **`GEMINI_API_KEY`**:
   - Your API key for the Gemini API.
-  - One of several available [authentication methods](./authentication.md).
+  - One of several available
+    [authentication methods](../get-started/authentication.md).
   - Set this in your shell profile (e.g., `~/.bashrc`, `~/.zshrc`) or an `.env`
     file.
 - **`GEMINI_MODEL`**:
@@ -1565,15 +1566,16 @@ conventions and context.
   about the active instructional context.
 - **Importing content:** You can modularize your context files by importing
   other Markdown files using the `@path/to/file.md` syntax. For more details,
-  see the [Memory Import Processor documentation](../core/memport.md).
+  see the [Memory Import Processor documentation](../reference/memport.md).
 - **Commands for memory management:**
   - Use `/memory refresh` to force a re-scan and reload of all context files
     from all configured locations. This updates the AI's instructional context.
   - Use `/memory show` to display the combined instructional context currently
     loaded, allowing you to verify the hierarchy and content being used by the
     AI.
-  - See the [Commands documentation](../cli/commands.md#memory) for full details
-    on the `/memory` command and its sub-commands (`show` and `refresh`).
+  - See the [Commands documentation](../reference/commands.md#memory) for full
+    details on the `/memory` command and its sub-commands (`show` and
+    `refresh`).
 
 By understanding and utilizing these configuration layers and the hierarchical
 nature of context files, you can effectively manage the AI's memory and tailor