fix(run): address gadfly review of the checkpoint PR

Real findings from the consensus review (44 raw; heavy devstral noise):

- finalizeCheckpoint is now fired from the top-of-Run defer, so it runs on
  EVERY exit: a panic, an early build-error return (before the run loop), AND
  normal completion. Previously an early return on a recovered run left its
  durable record unfinalized → boot recovery would retry it forever on a
  persistent build error. (opus + glm)
- Removed the dead ActivePhase field from run.RunCheckpointState +
  run.ResumeState (and the battery RunCheckpoint) — phase recovery is
  boundary-granular (skip completed phases; the interrupted phase re-runs from
  its start), so ActivePhase was never written nor read. Docs across
  ports/checkpoint/phases now state this plainly (5-model consensus that the
  field + docs over-promised mid-phase resume).
- CheckpointerFactory.Begin error is now logged (WARN) before degrading to
  non-durable, per the documented contract (was silently swallowed). (4 models)
- finalizeCheckpoint logs Complete/Fail errors (was silent).
- Resume phase-skip now keys off a SEPARATE resumeSkip set, not the live
  outputs map — a fresh run with two same-named phases no longer skips the
  second (the outputs map fills as phases run). (opus:max) + regression test.
- Removed the dead checkpoint.factory.now field (never set). (opus + glm)
- Fixed the stale phaseDeps doc (the step observer moved out of sharedOpts to
  per-path). Hoisted the resume guard to a local; dropped the wasted acc
  allocation on the resume path; documented that Save throttling is the
  Checkpointer's responsibility and the accumulated transcript is pre-compaction
  (host size-caps it).

Note (carried from the PR): classifyCheckpointOutcome keys shutdown on
run.ErrShutdown; mort stamps its own runengine.ErrShutdown — the mort wiring PR
aliases them so errors.Is matches.

New test: duplicate phase names both run on a fresh run. Full ./... green.

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

run/ports.go

@@ -199,15 +199,15 @@ type Checkpointer interface {
 
 // RunCheckpointState is the resumable snapshot a Checkpointer persists.
 type RunCheckpointState struct {
-	// Messages is the running transcript (single-loop run) OR the active phase's
-	// transcript (multi-phase run). May be nil.
+	// Messages is the running transcript of a SINGLE-LOOP run (grows each step;
+	// resumed via WithHistory). nil for multi-phase runs — phase recovery is
+	// boundary-granular (see CompletedPhases), not mid-phase transcript.
 	Messages  []llm.Message
 	Iteration int
 	// CompletedPhases is set only for multi-phase runs: the outputs of phases
-	// already finished, in phase order. nil for single-loop runs.
+	// already finished, in phase order, so a resumed run skips them and re-runs
+	// the interrupted phase from its start. nil for single-loop runs.
 	CompletedPhases []PhaseOutput
-	// ActivePhase is the name of the in-progress phase (multi-phase only).
-	ActivePhase string
 }
 
 // PhaseOutput is one completed pipeline phase's name and output text, recorded in