Refactor pipeline policies, MCP registry, and unified config/runtime

docs/pipeline-policies.md

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+# Pipeline Policies and Lifecycle Hooks
+
+## Why this exists
+
+`PipelineExecutor` previously handled DAG traversal, failure heuristics, state persistence, and domain-event emission in one execution loop. This made behavior harder to isolate and test.
+
+## Current structure
+
+- `FailurePolicy` (`src/agents/failure-policy.ts`)
+  - Owns hard vs soft failure classification.
+  - Determines whether a sequence of hard failures should abort execution.
+- `PersistenceLifecycleObserver` (`src/agents/lifecycle-observer.ts`)
+  - Handles state patching, project-context updates, and domain-event publishing for each node attempt.
+- `PipelineExecutor` (`src/agents/pipeline.ts`)
+  - Coordinates DAG traversal and retry behavior.
+  - Computes aggregate run status from executed terminal nodes plus critical-path failures.
+
+## Aggregate status semantics
+
+Run status is `success` only when both are true:
+
+1. All executed terminal nodes (leaves in the executed subgraph) have final status `success`.
+2. No executed node in the critical path has final status `failure`.
+
+Otherwise status is `failure`.
+
+## Persistence guarantees
+
+State and project-context writes are now atomic via temp-file + rename.
+Project-context patch/write operations are serialized both in-process (promise queue) and cross-process (lock file).