refactor: architecture improvements for contributor velocity (#198)

* refactor: split large files and consolidate test stubs for contributor velocity

- Extract 7 Database sub-traits (ConversationStore, JobStore, SandboxStore,
  RoutineStore, ToolFailureStore, SettingsStore, WorkspaceStore) with Database
  as a supertrait combining them all
- Split libsql_backend.rs (2769 lines) into src/db/libsql/ directory with
  one file per sub-trait implementation
- Split config.rs (1753 lines) into src/config/ directory with 16 domain files
- Consolidate 3 duplicate test LLM stubs into shared StubLlm in src/testing.rs
- Split server.rs handlers into src/channels/web/handlers/ directory
- Extract main.rs init phases into AppBuilder (src/app.rs)
- Add developer setup script (scripts/dev-setup.sh)

Co-Authored-By: Claude Opus 4.6 <[email protected]>

* refactor: move heartbeat test from examples/ to tests/

Convert standalone example binary into a proper #[ignore] integration
test, matching the convention of the other integration tests.

Co-Authored-By: Claude Opus 4.6 <[email protected]>

* style: fix rustfmt formatting for CI

Co-Authored-By: Claude Opus 4.6 <[email protected]>

* fix: address PR review comments from Copilot

- tunnel.rs: replace .ok().flatten() with ? to propagate env var errors
- secrets.rs: remove misleading "process-wide cache" comment
- database.rs: use uppercase "DATABASE_URL" in error key
- testing.rs: gate harness tests with #[cfg(feature = "libsql")]

Co-Authored-By: Claude Opus 4.6 <[email protected]>

---------

Co-authored-by: Illia Polosukhin <[email protected]>
Co-authored-by: Claude Opus 4.6 <[email protected]>

src/setup/wizard.rs

@@ -79,7 +79,7 @@ pub struct SetupWizard {
     db_pool: Option<deadpool_postgres::Pool>,
     /// libSQL backend (created during setup, libsql only).
     #[cfg(feature = "libsql")]
-    db_backend: Option<crate::db::libsql_backend::LibSqlBackend>,
+    db_backend: Option<crate::db::libsql::LibSqlBackend>,
     /// Secrets crypto (created during setup).
     secrets_crypto: Option<Arc<SecretsCrypto>>,
     /// Cached API key from provider setup (used by model fetcher without env mutation).
@@ -438,7 +438,7 @@ impl SetupWizard {
         turso_url: Option<&str>,
         turso_token: Option<&str>,
     ) -> Result<(), SetupError> {
-        use crate::db::libsql_backend::LibSqlBackend;
+        use crate::db::libsql::LibSqlBackend;
         use std::path::Path;
 
         let db_path = Path::new(path);
@@ -1486,7 +1486,7 @@ impl SetupWizard {
             #[cfg(feature = "libsql")]
             let saved = if !saved {
                 if let Some(ref backend) = self.db_backend {
-                    use crate::db::Database as _;
+                    use crate::db::SettingsStore as _;
                     backend
                         .set_all_settings("default", &db_map)
                         .await