fix(gsd-tools): support .planning/milestones/v*-phases/ layout in validators and find-phase

Fixes #3164

Validators and find-phase hardcoded phasesDir = .planning/phases/, so projects
using the milestone-archive layout (.planning/milestones/v*-phases/) had an empty
diskPhases set, triggering W006 for every active phase and find-phase returning
found:false.

Add collectDiskPhases(planBase) helper that scans both flat layout and all
.planning/milestones/v*-phases/ subdirs. Wire it into cmdValidateConsistency,
cmdValidateHealth (both the Check 4 validPhases set and Check 8 diskPhases),
and refactor cmdFindPhase to iterate candidate search dirs so it also searches
milestone-archive dirs.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

CHANGELOG.md

@@ -6,6 +6,10 @@ Format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 ## [Unreleased](https://github.com/gsd-build/get-shit-done/compare/v1.39.1...HEAD)
 
+### Fixed
+
+- **Milestone-archive layout support** — `validate consistency`, `validate health`, and `find-phase` now scan `.planning/milestones/v*-phases/` directories in addition to the flat `.planning/phases/` layout. Projects that have graduated to milestone-archive layout no longer receive spurious W006 "Phase N in ROADMAP.md but no directory on disk" warnings for every active phase. (#3164)
+
 ### Feature
 
 - **Six namespace meta-skills with keyword-tag descriptions** — replace the flat 86-skill