logiguard fork: GPUI xdg-activation keyboard-focus serial fix

Single-commit orphan branch: full zed-industries/zed @ 8c74db0 source tree
with a 3-file patch applied (no upstream history).

Patch (crates/gpui_linux/src/linux/wayland/):
  - serial.rs: add SerialKind::KeyboardEnter
  - client.rs: store wl_keyboard.enter serial; add latest_serial_of()
  - window.rs: activate() uses keyboard-enter serial (Mutter focus gate)

Mutter honors window activation only when the token carries the keyboard-
focus serial from wl_keyboard.enter; GPUI used a stale mouse-press serial.
See docs/tray-window-focus-wayland.md in logiguard.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

docs/.doc-examples/reference.md

@@ -0,0 +1,103 @@
+<!--
+  GOLD STANDARD EXAMPLE: Reference Documentation
+
+  This example demonstrates documentation for API/reference content like tools,
+  actions, or other enumerable items.
+
+  Key patterns to note:
+  - Anchor IDs on categories and individual items for deep-linking
+  - Opening paragraph explains what these are and where they're used
+  - Organized into logical categories
+  - Each item has a clear, actionable description
+  - Links to related configuration docs
+  - "See Also" section for related topics
+-->
+
+---
+
+title: AI Agent Tools - Zed
+description: Built-in tools for Zed's AI agent including file editing, code search, terminal commands, web search, and diagnostics.
+
+---
+
+# Tools
+
+Zed's built-in agent has access to these tools for reading, searching, and editing your codebase. These tools are used in the [Agent Panel](./agent-panel.md) during conversations with AI agents.
+
+You can configure permissions for tool actions, including situations where they are automatically approved, automatically denied, or require your confirmation on a case-by-case basis. See [Tool Permissions](./tool-permissions.md) for the list of permission-gated tools and details.
+
+To add custom tools beyond these built-in ones, see [MCP servers](./mcp.md).
+
+## Read & Search Tools {#read-search-tools}
+
+### `diagnostics` {#diagnostics}
+
+Gets errors and warnings for either a specific file or the entire project, useful after making edits to determine if further changes are needed.
+When a path is provided, shows all diagnostics for that specific file.
+When no path is provided, shows a summary of error and warning counts for all files in the project.
+
+### `fetch` {#fetch}
+
+Fetches a URL and returns the content as Markdown. Useful for providing docs as context.
+
+### `find_path` {#find-path}
+
+Quickly finds files by matching glob patterns (like `**/*.js`), returning matching file paths alphabetically.
+
+### `grep` {#grep}
+
+Searches file contents across the project using regular expressions, preferred for finding symbols in code without knowing exact file paths.
+
+### `list_directory` {#list-directory}
+
+Lists files and directories in a given path, providing an overview of filesystem contents.
+
+### `read_file` {#read-file}
+
+Reads the content of a specified file in the project, allowing access to file contents.
+
+### `search_web` {#search-web}
+
+Searches the web for information, providing results with snippets and links from relevant web pages, useful for accessing real-time information.
+
+## Edit Tools {#edit-tools}
+
+### `copy_path` {#copy-path}
+
+Copies a file or directory recursively in the project, more efficient than manually reading and writing files when duplicating content.
+
+### `create_directory` {#create-directory}
+
+Creates a new directory at the specified path within the project, creating all necessary parent directories (similar to `mkdir -p`).
+
+### `delete_path` {#delete-path}
+
+Deletes a file or directory (including contents recursively) at the specified path and confirms the deletion.
+
+### `edit_file` {#edit-file}
+
+Edits files by replacing specific text with new content.
+
+### `move_path` {#move-path}
+
+Moves or renames a file or directory in the project, performing a rename if only the filename differs.
+
+### `write_file` {#write-file}
+
+Creates a new file or overwrites an existing file with completely new contents.
+
+### `terminal` {#terminal}
+
+Executes shell commands and returns the combined output, creating a new shell process for each invocation.
+
+## Other Tools {#other-tools}
+
+### `spawn_agent` {#spawn-agent}
+
+Spawns a subagent with its own context window to perform a delegated task. Useful for running parallel investigations, completing self-contained tasks, or performing research where only the outcome matters. Each subagent has access to the same tools as the parent agent.
+
+## See Also {#see-also}
+
+- [Agent Panel](./agent-panel.md) — Where you interact with AI agents
+- [Tool Permissions](./tool-permissions.md) — Configure which tools require approval
+- [MCP Servers](./mcp.md) — Add custom tools via Model Context Protocol