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

outdated clone of docs/index.

docs/core/index.md

@@ -9,11 +9,11 @@ requests sent from `packages/cli`. For a general overview of Gemini CLI, see the
 
 - **[Sub-agents (experimental)](./subagents.md):** Learn how to create and use
   specialized sub-agents for complex tasks.
-- **[Core tools API](./tools-api.md):** Information on how tools are defined,
-  registered, and used by the core.
-- **[Memory Import Processor](./memport.md):** Documentation for the modular
-  GEMINI.md import feature using @file.md syntax.
-- **[Policy Engine](./policy-engine.md):** Use the Policy Engine for
+- **[Core tools API](../reference/tools-api.md):** Information on how tools are
+  defined, registered, and used by the core.
+- **[Memory Import Processor](../reference/memport.md):** Documentation for the
+  modular GEMINI.md import feature using @file.md syntax.
+- **[Policy Engine](../reference/policy-engine.md):** Use the Policy Engine for
   fine-grained control over tool execution.
 
 ## Role of the core
@@ -92,8 +92,8 @@ This allows you to have global, project-level, and component-level context
 files, which are all combined to provide the model with the most relevant
 information.
 
-You can use the [`/memory` command](../cli/commands.md) to `show`, `add`, and
-`refresh` the content of loaded `GEMINI.md` files.
+You can use the [`/memory` command](../reference/commands.md) to `show`, `add`,
+and `refresh` the content of loaded `GEMINI.md` files.
 
 ## Citations
 

docs/core/subagents.md

@@ -17,7 +17,7 @@ the main agent's context or toolset.
 > ```
 >
 > **Warning:** Sub-agents currently operate in
-> ["YOLO mode"](../get-started/configuration.md#command-line-arguments), meaning
+> ["YOLO mode"](../reference/configuration.md#command-line-arguments), meaning
 > they may execute tools without individual user confirmation for each step.
 > Proceed with caution when defining agents with powerful tools like
 > `run_shell_command` or `write_file`.