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/orchestrator/api.rs

@@ -449,48 +449,17 @@ mod tests {
     use tower::ServiceExt;
     use uuid::Uuid;
 
-    use crate::error::LlmError;
-    use crate::llm::{
-        CompletionRequest, CompletionResponse, ToolCompletionRequest, ToolCompletionResponse,
-    };
     use crate::orchestrator::auth::TokenStore;
     use crate::orchestrator::job_manager::{ContainerJobConfig, ContainerJobManager};
+    use crate::testing::StubLlm;
 
     use super::*;
 
-    /// Stub LLM provider that panics if called (tests only exercise routing/auth).
-    struct StubLlm;
-
-    #[async_trait::async_trait]
-    impl crate::llm::LlmProvider for StubLlm {
-        fn model_name(&self) -> &str {
-            "stub"
-        }
-        fn cost_per_token(&self) -> (rust_decimal::Decimal, rust_decimal::Decimal) {
-            (rust_decimal::Decimal::ZERO, rust_decimal::Decimal::ZERO)
-        }
-        async fn complete(&self, _req: CompletionRequest) -> Result<CompletionResponse, LlmError> {
-            Err(LlmError::RequestFailed {
-                provider: "stub".into(),
-                reason: "not implemented".into(),
-            })
-        }
-        async fn complete_with_tools(
-            &self,
-            _req: ToolCompletionRequest,
-        ) -> Result<ToolCompletionResponse, LlmError> {
-            Err(LlmError::RequestFailed {
-                provider: "stub".into(),
-                reason: "not implemented".into(),
-            })
-        }
-    }
-
     fn test_state() -> OrchestratorState {
         let token_store = TokenStore::new();
         let jm = ContainerJobManager::new(ContainerJobConfig::default(), token_store.clone());
         OrchestratorState {
-            llm: Arc::new(StubLlm),
+            llm: Arc::new(StubLlm::default()),
             job_manager: Arc::new(jm),
             token_store,
             job_event_tx: None,
@@ -722,7 +691,7 @@ mod tests {
             .await;
 
         let state = OrchestratorState {
-            llm: Arc::new(StubLlm),
+            llm: Arc::new(StubLlm::default()),
             job_manager: Arc::new(jm),
             token_store,
             job_event_tx: None,
@@ -757,7 +726,7 @@ mod tests {
         let token_store = TokenStore::new();
         let jm = ContainerJobManager::new(ContainerJobConfig::default(), token_store.clone());
         let state = OrchestratorState {
-            llm: Arc::new(StubLlm),
+            llm: Arc::new(StubLlm::default()),
             job_manager: Arc::new(jm),
             token_store: token_store.clone(),
             job_event_tx: Some(tx),
@@ -812,7 +781,7 @@ mod tests {
         let token_store = TokenStore::new();
         let jm = ContainerJobManager::new(ContainerJobConfig::default(), token_store.clone());
         let state = OrchestratorState {
-            llm: Arc::new(StubLlm),
+            llm: Arc::new(StubLlm::default()),
             job_manager: Arc::new(jm),
             token_store: token_store.clone(),
             job_event_tx: Some(tx),
@@ -860,7 +829,7 @@ mod tests {
         let token_store = TokenStore::new();
         let jm = ContainerJobManager::new(ContainerJobConfig::default(), token_store.clone());
         let state = OrchestratorState {
-            llm: Arc::new(StubLlm),
+            llm: Arc::new(StubLlm::default()),
             job_manager: Arc::new(jm),
             token_store: token_store.clone(),
             job_event_tx: Some(tx),