Fix IPC stdout corruption, dark window background, overlay timing

- Redirect sys.stdout to stderr in Python sidecar so library print()
  calls don't corrupt the JSON-line IPC stream
- Save real stdout fd for exclusive IPC use via init_ipc()
- Skip non-JSON lines in Rust reader instead of failing with parse error
- Set Tauri window background color to match dark theme (#0a0a23)
- Add inline dark background on html/body to prevent white flash
- Use Svelte tick() to ensure progress overlay renders before invoke
- Improve ProgressOverlay with spinner, better styling, z-index 9999

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

src-tauri/tauri.conf.json

@@ -16,7 +16,9 @@
         "width": 1200,
         "height": 800,
         "minWidth": 800,
-        "minHeight": 600
+        "minHeight": 600,
+        "decorations": true,
+        "transparent": false
       }
     ],
     "security": {