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

outdated clone of docs/index.

docs/tools/index.md

@@ -98,5 +98,5 @@ Always review confirmation prompts carefully before allowing a tool to execute.
 ## Next steps
 
 - Learn how to [Provide context](../cli/gemini-md.md) to guide tool use.
-- Explore the [Command reference](../cli/commands.md) for tool-related slash
-  commands.
+- Explore the [Command reference](../reference/commands.md) for tool-related
+  slash commands.

docs/tools/internal-docs.md

@@ -40,7 +40,7 @@ Gemini CLI uses this tool to ensure technical accuracy:
 
 ## Next steps
 
-- Explore the [Command reference](../cli/commands.md) for a detailed guide to
-  slash commands.
-- See the [Configuration guide](../get-started/configuration.md) for settings
+- Explore the [Command reference](../reference/commands.md) for a detailed guide
+  to slash commands.
+- See the [Configuration guide](../reference/configuration.md) for settings
   reference.

docs/tools/shell.md

@@ -131,9 +131,9 @@ configuration file.
   commands. Including the generic `run_shell_command` acts as a wildcard,
   allowing any command not explicitly blocked.
 - `tools.exclude` [DEPRECATED]: To block specific commands, use the
-  [Policy Engine](../core/policy-engine.md). Historically, this setting allowed
-  adding entries to the `exclude` list under the `tools` category in the format
-  `run_shell_command(<command>)`. For example,
+  [Policy Engine](../reference/policy-engine.md). Historically, this setting
+  allowed adding entries to the `exclude` list under the `tools` category in the
+  format `run_shell_command(<command>)`. For example,
   `"tools": {"exclude": ["run_shell_command(rm)"]}` will block `rm` commands.
 
 The validation logic is designed to be secure and flexible: