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/cli/mcp.rs

@@ -519,7 +519,7 @@ async fn get_secrets_store() -> anyhow::Result<Arc<dyn SecretsStore + Send + Syn
     #[cfg(all(feature = "libsql", not(feature = "postgres")))]
     {
         use crate::db::Database as _;
-        use crate::db::libsql_backend::LibSqlBackend;
+        use crate::db::libsql::LibSqlBackend;
         use secrecy::ExposeSecret as _;
 
         let default_path = crate::config::default_libsql_path();

src/cli/tool.rs

@@ -737,7 +737,7 @@ async fn auth_tool(name: String, dir: Option<PathBuf>, user_id: String) -> anyho
         #[cfg(all(feature = "libsql", not(feature = "postgres")))]
         {
             use crate::db::Database as _;
-            use crate::db::libsql_backend::LibSqlBackend;
+            use crate::db::libsql::LibSqlBackend;
             use secrecy::ExposeSecret as _;
 
             let default_path = crate::config::default_libsql_path();