diff --git a/.changeset/pr-3115-release-note.md b/.changeset/pr-3115-release-note.md
new file mode 100644
index 000000000..db3fa29a2
--- /dev/null
+++ b/.changeset/pr-3115-release-note.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 3115
+---
+Fixes for issue #3115 were applied to keep command/workflow behavior and SDK parity aligned with current documented usage.
diff --git a/get-shit-done/bin/lib/init.cjs b/get-shit-done/bin/lib/init.cjs
index 3eaa42374..952bdaaf4 100644
--- a/get-shit-done/bin/lib/init.cjs
+++ b/get-shit-done/bin/lib/init.cjs
@@ -14,6 +14,30 @@ const { maskIfSecret } = require('./secrets.cjs');
 // same in markdown but differ textually.
 const REQUIREMENTS_HEADER_RE = /^\*\*Requirements:?\*\*[^\S\n]*:?[^\S\n]*([^\n]*)$/m;
 
+function listPhaseSummaryFiles(phaseDir) {
+  const phaseFiles = fs.readdirSync(phaseDir);
+  const rootSummaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+  const plansDir = path.join(phaseDir, 'plans');
+  let nestedSummaries = [];
+  if (fs.existsSync(plansDir)) {
+    const files = fs.readdirSync(plansDir);
+    nestedSummaries = files.filter(f => /^SUMMARY-\d+.*\.md$/i.test(f));
+  }
+  return rootSummaries.concat(nestedSummaries);
+}
+
+function listPhasePlanFiles(phaseDir) {
+  const phaseFiles = fs.readdirSync(phaseDir);
+  const rootPlans = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md');
+  const plansDir = path.join(phaseDir, 'plans');
+  let nestedPlans = [];
+  if (fs.existsSync(plansDir)) {
+    const files = fs.readdirSync(plansDir);
+    nestedPlans = files.filter(f => /^PLAN-\d+.*\.md$/i.test(f));
+  }
+  return rootPlans.concat(nestedPlans);
+}
+
 function getLatestCompletedMilestone(cwd) {
   const milestonesPath = path.join(planningRoot(cwd), 'MILESTONES.md');
   if (!fs.existsSync(milestonesPath)) return null;
@@ -901,8 +925,7 @@ function cmdInitMilestoneOp(cwd, raw) {
       const dirName = diskPhaseDirs.get(canonicalizePhase(num));
       if (!dirName) continue;
       try {
-        const phaseFiles = fs.readdirSync(path.join(phasesDir, dirName));
-        const hasSummary = phaseFiles.some(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+        const hasSummary = listPhaseSummaryFiles(path.join(phasesDir, dirName)).length > 0;
         if (hasSummary) completedPhases++;
       } catch { /* intentionally empty */ }
     }
@@ -914,8 +937,7 @@ function cmdInitMilestoneOp(cwd, raw) {
       phaseCount = dirs.length;
       for (const dir of dirs) {
         try {
-          const phaseFiles = fs.readdirSync(path.join(phasesDir, dir));
-          const hasSummary = phaseFiles.some(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+          const hasSummary = listPhaseSummaryFiles(path.join(phasesDir, dir)).length > 0;
           if (hasSummary) completedPhases++;
         } catch { /* intentionally empty */ }
       }
@@ -1072,8 +1094,8 @@ function cmdInitManager(cwd, raw) {
       if (dirMatch) {
         const fullDir = path.join(phasesDir, dirMatch);
         const phaseFiles = fs.readdirSync(fullDir);
-        planCount = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md').length;
-        summaryCount = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md').length;
+        planCount = listPhasePlanFiles(fullDir).length;
+        summaryCount = listPhaseSummaryFiles(fullDir).length;
         hasContext = phaseFiles.some(f => f.endsWith('-CONTEXT.md') || f === 'CONTEXT.md');
         hasResearch = phaseFiles.some(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md');
 
@@ -1353,8 +1375,8 @@ function cmdInitProgress(cwd, raw) {
       const phasePath = path.join(phasesDir, dir);
       const phaseFiles = fs.readdirSync(phasePath);
 
-      const plans = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md');
-      const summaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+      const plans = listPhasePlanFiles(phasePath);
+      const summaries = listPhaseSummaryFiles(phasePath);
       const hasResearch = phaseFiles.some(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md');
 
       const status = summaries.length >= plans.length && plans.length > 0 ? 'complete' :
diff --git a/get-shit-done/bin/lib/roadmap.cjs b/get-shit-done/bin/lib/roadmap.cjs
index 133f9b4d9..930eb8b94 100644
--- a/get-shit-done/bin/lib/roadmap.cjs
+++ b/get-shit-done/bin/lib/roadmap.cjs
@@ -36,6 +36,28 @@ function coerceTruthToString(t) {
   return '';
 }
 
+function countPhasePlansAndSummaries(phaseDir) {
+  const phaseFiles = fs.readdirSync(phaseDir);
+  const rootPlans = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md');
+  const rootSummaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+
+  let nestedPlans = [];
+  let nestedSummaries = [];
+  const plansDir = path.join(phaseDir, 'plans');
+  if (fs.existsSync(plansDir)) {
+    const planFiles = fs.readdirSync(plansDir);
+    nestedPlans = planFiles.filter(f => /^PLAN-\d+.*\.md$/i.test(f));
+    nestedSummaries = planFiles.filter(f => /^SUMMARY-\d+.*\.md$/i.test(f));
+  }
+
+  return {
+    planCount: rootPlans.length + nestedPlans.length,
+    summaryCount: rootSummaries.length + nestedSummaries.length,
+    hasContext: phaseFiles.some(f => f.endsWith('-CONTEXT.md') || f === 'CONTEXT.md'),
+    hasResearch: phaseFiles.some(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md'),
+  };
+}
+
 /**
  * Search for a phase header (and its section) within the given content string.
  * Returns a result object if found (either a full match or a malformed_roadmap
@@ -197,11 +219,11 @@ function cmdRoadmapAnalyze(cwd, raw) {
       const dirMatch = _phaseDirNames.find(d => phaseTokenMatches(d, normalized));
 
       if (dirMatch) {
-        const phaseFiles = fs.readdirSync(path.join(phasesDir, dirMatch));
-        planCount = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md').length;
-        summaryCount = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md').length;
-        hasContext = phaseFiles.some(f => f.endsWith('-CONTEXT.md') || f === 'CONTEXT.md');
-        hasResearch = phaseFiles.some(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md');
+        const counts = countPhasePlansAndSummaries(path.join(phasesDir, dirMatch));
+        planCount = counts.planCount;
+        summaryCount = counts.summaryCount;
+        hasContext = counts.hasContext;
+        hasResearch = counts.hasResearch;
 
         if (summaryCount >= planCount && planCount > 0) diskStatus = 'complete';
         else if (summaryCount > 0) diskStatus = 'partial';
diff --git a/sdk/src/query/init-complex.ts b/sdk/src/query/init-complex.ts
index d85e19a03..bb0f13f84 100644
--- a/sdk/src/query/init-complex.ts
+++ b/sdk/src/query/init-complex.ts
@@ -83,6 +83,26 @@ function deriveStatusFromCheckbox(
   return 'not_started';
 }
 
+function listPhasePlanAndSummaryCounts(phasePath: string): { plans: string[]; summaries: string[] } {
+  const phaseFiles = readdirSync(phasePath);
+  const rootPlans = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md');
+  const rootSummaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+
+  const plansDir = join(phasePath, 'plans');
+  let nestedPlans: string[] = [];
+  let nestedSummaries: string[] = [];
+  if (existsSync(plansDir)) {
+    const files = readdirSync(plansDir);
+    nestedPlans = files.filter(f => /^PLAN-\d+.*\.md$/i.test(f));
+    nestedSummaries = files.filter(f => /^SUMMARY-\d+.*\.md$/i.test(f));
+  }
+
+  return {
+    plans: rootPlans.concat(nestedPlans),
+    summaries: rootSummaries.concat(nestedSummaries),
+  };
+}
+
 // ─── initNewProject ───────────────────────────────────────────────────────
 
 /**
@@ -258,8 +278,7 @@ export const initProgress: QueryHandler = async (_args, projectDir, workstream)
       const phasePath = join(paths.phases, dir);
       const phaseFiles = readdirSync(phasePath);
 
-      const plans = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md');
-      const summaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+      const { plans, summaries } = listPhasePlanAndSummaryCounts(phasePath);
       const hasResearch = phaseFiles.some(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md');
 
       let status =
@@ -431,8 +450,9 @@ export const initManager: QueryHandler = async (_args, projectDir, workstream) =
       if (dirMatch) {
         const fullDir = join(paths.phases, dirMatch);
         const phaseFiles = readdirSync(fullDir);
-        planCount = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md').length;
-        summaryCount = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md').length;
+        const counts = listPhasePlanAndSummaryCounts(fullDir);
+        planCount = counts.plans.length;
+        summaryCount = counts.summaries.length;
         hasContext = phaseFiles.some(f => f.endsWith('-CONTEXT.md') || f === 'CONTEXT.md');
         hasResearch = phaseFiles.some(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md');
 
diff --git a/sdk/src/query/roadmap.ts b/sdk/src/query/roadmap.ts
index ad139faef..ed0cb003e 100644
--- a/sdk/src/query/roadmap.ts
+++ b/sdk/src/query/roadmap.ts
@@ -404,6 +404,28 @@ function searchPhaseInContent(content: string, escapedPhase: string, phaseNum: s
   };
 }
 
+async function countPhasePlansAndSummaries(phaseDir: string): Promise<{ planCount: number; summaryCount: number; hasContext: boolean; hasResearch: boolean; }> {
+  const phaseFiles = await readdir(phaseDir);
+  const rootPlans = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md');
+  const rootSummaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+
+  let nestedPlans: string[] = [];
+  let nestedSummaries: string[] = [];
+  const plansDir = join(phaseDir, 'plans');
+  if (existsSync(plansDir)) {
+    const files = await readdir(plansDir);
+    nestedPlans = files.filter(f => /^PLAN-\d+.*\.md$/i.test(f));
+    nestedSummaries = files.filter(f => /^SUMMARY-\d+.*\.md$/i.test(f));
+  }
+
+  return {
+    planCount: rootPlans.length + nestedPlans.length,
+    summaryCount: rootSummaries.length + nestedSummaries.length,
+    hasContext: phaseFiles.some(f => f.endsWith('-CONTEXT.md') || f === 'CONTEXT.md'),
+    hasResearch: phaseFiles.some(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md'),
+  };
+}
+
 // ─── Exported handlers ────────────────────────────────────────────────────
 
 /**
@@ -509,11 +531,11 @@ export const roadmapAnalyze: QueryHandler = async (_args, projectDir, workstream
       const dirMatch = dirs.find(d => phaseTokenMatches(d, normalized));
 
       if (dirMatch) {
-        const phaseFiles = await readdir(join(phasesDir, dirMatch));
-        planCount = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md').length;
-        summaryCount = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md').length;
-        hasContext = phaseFiles.some(f => f.endsWith('-CONTEXT.md') || f === 'CONTEXT.md');
-        hasResearch = phaseFiles.some(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md');
+        const counts = await countPhasePlansAndSummaries(join(phasesDir, dirMatch));
+        planCount = counts.planCount;
+        summaryCount = counts.summaryCount;
+        hasContext = counts.hasContext;
+        hasResearch = counts.hasResearch;
 
         if (summaryCount >= planCount && planCount > 0) diskStatus = 'complete';
         else if (summaryCount > 0) diskStatus = 'partial';
diff --git a/tests/init-manager.test.cjs b/tests/init-manager.test.cjs
index de31a77f3..5e5eae6e1 100644
--- a/tests/init-manager.test.cjs
+++ b/tests/init-manager.test.cjs
@@ -131,6 +131,27 @@ describe('init manager', () => {
     assert.strictEqual(output.phases[4].disk_status, 'no_directory');
   });
 
+  test('treats plans/PLAN-NN.md layout as planned/complete counts (#3053)', () => {
+    writeState(tmpDir);
+    writeRoadmap(tmpDir, [
+      { number: '1', name: 'Nested Plans' },
+    ]);
+
+    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-nested-plans');
+    fs.mkdirSync(path.join(phaseDir, 'plans'), { recursive: true });
+    fs.writeFileSync(path.join(phaseDir, 'plans', 'PLAN-01.md'), '# Plan 1');
+    fs.writeFileSync(path.join(phaseDir, 'plans', 'PLAN-02.md'), '# Plan 2');
+    fs.writeFileSync(path.join(phaseDir, 'plans', 'SUMMARY-01.md'), '# Summary 1');
+
+    const result = runGsdTools('init manager', tmpDir);
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const output = JSON.parse(result.output);
+    assert.strictEqual(output.phases[0].plan_count, 2);
+    assert.strictEqual(output.phases[0].summary_count, 1);
+    assert.strictEqual(output.phases[0].disk_status, 'partial');
+  });
+
   test('dependency satisfaction: deps on complete phases = satisfied', () => {
     writeState(tmpDir);
     writeRoadmap(tmpDir, [
diff --git a/tests/roadmap.test.cjs b/tests/roadmap.test.cjs
index ab05926ca..1e6420652 100644
--- a/tests/roadmap.test.cjs
+++ b/tests/roadmap.test.cjs
@@ -706,6 +706,31 @@ describe('roadmap update-plan-progress command', () => {
     assert.ok(roadmapContent.includes('1/2'), 'roadmap should contain updated plan count');
   });
 
+  test('counts plans and summaries from plans/ subdirectory layout (#3053)', () => {
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'ROADMAP.md'),
+      `# Roadmap
+
+### Phase 1: Test
+**Goal:** Test goal
+`
+    );
+
+    const p1 = path.join(tmpDir, '.planning', 'phases', '01-test', 'plans');
+    fs.mkdirSync(p1, { recursive: true });
+    fs.writeFileSync(path.join(p1, 'PLAN-01.md'), '# Plan 1');
+    fs.writeFileSync(path.join(p1, 'PLAN-02.md'), '# Plan 2');
+    fs.writeFileSync(path.join(p1, 'SUMMARY-01.md'), '# Summary 1');
+
+    const result = runGsdTools('roadmap analyze', tmpDir);
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const output = JSON.parse(result.output);
+    assert.strictEqual(output.phases[0].plan_count, 2);
+    assert.strictEqual(output.phases[0].summary_count, 1);
+    assert.strictEqual(output.phases[0].disk_status, 'partial');
+  });
+
   test('updates progress and checks checkbox on completion', () => {
     fs.writeFileSync(
       path.join(tmpDir, '.planning', 'ROADMAP.md'),