Restructure project and add user settings persistence

- Move src/clide/ to clide/ (flatten directory structure)
- Add SettingsService for persistent user preferences
- Settings stored in ~/.clide/settings.json
- Persist theme, panel visibility, and compact mode state
- Fix terminal rendering glitch with throttled refresh (~60fps)
- Update pyproject.toml, Makefile, and tests for new structure

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

pyproject.toml

@@ -54,7 +54,7 @@ clide = "clide.cli:app"
 # example = "clide.extensions.builtin.example:ExampleExtension"
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/clide"]
+packages = ["clide"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
@@ -75,7 +75,7 @@ exclude = ["tests", "dist", "build"]
 [tool.ruff]
 target-version = "py312"
 line-length = 100
-src = ["src", "tests"]
+src = ["clide", "tests"]
 
 [tool.ruff.lint]
 select = [
@@ -100,7 +100,7 @@ ignore = [
 known-first-party = ["clide"]
 
 [tool.coverage.run]
-source = ["src/clide"]
+source = ["clide"]
 branch = true
 
 [tool.coverage.report]