Update callouts to work on github.

docs/reference/commands.md

@@ -35,8 +35,8 @@ Slash commands provide meta-level control over the CLI itself.
     - `list` (selecting this opens the auto-saved session browser)
   - `-- checkpoints --`
     - `list`, `save`, `resume`, `delete`, `share` (manual tagged checkpoints)
-  - **Note:** Unique prefixes (for example `/cha` or `/resum`) resolve to the
-    same grouped menu.
+  - Unique prefixes (for example `/chat` or `/resume`) resolve to the same
+    grouped menu.
 - **Sub-commands:**
   - **`debug`**
     - **Description:** Export the most recent API request as a JSON payload.

docs/reference/configuration.md

@@ -25,7 +25,9 @@ overridden by higher numbers):
 Gemini CLI uses JSON settings files for persistent configuration. There are four
 locations for these files:
 
-> **Tip:** JSON-aware editors can use autocomplete and validation by pointing to
+<!-- prettier-ignore -->
+> [!TIP]
+> JSON-aware editors can use autocomplete and validation by pointing to
 > the generated schema at `schemas/settings.schema.json` in this repository.
 > When working outside the repo, reference the hosted schema at
 > `https://raw.githubusercontent.com/google-gemini/gemini-cli/main/schemas/settings.schema.json`.
@@ -990,9 +992,12 @@ their corresponding top-level category object in your `settings.json` file.
   - **Default:** `true`
   - **Requires restart:** Yes
 
+<!-- prettier-ignore -->
+> [!WARNING]
+> Subagents is an experimental feature. Uses YOLO mode for subagents.
+
 - **`experimental.enableAgents`** (boolean):
-  - **Description:** Enable local and remote subagents. Warning: Experimental
-    feature, uses YOLO mode for subagents
+  - **Description:** Enable local and remote subagents.
   - **Default:** `false`
   - **Requires restart:** Yes
 
@@ -1198,7 +1203,9 @@ for compatibility. At least one of `command`, `url`, or `httpUrl` must be
 provided. If multiple are specified, the order of precedence is `httpUrl`, then
 `url`, then `command`.
 
-> **Warning:** Avoid using underscores (`_`) in your server aliases (e.g., use
+<!-- prettier-ignore -->
+> [!WARNING]
+> Avoid using underscores (`_`) in your server aliases (e.g., use
 > `my-server` instead of `my_server`). The underlying policy engine parses Fully
 > Qualified Names (`mcp_server_tool`) using the first underscore after the
 > `mcp_` prefix. An underscore in your server alias will cause the parser to

docs/reference/policy-engine.md

@@ -102,7 +102,9 @@ There are three possible decisions a rule can enforce:
 - `ask_user`: The user is prompted to approve or deny the tool call. (In
   non-interactive mode, this is treated as `deny`.)
 
-> **Note:** The `deny` decision is the recommended way to exclude tools. The
+<!-- prettier-ignore -->
+> [!NOTE]
+> The `deny` decision is the recommended way to exclude tools. The
 > legacy `tools.exclude` setting in `settings.json` is deprecated in favor of
 > policy rules with a `deny` decision.
 
@@ -228,15 +230,17 @@ directory are **ignored**.
 - **Linux / macOS:** Must be owned by `root` (UID 0) and NOT writable by group
   or others (e.g., `chmod 755`).
 - **Windows:** Must be in `C:\ProgramData`. Standard users (`Users`, `Everyone`)
-  must NOT have `Write`, `Modify`, or `Full Control` permissions. _Tip: If you
-  see a security warning, use the folder properties to remove write permissions
-  for non-admin groups. You may need to "Disable inheritance" in Advanced
-  Security Settings._
+  must NOT have `Write`, `Modify`, or `Full Control` permissions. If you see a
+  security warning, use the folder properties to remove write permissions for
+  non-admin groups. You may need to "Disable inheritance" in Advanced Security
+  Settings.
 
-**Note:** Supplemental admin policies (provided via `--admin-policy` or
-`adminPolicyPaths` settings) are **NOT** subject to these strict ownership
-checks, as they are explicitly provided by the user or administrator in their
-current execution context.
+<!-- prettier-ignore -->
+> [!NOTE]
+> Supplemental admin policies (provided via `--admin-policy` or
+> `adminPolicyPaths` settings) are **NOT** subject to these strict ownership
+> checks, as they are explicitly provided by the user or administrator in their
+> current execution context.
 
 ### TOML rule schema
 
@@ -333,7 +337,9 @@ using the `mcpName` field. **This is the recommended approach** for defining MCP
 policies, as it is much more robust than manually writing Fully Qualified Names
 (FQNs) or string wildcards.
 
-> **Warning:** Do not use underscores (`_`) in your MCP server names (e.g., use
+<!-- prettier-ignore -->
+> [!WARNING]
+> Do not use underscores (`_`) in your MCP server names (e.g., use
 > `my-server` rather than `my_server`). The policy parser splits Fully Qualified
 > Names (`mcp_server_tool`) on the _first_ underscore following the `mcp_`
 > prefix. If your server name contains an underscore, the parser will

docs/reference/tools.md

@@ -95,7 +95,9 @@ For developers, the tool system is designed to be extensible and robust. The
 You can extend Gemini CLI with custom tools by configuring
 `tools.discoveryCommand` in your settings or by connecting to MCP servers.
 
-> **Note:** For a deep dive into the internal Tool API and how to implement your
+<!-- prettier-ignore -->
+> [!NOTE]
+> For a deep dive into the internal Tool API and how to implement your
 > own tools in the codebase, see the `packages/core/src/tools/` directory in
 > GitHub.