fix(coding-agent): use tool-name allowlists and remove cwd-bound singletons

- treat tools as a global allowlist across built-in, extension, and SDK tools
- remove process-cwd singleton tool usage from SDK and CLI paths
- add regression coverage for extension tool filtering

closes #3452
closes #2835

packages/coding-agent/docs/extensions.md

@@ -2049,8 +2049,16 @@ ctx.ui.setWorkingMessage("Thinking deeply...");
 ctx.ui.setWorkingMessage();  // Restore default
 
 // Working indicator (shown during streaming)
-ctx.ui.setWorkingIndicator({ frames: ["●"] });  // Static dot
-ctx.ui.setWorkingIndicator({ frames: ["·", "•", "●", "•"], intervalMs: 120 });
+ctx.ui.setWorkingIndicator({ frames: [ctx.ui.theme.fg("accent", "●")] });  // Static dot
+ctx.ui.setWorkingIndicator({
+  frames: [
+    ctx.ui.theme.fg("dim", "·"),
+    ctx.ui.theme.fg("muted", "•"),
+    ctx.ui.theme.fg("accent", "●"),
+    ctx.ui.theme.fg("muted", "•"),
+  ],
+  intervalMs: 120,
+});
 ctx.ui.setWorkingIndicator({ frames: [] });  // Hide indicator
 ctx.ui.setWorkingIndicator();  // Restore default spinner
 
@@ -2098,6 +2106,8 @@ ctx.ui.setTheme(lightTheme!);  // Or switch by Theme object
 ctx.ui.theme.fg("accent", "styled text");  // Access current theme
 ```
 
+Custom working-indicator frames are rendered verbatim. If you want colors, add them to the frame strings yourself, for example with `ctx.ui.theme.fg(...)`.
+
 ### Custom Components
 
 For complex UI, use `ctx.ui.custom()`. This temporarily replaces the editor with your component until `done()` is called: