diff --git a/.changeset/witty-wasps-hum.md b/.changeset/witty-wasps-hum.md
new file mode 100644
index 000000000..8a0d4db16
--- /dev/null
+++ b/.changeset/witty-wasps-hum.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 3191
+---
+validate consistency, validate health, and find-phase now scan .planning/milestones/v*-phases/ dirs in addition to the flat .planning/phases/ layout. Projects using milestone-archive layout no longer receive spurious W006 warnings for every active phase. Fixes #3164.
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9766aa24a..8b4b6c029 100644
--- a/CHANGELOG.md
+++ b/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
diff --git a/get-shit-done/bin/lib/phase.cjs b/get-shit-done/bin/lib/phase.cjs
index 3ad552c10..4f9177171 100644
--- a/get-shit-done/bin/lib/phase.cjs
+++ b/get-shit-done/bin/lib/phase.cjs
@@ -212,48 +212,64 @@ function cmdFindPhase(cwd, phase, raw) {
     error('phase identifier required');
   }
 
-  const phasesDir = path.join(planningDir(cwd), 'phases');
+  const planBase = planningDir(cwd);
   const normalized = normalizePhaseName(phase);
+  const notFound = { found: false, directory: null, phase_number: null, phase_name: null, plans: [], summaries: [], searched_directories: [] };
 
-  const notFound = { found: false, directory: null, phase_number: null, phase_name: null, plans: [], summaries: [] };
-
+  // Build candidate search dirs: flat layout first, then milestone-archive layout.
+  const searchDirs = [];
+  const flatPhasesDir = path.join(planBase, 'phases');
+  if (fs.existsSync(flatPhasesDir)) searchDirs.push(flatPhasesDir);
   try {
-    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
-    const dirs = entries.filter(e => e.isDirectory()).map(e => e.name).sort((a, b) => comparePhaseNum(a, b));
-
-    const match = dirs.find(d => phaseTokenMatches(d, normalized));
-    if (!match) {
-      output(notFound, raw, '');
-      return;
+    const milestonesDir = path.join(planBase, 'milestones');
+    const entries = fs.readdirSync(milestonesDir, { withFileTypes: true })
+      .filter(e => e.isDirectory() && /^v\d+.*-phases$/.test(e.name))
+      .sort((a, b) => a.name.localeCompare(b.name, undefined, { numeric: true }));
+    for (const e of entries) {
+      searchDirs.push(path.join(milestonesDir, e.name));
     }
+  } catch { /* no milestones dir */ }
 
-    // Extract phase number — supports project-code-prefixed (CK-01-name), numeric (01-name), and custom IDs
-    const dirMatch = match.match(/^(?:[A-Z]{1,6}-)(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i)
-      || match.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i);
-    const phaseNumber = dirMatch ? dirMatch[1] : normalized;
-    const phaseName = dirMatch && dirMatch[2] ? dirMatch[2] : null;
+  notFound.searched_directories = searchDirs.map((searchDir) =>
+    toPosixPath(path.join(path.relative(cwd, planBase), path.relative(planBase, searchDir))));
 
-    const phaseDir = path.join(phasesDir, match);
-    const phaseFiles = fs.readdirSync(phaseDir);
-    const plans = phaseFiles.filter(isCanonicalPlanFile).sort();
-    const summaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md').sort();
-    // #2893 — same diagnostic as phase-plan-index for consistency.
-    const planNamingWarning = describeNonCanonicalPlans(phaseFiles, plans);
+  for (const searchDir of searchDirs) {
+    try {
+      const entries = fs.readdirSync(searchDir, { withFileTypes: true });
+      const dirs = entries.filter(e => e.isDirectory()).map(e => e.name).sort((a, b) => comparePhaseNum(a, b));
 
-    const result = {
-      found: true,
-      directory: toPosixPath(path.join(path.relative(cwd, planningDir(cwd)), 'phases', match)),
-      phase_number: phaseNumber,
-      phase_name: phaseName,
-      plans,
-      summaries,
-    };
-    if (planNamingWarning) result.warning = planNamingWarning;
+      const match = dirs.find(d => phaseTokenMatches(d, normalized));
+      if (!match) continue;
 
-    output(result, raw, result.directory);
-  } catch {
-    output(notFound, raw, '');
+      // Extract phase number — supports project-code-prefixed (CK-01-name), numeric (01-name), and custom IDs
+      const dirMatch = match.match(/^(?:[A-Z]{1,6}-)(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i)
+        || match.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i);
+      const phaseNumber = dirMatch ? dirMatch[1] : normalized;
+      const phaseName = dirMatch && dirMatch[2] ? dirMatch[2] : null;
+
+      const phaseDir = path.join(searchDir, match);
+      const phaseFiles = fs.readdirSync(phaseDir);
+      const plans = phaseFiles.filter(isCanonicalPlanFile).sort();
+      const summaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md').sort();
+      // #2893 — same diagnostic as phase-plan-index for consistency.
+      const planNamingWarning = describeNonCanonicalPlans(phaseFiles, plans);
+
+      const result = {
+        found: true,
+        directory: toPosixPath(path.join(path.relative(cwd, planBase), path.relative(planBase, searchDir), match)),
+        phase_number: phaseNumber,
+        phase_name: phaseName,
+        plans,
+        summaries,
+      };
+      if (planNamingWarning) result.warning = planNamingWarning;
+
+      output(result, raw, result.directory);
+      return;
+    } catch { continue; }
   }
+
+  output(notFound, raw, '');
 }
 
 function extractObjective(content) {
diff --git a/get-shit-done/bin/lib/verify.cjs b/get-shit-done/bin/lib/verify.cjs
index 9de714c6a..d5d6585be 100644
--- a/get-shit-done/bin/lib/verify.cjs
+++ b/get-shit-done/bin/lib/verify.cjs
@@ -396,9 +396,76 @@ function cmdVerifyKeyLinks(cwd, planFilePath, raw) {
   }, raw, verified === results.length ? 'valid' : 'invalid');
 }
 
+const PHASE_TOKEN_FROM_DIR_RE = /^(?:[A-Z]{1,6}-)?(\d+[A-Z]?(?:\.\d+)*)(?:-|$)/i;
+const MILESTONE_ARCHIVE_DIR_RE = /^v\d+.*-phases$/i;
+
+function listMilestoneArchiveDirs(planBase) {
+  const milestonesDir = path.join(planBase, 'milestones');
+  try {
+    return fs.readdirSync(milestonesDir, { withFileTypes: true })
+      .filter((e) => e.isDirectory() && MILESTONE_ARCHIVE_DIR_RE.test(e.name))
+      .map((e) => path.join(milestonesDir, e.name))
+      .sort((a, b) => path.basename(a).localeCompare(path.basename(b), undefined, { numeric: true }));
+  } catch {
+    return [];
+  }
+}
+
+function getActiveMilestoneArchiveDir(planBase) {
+  const archiveDirs = listMilestoneArchiveDirs(planBase);
+  if (archiveDirs.length === 0) return null;
+
+  // Prefer STATE.md milestone when it maps to an on-disk archive dir.
+  try {
+    const statePath = path.join(planBase, 'STATE.md');
+    if (fs.existsSync(statePath)) {
+      const state = fs.readFileSync(statePath, 'utf-8');
+      const m = state.match(/^\s*(?:\*\*)?milestone(?:\*\*)?:\s*([^\s\r\n#]+).*$/mi);
+      if (m && m[1]) {
+        const milestone = m[1].trim();
+        const candidate = path.join(planBase, 'milestones', `${milestone}-phases`);
+        if (archiveDirs.includes(candidate)) return candidate;
+      }
+    }
+  } catch { /* intentionally empty */ }
+
+  // Fallback when STATE.md is absent/stale: highest (most recent) archive by version-ish name.
+  return archiveDirs[archiveDirs.length - 1];
+}
+
+function collectPhaseRoots(planBase) {
+  const roots = [];
+  const flatPhasesDir = path.join(planBase, 'phases');
+  if (fs.existsSync(flatPhasesDir)) roots.push(flatPhasesDir);
+  const activeArchive = getActiveMilestoneArchiveDir(planBase);
+  if (activeArchive) roots.push(activeArchive);
+  return roots;
+}
+
+// Returns a Set of phase numbers found on disk across active phase roots.
+function collectDiskPhases(planBase) {
+  const diskPhases = new Set();
+  const phaseRoots = collectPhaseRoots(planBase);
+  const scanDir = (dir) => {
+    try {
+      const entries = fs.readdirSync(dir, { withFileTypes: true });
+      for (const e of entries) {
+        if (e.isDirectory()) {
+          const m = e.name.match(PHASE_TOKEN_FROM_DIR_RE);
+          if (m) diskPhases.add(m[1]);
+        }
+      }
+    } catch { /* dir absent */ }
+  };
+
+  for (const root of phaseRoots) scanDir(root);
+
+  return diskPhases;
+}
+
 function cmdValidateConsistency(cwd, raw) {
-  const roadmapPath = path.join(planningDir(cwd), 'ROADMAP.md');
-  const phasesDir = path.join(planningDir(cwd), 'phases');
+  const planBase = planningDir(cwd);
+  const roadmapPath = path.join(planBase, 'ROADMAP.md');
   const errors = [];
   const warnings = [];
 
@@ -420,16 +487,8 @@ function cmdValidateConsistency(cwd, raw) {
     roadmapPhases.add(m[1]);
   }
 
-  // Get phases on disk
-  const diskPhases = new Set();
-  try {
-    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
-    const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
-    for (const dir of dirs) {
-      const dm = dir.match(/^(\d+[A-Z]?(?:\.\d+)*)/i);
-      if (dm) diskPhases.add(dm[1]);
-    }
-  } catch { /* intentionally empty */ }
+  // Get phases on disk (flat layout + milestone-archive layout)
+  const diskPhases = collectDiskPhases(planBase);
 
   // Check: phases in ROADMAP but not on disk
   for (const p of roadmapPhases) {
@@ -461,60 +520,53 @@ function cmdValidateConsistency(cwd, raw) {
     }
   }
 
-  // Check: plan numbering within phases
-  try {
-    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
-    const dirs = entries.filter(e => e.isDirectory()).map(e => e.name).sort();
+  const phaseRoots = collectPhaseRoots(planBase);
+  for (const phaseRoot of phaseRoots) {
+    try {
+      const entries = fs.readdirSync(phaseRoot, { withFileTypes: true });
+      const dirs = entries.filter(e => e.isDirectory()).map(e => e.name).sort();
 
-    for (const dir of dirs) {
-      const phaseFiles = fs.readdirSync(path.join(phasesDir, dir));
-      const plans = phaseFiles.filter(f => f.endsWith('-PLAN.md')).sort();
+      for (const dir of dirs) {
+        const phasePath = path.join(phaseRoot, dir);
+        const phaseLabel = path.relative(planBase, phasePath).replace(/\\/g, '/');
+        const phaseFiles = fs.readdirSync(phasePath);
+        const plans = phaseFiles.filter(f => f.endsWith('-PLAN.md')).sort();
 
-      // Extract plan numbers
-      const planNums = plans.map(p => {
-        const pm = p.match(/-(\d{2})-PLAN\.md$/);
-        return pm ? parseInt(pm[1], 10) : null;
-      }).filter(n => n !== null);
+        // Extract plan numbers
+        const planNums = plans.map(p => {
+          const pm = p.match(/-(\d{2})-PLAN\.md$/);
+          return pm ? parseInt(pm[1], 10) : null;
+        }).filter(n => n !== null);
 
-      for (let i = 1; i < planNums.length; i++) {
-        if (planNums[i] !== planNums[i - 1] + 1) {
-          warnings.push(`Gap in plan numbering in ${dir}: plan ${planNums[i - 1]} → ${planNums[i]}`);
+        for (let i = 1; i < planNums.length; i++) {
+          if (planNums[i] !== planNums[i - 1] + 1) {
+            warnings.push(`Gap in plan numbering in ${phaseLabel}: plan ${planNums[i - 1]} → ${planNums[i]}`);
+          }
+        }
+
+        // Check: plans without summaries (completed plans)
+        const summaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md'));
+        const planIds = new Set(plans.map(p => p.replace('-PLAN.md', '')));
+        const summaryIds = new Set(summaries.map(s => s.replace('-SUMMARY.md', '')));
+
+        // Summary without matching plan is suspicious
+        for (const sid of summaryIds) {
+          if (!planIds.has(sid)) {
+            warnings.push(`Summary ${sid}-SUMMARY.md in ${phaseLabel} has no matching PLAN.md`);
+          }
+        }
+
+        // Check: frontmatter in plans has required fields
+        for (const plan of plans) {
+          const content = fs.readFileSync(path.join(phasePath, plan), 'utf-8');
+          const fm = extractFrontmatter(content);
+          if (!fm.wave) {
+            warnings.push(`${phaseLabel}/${plan}: missing 'wave' in frontmatter`);
+          }
         }
       }
-
-      // Check: plans without summaries (completed plans)
-      const summaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md'));
-      const planIds = new Set(plans.map(p => p.replace('-PLAN.md', '')));
-      const summaryIds = new Set(summaries.map(s => s.replace('-SUMMARY.md', '')));
-
-      // Summary without matching plan is suspicious
-      for (const sid of summaryIds) {
-        if (!planIds.has(sid)) {
-          warnings.push(`Summary ${sid}-SUMMARY.md in ${dir} has no matching PLAN.md`);
-        }
-      }
-    }
-  } catch { /* intentionally empty */ }
-
-  // Check: frontmatter in plans has required fields
-  try {
-    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
-    const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
-
-    for (const dir of dirs) {
-      const phaseFiles = fs.readdirSync(path.join(phasesDir, dir));
-      const plans = phaseFiles.filter(f => f.endsWith('-PLAN.md'));
-
-      for (const plan of plans) {
-        const content = fs.readFileSync(path.join(phasesDir, dir, plan), 'utf-8');
-        const fm = extractFrontmatter(content);
-
-        if (!fm.wave) {
-          warnings.push(`${dir}/${plan}: missing 'wave' in frontmatter`);
-        }
-      }
-    }
-  } catch { /* intentionally empty */ }
+    } catch { /* intentionally empty */ }
+  }
 
   const passed = errors.length === 0;
   output({ passed, errors, warnings, warning_count: warnings.length }, raw, passed ? 'passed' : 'failed');
@@ -598,16 +650,7 @@ function cmdValidateHealth(cwd, options, raw) {
     // (not yet materialized on disk) and shipped-milestone history phases
     // (archived / cleared off disk). Matching only against on-disk dirs
     // produces false W002 warnings in both cases.
-    const validPhases = new Set();
-    try {
-      const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
-      for (const e of entries) {
-        if (e.isDirectory()) {
-          const m = e.name.match(/^(\d+[A-Z]?(?:\.\d+)*)/);
-          if (m) validPhases.add(m[1]);
-        }
-      }
-    } catch { /* intentionally empty */ }
+    const validPhases = collectDiskPhases(planBase);
     // Union in every phase declared anywhere in ROADMAP.md (current + shipped + backlog).
     try {
       if (fs.existsSync(roadmapPath)) {
@@ -765,11 +808,7 @@ function cmdValidateHealth(cwd, options, raw) {
       roadmapPhases.add(m[1]);
     }
 
-    const diskPhases = new Set();
-    for (const e of phaseDirEntries) {
-      const dm = e.name.match(/^(\d+[A-Z]?(?:\.\d+)*)/i);
-      if (dm) diskPhases.add(dm[1]);
-    }
+    const diskPhases = collectDiskPhases(planBase);
 
     // Build a set of phases explicitly marked not-yet-started in the ROADMAP
     // summary list (- [ ] **Phase N:**). These phases are intentionally absent
diff --git a/tests/bug-3164-milestone-archive-layout.test.cjs b/tests/bug-3164-milestone-archive-layout.test.cjs
new file mode 100644
index 000000000..72563bd72
--- /dev/null
+++ b/tests/bug-3164-milestone-archive-layout.test.cjs
@@ -0,0 +1,262 @@
+'use strict';
+
+/**
+ * #3164 — gsd-tools doesn't support .planning/milestones/v*-phases/ layout.
+ *
+ * Validators hardcode `phasesDir = .planning/phases/`. On projects that have
+ * graduated to milestone-archive layout (.planning/milestones/v*-phases/),
+ * the old path doesn't exist and diskPhases stays empty, triggering W006
+ * "Phase N in ROADMAP.md but no directory on disk" for every active phase.
+ *
+ * Fix: resolve phasesDir to the active milestone's archive dir when
+ * .planning/phases/ does not exist.
+ */
+
+const { describe, test, beforeEach, afterEach } = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('node:fs');
+const path = require('node:path');
+const { createTempProject, cleanup, runGsdTools } = require('./helpers.cjs');
+
+function setupMilestoneArchiveProject(tmpDir, options = {}) {
+  const {
+    milestone = 'v1.7',
+    phases = ['64-secondary-grader-fix'],
+    roadmapPhases = ['64'],
+  } = options;
+
+  // Remove the default .planning/phases/ dir (milestone-archive layout has no flat phases/)
+  fs.rmSync(path.join(tmpDir, '.planning', 'phases'), { recursive: true, force: true });
+
+  // Create milestone-archive phase directories
+  const archiveDir = path.join(tmpDir, '.planning', 'milestones', `${milestone}-phases`);
+  for (const phase of phases) {
+    const phaseDir = path.join(archiveDir, phase);
+    fs.mkdirSync(phaseDir, { recursive: true });
+    fs.writeFileSync(path.join(phaseDir, 'PLAN.md'), `# Plan\nPhase ${phase}\n`);
+  }
+
+  // Write STATE.md with current milestone
+  fs.writeFileSync(
+    path.join(tmpDir, '.planning', 'STATE.md'),
+    `milestone: ${milestone}\n# Session State\n\nPhase: ${roadmapPhases[0]}\n`
+  );
+
+  // Write PROJECT.md
+  fs.writeFileSync(
+    path.join(tmpDir, '.planning', 'PROJECT.md'),
+    '# Project\n\n## What This Is\nTest.\n## Core Value\nTest.\n## Requirements\nTest.\n'
+  );
+
+  // Write ROADMAP.md with phases in the milestone section
+  const phaseLines = roadmapPhases.map(n => `### Phase ${n}: Description\n\nGoal: implement it.\n`).join('\n');
+  fs.writeFileSync(
+    path.join(tmpDir, '.planning', 'ROADMAP.md'),
+    `# Roadmap\n\n## Roadmap ${milestone}: Current\n\n${phaseLines}\n`
+  );
+
+  // Write config.json
+  fs.writeFileSync(
+    path.join(tmpDir, '.planning', 'config.json'),
+    JSON.stringify({ model_profile: 'balanced', commit_docs: true }, null, 2)
+  );
+}
+
+describe('#3164 — validate consistency: milestone-archive layout', () => {
+  let tmpDir;
+
+  beforeEach(() => { tmpDir = createTempProject(); });
+  afterEach(() => { cleanup(tmpDir); });
+
+  test('no W006 warnings for phases that exist in .planning/milestones/v*-phases/', () => {
+    setupMilestoneArchiveProject(tmpDir, {
+      milestone: 'v1.7',
+      phases: ['64-secondary-grader-fix'],
+      roadmapPhases: ['64'],
+    });
+
+    const result = runGsdTools('validate consistency', tmpDir);
+    assert.ok(result.success, `validate consistency should succeed: ${result.error}`);
+
+    const out = JSON.parse(result.output);
+    const w006 = (out.warnings || []).filter(w => w.includes('Phase 64') && w.includes('no directory'));
+    assert.deepStrictEqual(
+      w006, [],
+      `Got spurious W006 for phase 64 in milestone-archive layout:\n  ${w006.join('\n  ')}`
+    );
+  });
+
+  test('no W006 when multiple phases exist in milestone-archive layout', () => {
+    setupMilestoneArchiveProject(tmpDir, {
+      milestone: 'v1.7',
+      phases: ['48-feature-a', '51-feature-b', '64-feature-c'],
+      roadmapPhases: ['48', '51', '64'],
+    });
+
+    const result = runGsdTools('validate consistency', tmpDir);
+    assert.ok(result.success, `validate consistency should succeed: ${result.error}`);
+
+    const out = JSON.parse(result.output);
+    const w006 = (out.warnings || []).filter(w => w.includes('no directory'));
+    assert.deepStrictEqual(
+      w006, [],
+      `Got spurious W006 warnings in milestone-archive layout:\n  ${w006.join('\n  ')}`
+    );
+  });
+
+  test('prefixed archive dir names (CK-64-...) are recognized as phase 64', () => {
+    setupMilestoneArchiveProject(tmpDir, {
+      milestone: 'v1.7',
+      phases: ['CK-64-secondary-grader-fix'],
+      roadmapPhases: ['64'],
+    });
+
+    const result = runGsdTools('validate consistency', tmpDir);
+    assert.ok(result.success, `validate consistency should succeed: ${result.error}`);
+
+    const out = JSON.parse(result.output);
+    const w006 = (out.warnings || []).filter(w => w.includes('Phase 64') && w.includes('no directory'));
+    assert.deepStrictEqual(
+      w006, [],
+      `Prefixed phase dir should count as phase 64, got W006:\n  ${w006.join('\n  ')}`
+    );
+  });
+
+  test('consistency scans only active milestone archive and still validates plans/frontmatter', () => {
+    // Remove default flat phases dir; this project is archive-only.
+    fs.rmSync(path.join(tmpDir, '.planning', 'phases'), { recursive: true, force: true });
+
+    // Old archived milestone should NOT be treated as active on-disk phase roots.
+    const oldDir = path.join(tmpDir, '.planning', 'milestones', 'v1.6-phases', '64-legacy');
+    fs.mkdirSync(oldDir, { recursive: true });
+    fs.writeFileSync(path.join(oldDir, '64-01-PLAN.md'), '# legacy plan\n');
+
+    // Active milestone includes intentionally malformed plan numbering/frontmatter.
+    const activeDir = path.join(tmpDir, '.planning', 'milestones', 'v1.7-phases', '65-current');
+    fs.mkdirSync(activeDir, { recursive: true });
+    fs.writeFileSync(path.join(activeDir, '65-01-PLAN.md'), '# plan 1\n');
+    fs.writeFileSync(path.join(activeDir, '65-03-PLAN.md'), '# plan 3\n');
+
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'STATE.md'),
+      '# Session State\n\n**Milestone:** v1.7 Current Milestone\nPhase: 65\n'
+    );
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'ROADMAP.md'),
+      '# Roadmap\n\n## Roadmap v1.7: Current\n\n### Phase 65: Current work\n\nGoal: test.\n'
+    );
+
+    const result = runGsdTools('validate consistency', tmpDir);
+    assert.ok(result.success, `validate consistency should succeed: ${result.error}`);
+
+    const out = JSON.parse(result.output);
+    const warnings = out.warnings || [];
+    const phase64Warnings = warnings.filter(w => w.includes('Phase 64 exists on disk but not in ROADMAP.md'));
+    assert.deepStrictEqual(
+      phase64Warnings,
+      [],
+      `Old archived milestone phase 64 should not be treated as active:\n  ${phase64Warnings.join('\n  ')}`
+    );
+    assert.ok(
+      warnings.some(w => w.includes('Gap in plan numbering in milestones/v1.7-phases/65-current')),
+      `Expected plan numbering warning from active archive root, got:\n  ${warnings.join('\n  ')}`
+    );
+    assert.ok(
+      warnings.some(w => w.includes("milestones/v1.7-phases/65-current/65-01-PLAN.md: missing 'wave'"))
+        || warnings.some(w => w.includes("milestones/v1.7-phases/65-current/65-03-PLAN.md: missing 'wave'")),
+      `Expected frontmatter warning from active archive plans, got:\n  ${warnings.join('\n  ')}`
+    );
+  });
+});
+
+describe('#3164 — validate health: milestone-archive layout', () => {
+  let tmpDir;
+
+  beforeEach(() => { tmpDir = createTempProject(); });
+  afterEach(() => { cleanup(tmpDir); });
+
+  test('no W006 warnings for phases that exist in .planning/milestones/v*-phases/', () => {
+    setupMilestoneArchiveProject(tmpDir, {
+      milestone: 'v1.7',
+      phases: ['64-secondary-grader-fix'],
+      roadmapPhases: ['64'],
+    });
+
+    const result = runGsdTools('validate health', tmpDir);
+    assert.ok(result.success, `validate health should succeed: ${result.error}`);
+
+    const out = JSON.parse(result.output);
+    const w006 = (out.warnings || []).filter(w => {
+      const msg = typeof w === 'string' ? w : w.message;
+      return msg && msg.includes('Phase 64') && msg.includes('no directory');
+    });
+    assert.deepStrictEqual(
+      w006, [],
+      `Got spurious W006 for phase 64 in milestone-archive validate health:\n  ${w006.map(w => typeof w === 'string' ? w : w.message).join('\n  ')}`
+    );
+  });
+});
+
+describe('#3164 — find-phase: milestone-archive layout', () => {
+  let tmpDir;
+
+  beforeEach(() => { tmpDir = createTempProject(); });
+  afterEach(() => { cleanup(tmpDir); });
+
+  test('find-phase 64 returns found:true for phase in .planning/milestones/v*-phases/', () => {
+    setupMilestoneArchiveProject(tmpDir, {
+      milestone: 'v1.7',
+      phases: ['64-secondary-grader-fix'],
+      roadmapPhases: ['64'],
+    });
+
+    const result = runGsdTools('find-phase 64', tmpDir);
+    assert.ok(result.success, `find-phase should succeed: ${result.error}`);
+
+    const out = JSON.parse(result.output);
+    assert.strictEqual(out.found, true, `find-phase 64 should return found:true, got: ${JSON.stringify(out)}`);
+  });
+
+  test('find-phase searches milestone archives in deterministic sorted order', () => {
+    // Remove flat phases dir so search relies on milestone archives only.
+    fs.rmSync(path.join(tmpDir, '.planning', 'phases'), { recursive: true, force: true });
+
+    const milestonesDir = path.join(tmpDir, '.planning', 'milestones');
+    const v110 = path.join(milestonesDir, 'v1.10-phases', '64-from-110');
+    const v12 = path.join(milestonesDir, 'v1.2-phases', '64-from-12');
+    fs.mkdirSync(v110, { recursive: true });
+    fs.mkdirSync(v12, { recursive: true });
+    fs.writeFileSync(path.join(v110, 'PLAN.md'), '# v1.10 plan\n');
+    fs.writeFileSync(path.join(v12, 'PLAN.md'), '# v1.2 plan\n');
+
+    const result = runGsdTools('find-phase 64', tmpDir);
+    assert.ok(result.success, `find-phase should succeed: ${result.error}`);
+
+    const out = JSON.parse(result.output);
+    assert.strictEqual(out.found, true, `find-phase 64 should return found:true, got: ${JSON.stringify(out)}`);
+    assert.strictEqual(
+      out.directory,
+      '.planning/milestones/v1.2-phases/64-from-12',
+      `Expected deterministic archive ordering (v1.2 before v1.10), got directory: ${out.directory}`
+    );
+  });
+
+  test('find-phase not-found payload includes searched_directories', () => {
+    setupMilestoneArchiveProject(tmpDir, {
+      milestone: 'v1.7',
+      phases: ['64-secondary-grader-fix'],
+      roadmapPhases: ['64'],
+    });
+
+    const result = runGsdTools('find-phase 999', tmpDir);
+    assert.ok(result.success, `find-phase should succeed with found:false payload: ${result.error}`);
+
+    const out = JSON.parse(result.output);
+    assert.strictEqual(out.found, false, `find-phase 999 should return found:false, got: ${JSON.stringify(out)}`);
+    assert.ok(Array.isArray(out.searched_directories), 'searched_directories should be an array on not-found payload');
+    assert.ok(
+      out.searched_directories.includes('.planning/milestones/v1.7-phases'),
+      `searched_directories should include active archive dir, got: ${JSON.stringify(out.searched_directories)}`
+    );
+  });
+});