feat(run): execute multi-phase pipelines (RunnableAgent.Phases)

The kernel carried RunnableAgent.Phases as a DTO but never executed it —
Run always ran a single agent loop with ra.SystemPrompt, so a phased agent
(mort's deepresearch/research) silently ran one loop with the base prompt
instead of its pipeline. This implements the phase loop, ported from mort's
agentexec pipeline but reusing the kernel's own machinery.

- run/phases.go: runPhases / runOnePhase. Phases run sequentially; each is a
  fresh agent loop (or a bare LLM call for IsRunFunc phases) with its own
  template-expanded system prompt ({{.Query}} + {{.<PhaseName>}}), model
  tier, step cap, and tool subset. Outputs thread into later phases; the
  final phase's output is the run output. Optional phases swallow errors and
  substitute FallbackMessage; a non-optional phase that merely exhausts its
  step/tool budget salvages its partial transcript and continues (a hard
  error still aborts); per-phase tier-resolve failures fall back with a WARN.
- run/agent.go: Phase gains IsRunFunc + FallbackMessage (the kernel Phase
  struct previously omitted them).
- run/executor.go: Run factors the shared agent options (tool-error limits,
  step observer, compactor) and branches — single loop (critic's dynamic
  step ceiling) vs the phase runner (fixed per-phase caps; the run-level
  critic's steer + hard deadline still apply across phases). systemPrompt
  now delegates to systemPromptWithBody so each phase keeps the platform
  header. The same step observer feeds audit/steps/critic across all phases.

Tests (run/phases_test.go): sequential output threading + template
expansion, Optional-failure → FallbackMessage continues, hard-error abort,
IsRunFunc bare call, per-phase SystemHeader, filterToolbox subset, template
expansion. Full ./... suite green.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

run/agent.go

@@ -55,15 +55,27 @@ type RunnableAgent struct {
 }
 
 // Phase is one step of a multi-step run: its own system prompt, model tier,
-// iteration cap, and tool subset. Optional phases may be skipped by the
-// pipeline when their precondition isn't met.
+// iteration cap, and tool subset. Phase prompts are Go text/template strings
+// expanded against {{.Query}} (the original input) and {{.<PhaseName>}} (a
+// prior phase's output) before the phase runs, so a phase can consume earlier
+// work. The final phase's output is the run's output.
 type Phase struct {
 	Name          string
 	SystemPrompt  string
 	ModelTier     string
 	MaxIterations int
 	Tools         []string
-	Optional      bool
+	// Optional swallows a phase's error and substitutes FallbackMessage (or a
+	// generated note) as its output, so a non-critical phase failing does not
+	// abort the pipeline.
+	Optional bool
+	// FallbackMessage is the substitute output when an Optional phase fails.
+	// Empty → a generated "(phase %q encountered an error…)" note.
+	FallbackMessage string
+	// IsRunFunc marks a phase as a single bare LLM call (no tool loop, no tools
+	// array) — a deterministic transform step (plan/synthesize) rather than an
+	// agentic loop. Its Tools/MaxIterations are ignored.
+	IsRunFunc bool
 }
 
 // CriticConfig configures the optional run-critic. Enabled gates whether a