feat: phases + tasks — per-task execution with phase directories

- A phase is now a directory: 00_phase.md (overview + task index) plus
  small, quick NN_task.md task files; complete/ mirrors todo/
- Task is the unit of execution: run-task.sh (one unit), run-phase.sh
  (phase to completion incl. 00_phase.md final pass), auto-phase.sh
  (all units in order); validate.sh gate runs after every task
- PHASE_COMMIT commits at phase boundaries (00_phase.md / legacy file moves)
- Legacy flat todo/NN_name.md files still execute as a single unit;
  new migrate-phases-to-tasks.sh converts them to the directory layout
- phase-status.sh reports per-task state and the next unit
- New task-template.md; phase templates now carry a Tasks index

phase-authoring/scripts/migrate-phases-to-tasks.sh

@@ -0,0 +1,72 @@
+#!/usr/bin/env bash
+# migrate-phases-to-tasks.sh — convert the flat phase-file layout to the
+# phase-directory + task-file layout.
+#
+# Each numeric-prefixed flat phase file in {todo,complete}/ is wrapped into a
+# directory of the same name with the file renamed to 00_phase.md:
+#
+#   todo/03_api.md          →  todo/03_api/00_phase.md
+#   complete/01_init.md     →  complete/01_init/00_phase.md
+#
+# The harness still executes wrapped phases: their inline task lists are
+# picked up by the phase's 00_phase.md final pass, so this is safe
+# mid-pipeline. Splitting a wrapped todo phase into real task files is the
+# phase-authoring skill's job, not this script's. Already-migrated phases are
+# left alone; a flat file colliding with an existing same-name directory is
+# reported and skipped.
+#
+# Usage: bash migrate-phases-to-tasks.sh [project-root]
+#   project-root defaults to the nearest ancestor containing
+#   .agent/phases/todo or agent/phases/todo (older projects).
+set -euo pipefail
+
+root="${1:-}"
+if [[ -n "$root" ]]; then
+  [[ -d "$root" ]] || { echo "✗ ERROR: $root is not a directory" >&2; exit 1; }
+else
+  root="$(pwd)"
+  while :; do
+    if [[ -d "$root/.agent/phases/todo" || -d "$root/agent/phases/todo" ]]; then break; fi
+    [[ "$root" == "/" ]] && { echo "✗ ERROR: no phases/todo found at or above $(pwd)" >&2; exit 1; }
+    root="$(dirname "$root")"
+  done
+fi
+
+if [[ -d "$root/.agent/phases" ]]; then
+  phases="$root/.agent/phases"
+elif [[ -d "$root/agent/phases" ]]; then
+  phases="$root/agent/phases"
+else
+  echo "✗ ERROR: no phases directory under $root" >&2
+  exit 1
+fi
+
+echo "project root: $root"
+echo "phases:       $phases"
+echo
+
+moved=0 skipped=0
+for d in todo complete; do
+  [[ -d "$phases/$d" ]] || continue
+  for f in "$phases/$d"/*.md; do
+    [[ -e "$f" ]] || continue
+    base="$(basename "$f" .md)"
+    [[ "$base" =~ ^[0-9] ]] || continue
+    if [[ -d "$phases/$d/$base" ]]; then
+      echo "⚠ skip: $d/$base.md — directory $d/$base/ already exists (conflict)" >&2
+      skipped=$((skipped + 1))
+      continue
+    fi
+    mkdir -p "$phases/$d/$base"
+    mv -f "$f" "$phases/$d/$base/00_phase.md"
+    echo "  $d/$base.md → $d/$base/00_phase.md"
+    moved=$((moved + 1))
+  done
+done
+
+echo
+echo "migrated: $moved phase file(s) → 00_phase.md directory layout; skipped: $skipped"
+if (( moved > 0 )); then
+  echo "wrapped todo phases now run as a single final pass; use the phase-authoring"
+  echo "skill to split their inline task lists into real task files."
+fi