Add directive-first chain system redesign

Redesigns the chain system with a directive-first architecture where
Directive is the top-level entity (the "why/what") and Chains are
generated execution plans (the "how") that can be dynamically modified.

Backend:
- Add database migration for directive system tables
- Add Directive, DirectiveChain, ChainStep, DirectiveEvent models
- Add DirectiveVerifier and DirectiveApproval models
- Add orchestration module with engine, planner, and verifier
- Add comprehensive API handlers for directives
- Add daemon CLI commands for directive management
- Add directive skill documentation
- Integrate contract completion with directive engine
- Add SSE endpoint for real-time directive events

Frontend:
- Add directives route with split-view layout
- Add 6-tab detail view (Overview, Chain, Events, Evaluations, Approvals, Verifiers)
- Add React Flow DAG visualization for chain steps
- Add SSE subscription hook for real-time event updates
- Add useDirectives and useDirectiveEventSubscription hooks
- Add directive types and API functions

Fixes:
- Fix test failures in ws/protocol, task_output, completion_gate, patch
- Fix word boundary matching in looks_like_task()
- Fix parse_last() to find actual last completion gate
- Fix create_export_patch when merge-base equals HEAD
- Clean up clippy warnings in new code

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

1 files changed, 10 insertions, 2 deletions

diff --git a/makima/src/daemon/chain/runner.rs b/makima/src/daemon/chain/runner.rs
index dfbcfa7..1814581 100644
--- a/makima/src/daemon/chain/runner.rs
+++ b/makima/src/daemon/chain/runner.rs
@@ -37,8 +37,10 @@ pub enum RunnerError {
 /// Chain runner for creating and managing chains.
 pub struct ChainRunner {
     /// Base API URL
+    #[allow(dead_code)]
     api_url: String,
     /// API key for authentication
+    #[allow(dead_code)]
     api_key: String,
 }
 
@@ -116,6 +118,7 @@ impl ChainRunner {
         CreateChainRequest {
             name: chain.name.clone(),
             description: chain.description.clone(),
+            repository_url: None, // Legacy field, repositories take precedence
             repositories: if repositories.is_empty() {
                 None
             } else {
@@ -242,7 +245,9 @@ mod tests {
         let yaml = r#"
 name: Test Chain
 description: A test chain
-repo: https://github.com/test/repo
+repositories:
+  - name: main
+    repository_url: https://github.com/test/repo
 contracts:
   - name: Research
     type: simple
@@ -270,8 +275,11 @@ loop:
 
         assert_eq!(request.name, "Test Chain");
         assert_eq!(request.description, Some("A test chain".to_string()));
+        // Repositories are now in a separate array
+        let repos = request.repositories.unwrap();
+        assert_eq!(repos.len(), 1);
         assert_eq!(
-            request.repository_url,
+            repos[0].repository_url,
             Some("https://github.com/test/repo".to_string())
         );
         assert_eq!(request.loop_enabled, Some(true));