feat(gui): Implement selectable thinking monologs and fix UI regressions

- Implement [Pure]/[Read] toggle for AI thinking monologues to allow text selection/copying.
- Fix TypeError: render_thinking_trace() missing 'entry_index' argument.
- Fix [+] buttons in Discussion and Comms history by correctly updating window state registry.
- Remove ListClipper from Discussion and Comms panels to fix variable-height clipping issues.
- Increase clipping heights for large entries to improve visibility.
- Fix code block scroll snapping in Markdown helper by robustifying text synchronization.

src/markdown_helper.py

@@ -126,13 +126,13 @@ class MarkdownRenderer:
   
   # Sync text and language
   lang_id = self._lang_map.get(lang_tag, ed.TextEditor.LanguageDefinitionId.none)
-  target_text = code + "\n"
   
-  if editor.get_text() != target_text:
+  # Robust check to avoid re-setting text every frame (which resets scroll)
+  curr_text = editor.get_text().replace('\r\n', '\n').strip()
+  if curr_text != code.replace('\r\n', '\n').strip():
    editor.set_text(code)
    editor.set_language_definition(lang_id)
   elif editor.get_language_definition_name().lower() != lang_tag:
-   # get_language_definition_name might not match exactly but good enough check
    editor.set_language_definition(lang_id)
 
   # Dynamic height calculation