diff --git a/.changeset/fix-3-milestone-complete-noise.md b/.changeset/fix-3-milestone-complete-noise.md
new file mode 100644
index 000000000..979b4f38a
--- /dev/null
+++ b/.changeset/fix-3-milestone-complete-noise.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 146
+---
+milestone.complete no longer produces a doubled version in the MILESTONES.md header (`v1.0 v1.0`), leaks phases declared via checkbox bullets into the "all phases" fallback, or extracts one-liner text from sections beyond the first heading boundary. (#3)
diff --git a/sdk/src/query/phase-lifecycle-policy.ts b/sdk/src/query/phase-lifecycle-policy.ts
index 4232d27e5..b1db23ed6 100644
--- a/sdk/src/query/phase-lifecycle-policy.ts
+++ b/sdk/src/query/phase-lifecycle-policy.ts
@@ -51,11 +51,32 @@ export function parseMultiwordArg(args: string[], flag: string): string | null {
   return tokens.length > 0 ? tokens.join(' ') : null;
 }
 
+/**
+ * Extract a one-liner from the summary body when it is not in frontmatter.
+ *
+ * Scope: content from the first heading to the next heading of ANY level.
+ * Per GFM ATX headings (https://github.github.com/gfm/#atx-headings),
+ * a heading of any level terminates the scope -- including sub-headings
+ * even when the title heading is H1.
+ *
+ * #3 defect-3: the original regex matched the first bold in the entire body
+ * after any heading, leaking bold text from later sections (e.g. deviation
+ * entries) into the one-liner.
+ */
 export function extractOneLinerFromBody(content: string): string | null {
   if (!content) return null;
   const body = content.replace(/^---\r?\n[\s\S]*?\r?\n---\r?\n*/, '');
-  const match = body.match(/^#[^\n]*\n+\*\*([^*]+)\*\*/m);
-  return match ? match[1]!.trim() : null;
+  // Find the first heading of any level (GFM section ATX headings)
+  const headingMatch = body.match(/^(#{1,6}\s[^\n]+\n)/m);
+  if (!headingMatch || headingMatch.index === undefined) return null;
+  const afterHeading = body.slice(headingMatch.index + headingMatch[0].length);
+  // Bound to the first section: truncate at the next heading of any level
+  const nextHeadingMatch = afterHeading.match(/^#{1,6}\s/m);
+  const sectionScope = nextHeadingMatch && nextHeadingMatch.index !== undefined
+    ? afterHeading.slice(0, nextHeadingMatch.index)
+    : afterHeading;
+  const boldMatch = sectionScope.match(/\*\*([^*]+)\*\*/);
+  return boldMatch ? boldMatch[1]!.trim() : null;
 }
 
 /**
diff --git a/sdk/src/query/phase-lifecycle.test.ts b/sdk/src/query/phase-lifecycle.test.ts
index 44f8221b5..d5a4a7d2c 100644
--- a/sdk/src/query/phase-lifecycle.test.ts
+++ b/sdk/src/query/phase-lifecycle.test.ts
@@ -1969,3 +1969,132 @@ describe('collectDecimalSuffixesFromDirNames — CR-3267 finding 3: alphanumeric
     expect(result.has(2)).toBe(true);
   });
 });
+
+// ─── #3 defect-1: milestone.complete header duplication ───────────────────
+//
+// Historical evidence: `## v1.8.0 Quick Mode (Shipped: 2026-01-19)`
+// Canonical template: `## ${version}${nameOpt ? ` ${nameOpt}` : ''} (Shipped: ${today})`
+// GFM § ATX headings: https://github.github.com/gfm/#atx-headings
+
+describe('milestoneComplete (#3 defect-1): header version/name rendering', () => {
+  it('no --name: header is "## v1.0 (Shipped: <date>)" — version appears exactly once', async () => {
+    const { milestoneComplete } = await import('./phase-lifecycle.js');
+    const today = new Date().toISOString().split('T')[0]!;
+    const roadmap = `# Roadmap\n\n## Current Milestone: v1.0\n\n### Phase 1: Foundation\n\n**Goal:** TBD\n**Plans:** 1 plan\n\nPlans:\n- [ ] 01-01\n`;
+    const state = `---\ngsd_state_version: 1.0\nmilestone: v1.0\nstatus: executing\n---\n\n# Project State\n\n## Current Position\n\nPhase: 1\nStatus: Executing\n`;
+    await setupTestProject(tmpDir, { roadmap, state });
+    const milestonesPath = join(tmpDir, '.planning', 'MILESTONES.md');
+    await writeFile(milestonesPath, '# Milestones\n\n', 'utf-8');
+    await mkdir(join(tmpDir, '.planning', 'phases', '01-foundation'), { recursive: true });
+
+    await milestoneComplete(['v1.0'], tmpDir);
+
+    const content = await readFile(milestonesPath, 'utf-8');
+    // Must match exactly "## v1.0 (Shipped: <date>)" — version must NOT be doubled
+    expect(content).toContain(`## v1.0 (Shipped: ${today})`);
+    expect(content).not.toMatch(/## v1\.0 v1\.0/);
+  });
+
+  it('with --name "Foundation Release": header is "## v1.0 Foundation Release (Shipped: <date>)"', async () => {
+    const { milestoneComplete } = await import('./phase-lifecycle.js');
+    const today = new Date().toISOString().split('T')[0]!;
+    const roadmap = `# Roadmap\n\n## Current Milestone: v1.0\n\n### Phase 1: Foundation\n\n**Goal:** TBD\n**Plans:** 1 plan\n\nPlans:\n- [ ] 01-01\n`;
+    const state = `---\ngsd_state_version: 1.0\nmilestone: v1.0\nstatus: executing\n---\n\n# Project State\n\n## Current Position\n\nPhase: 1\nStatus: Executing\n`;
+    await setupTestProject(tmpDir, { roadmap, state });
+    const milestonesPath = join(tmpDir, '.planning', 'MILESTONES.md');
+    await writeFile(milestonesPath, '# Milestones\n\n', 'utf-8');
+    await mkdir(join(tmpDir, '.planning', 'phases', '01-foundation'), { recursive: true });
+
+    await milestoneComplete(['v1.0', '--name', 'Foundation', 'Release'], tmpDir);
+
+    const content = await readFile(milestonesPath, 'utf-8');
+    // version + name appended: "## v1.0 Foundation Release (Shipped: ...)"
+    expect(content).toContain(`## v1.0 Foundation Release (Shipped: ${today})`);
+    expect(content).not.toMatch(/## v1\.0 v1\.0/);
+  });
+});
+
+// ─── #3 defect-2: bullet-declared phases leak phase 99 into milestone ─────
+//
+// ROADMAP declares phases via checkbox bullets ONLY (GFM task list items:
+// https://github.github.com/gfm/#task-list-items-extension-).
+// When there are no `### Phase N:` headings in the milestone section,
+// getMilestonePhaseFilter falls back to passAll (milestonePhaseNums.size === 0),
+// admitting unrelated phase dirs like 99-unrelated.
+// The fix: extend the phase-extraction regex to also match checkbox-bullet
+// declarations so passAll is not triggered spuriously.
+
+describe('milestoneComplete (#3 defect-2): checkbox-bullet phase declarations filter correctly', () => {
+  it('collects only phases 1 and 2 from bullet-only declarations — never phase 99', async () => {
+    const { milestoneComplete } = await import('./phase-lifecycle.js');
+    // Roadmap declares phases via GFM task-list bullets ONLY — no ### Phase N:
+    // headings exist anywhere in the document. This is the exact shape that
+    // triggers passAll in the current code (milestonePhaseNums.size === 0).
+    const roadmap = `# Roadmap
+
+## Current Milestone: v1.0 Foundation
+
+- [ ] **Phase 1: Foundation**
+- [ ] **Phase 2: API**
+
+---
+*Last updated: 2026-01-01*
+`;
+    const state = `---\ngsd_state_version: 1.0\nmilestone: v1.0\nstatus: executing\n---\n\n# Project State\n\n## Current Position\n\nPhase: 1\nStatus: Executing\n`;
+    await setupTestProject(tmpDir, { roadmap, state });
+
+    const phasesDir = join(tmpDir, '.planning', 'phases');
+    await mkdir(join(phasesDir, '01-foundation'), { recursive: true });
+    await mkdir(join(phasesDir, '02-api'), { recursive: true });
+    await mkdir(join(phasesDir, '99-unrelated'), { recursive: true });
+
+    const summaryContent = `# Phase Summary\n\n**Shipped the feature.**\n`;
+    await writeFile(join(phasesDir, '01-foundation', 'SUMMARY.md'), summaryContent, 'utf-8');
+    await writeFile(join(phasesDir, '02-api', 'SUMMARY.md'), summaryContent, 'utf-8');
+    // Phase 99 has a summary too — should NOT appear in accomplishments
+    await writeFile(join(phasesDir, '99-unrelated', 'SUMMARY.md'), '# Phase Summary\n\n**Should NOT appear.**\n', 'utf-8');
+
+    const milestonesPath = join(tmpDir, '.planning', 'MILESTONES.md');
+    await writeFile(milestonesPath, '# Milestones\n\n', 'utf-8');
+
+    const result = await milestoneComplete(['v1.0'], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const accomplishments = data.accomplishments as string[];
+
+    // phases 1 and 2 should be counted, 99 must be excluded
+    expect(data.phases).toBe(2);
+    expect(accomplishments.some(a => a.includes('Should NOT appear'))).toBe(false);
+  });
+});
+
+// ─── #3 defect-3: extractOneLinerFromBody section-scope leak ──────────────
+//
+// extractOneLinerFromBody must be bounded to the content between the first
+// heading and the next heading of ANY level (GFM § ATX headings:
+// https://github.github.com/gfm/#atx-headings).
+// A bold match inside a subsequent subsection (e.g. "### Deviation 1 — bar")
+// must NOT be returned.
+
+describe('extractOneLinerFromBody (#3 defect-3): bounded to first heading section', () => {
+  it('returns the real one-liner and NOT the bold inside a following sub-heading', async () => {
+    const { extractOneLinerFromBody } = await import('./phase-lifecycle-policy.js');
+    const body = [
+      '# Phase Summary',
+      '',
+      '> This is a blockquote intro — not a one-liner.',
+      '',
+      '**Real one-liner: shipped the foo system.**',
+      '',
+      'Some prose.',
+      '',
+      '### Deviation 1 — bar',
+      '',
+      '**This bold should NOT be picked up.**',
+      '',
+    ].join('\n');
+
+    const result = extractOneLinerFromBody(body);
+    expect(result).toBe('Real one-liner: shipped the foo system.');
+    expect(result).not.toContain('should NOT be picked up');
+  });
+});
diff --git a/sdk/src/query/phase-lifecycle.ts b/sdk/src/query/phase-lifecycle.ts
index 5dfc9a959..f40e0a621 100644
--- a/sdk/src/query/phase-lifecycle.ts
+++ b/sdk/src/query/phase-lifecycle.ts
@@ -2039,7 +2039,11 @@ export const milestoneComplete: QueryHandler = async (args, projectDir, workstre
   const archiveDir = join(paths.planning, 'milestones');
   const phasesDir = paths.phases;
   const today = new Date().toISOString().split('T')[0]!;
-  const milestoneName = nameOpt || version;
+  // #3 defect-1: preserve version in header, append optional name only when
+  // explicitly provided. Historical template: `## v1.8.0 Quick Mode (Shipped: ...)`.
+  // When no --name is given, milestoneName is undefined so the header is
+  // `## ${version} (Shipped: ...)` — version appears exactly once.
+  const milestoneName = nameOpt ?? undefined;
 
   await mkdir(archiveDir, { recursive: true });
 
@@ -2095,8 +2099,10 @@ export const milestoneComplete: QueryHandler = async (args, projectDir, workstre
 
   if (existsSync(reqPath)) {
     const reqContent = await readFile(reqPath, 'utf-8');
+    // #3 defect-1: canonical header: version + optional name appended only when provided.
+    const reqTitle = milestoneName ? `${version} ${milestoneName}` : version;
     const archiveHeader =
-      `# Requirements Archive: ${version} ${milestoneName}\n\n` +
+      `# Requirements Archive: ${reqTitle}\n\n` +
       `**Archived:** ${today}\n**Status:** SHIPPED\n\n` +
       `For current requirements, see \`.planning/REQUIREMENTS.md\`.\n\n---\n\n`;
     await writeFile(join(archiveDir, `${version}-REQUIREMENTS.md`), archiveHeader + reqContent, 'utf-8');
@@ -2108,8 +2114,12 @@ export const milestoneComplete: QueryHandler = async (args, projectDir, workstre
   }
 
   const accomplishmentsList = accomplishments.map((a) => `- ${a}`).join('\n');
+  // #3 defect-1 (GFM § ATX headings: https://github.github.com/gfm/#atx-headings)
+  // Canonical template: `## ${version}${nameOpt ? ` ${nameOpt}` : ''} (Shipped: ${today})`
+  // Historical evidence: `## v1.8.0 Quick Mode (Shipped: 2026-01-19)`
+  const milestoneTitle = milestoneName ? `${version} ${milestoneName}` : version;
   const milestoneEntry =
-    `## ${version} ${milestoneName} (Shipped: ${today})\n\n` +
+    `## ${milestoneTitle} (Shipped: ${today})\n\n` +
     `**Phases completed:** ${phaseCount} phases, ${totalPlans} plans, ${totalTasks} tasks\n\n` +
     `**Key accomplishments:**\n${accomplishmentsList || '- (none recorded)'}\n\n---\n\n`;
 
diff --git a/sdk/src/query/state.ts b/sdk/src/query/state.ts
index 2b6cc59ae..3e6095d86 100644
--- a/sdk/src/query/state.ts
+++ b/sdk/src/query/state.ts
@@ -47,7 +47,13 @@ export async function getMilestonePhaseFilter(projectDir: string, workstream?: s
   try {
     const roadmapContent = await readFile(planningPaths(projectDir, workstream).roadmap, 'utf-8');
     const roadmap = await extractCurrentMilestone(roadmapContent, projectDir, workstream);
-    const phasePattern = /#{2,4}\s*Phase\s+([\w][\w.-]*)\s*:/gi;
+    // Match both heading-style (### Phase N:) and GFM task-list bullet-style
+    // (- [ ] **Phase N: title**) declarations.
+    // GFM § ATX headings: https://github.github.com/gfm/#atx-headings
+    // GFM § Task list items: https://github.github.com/gfm/#task-list-items-extension-
+    // #3 defect-2: the original regex matched only heading-style declarations;
+    // bullet-only ROADMAPs caused milestonePhaseNums.size === 0 -> passAll -> phase 99 leakage.
+    const phasePattern = /(?:#{2,4}\s*|-\s*(?:\[[x ]\]\s*)?\*{0,2}\s*)Phase\s+([\w][\w.-]*)\s*:/gi;
     let m: RegExpExecArray | null;
     while ((m = phasePattern.exec(roadmap)) !== null) {
       milestonePhaseNums.add(m[1]);
diff --git a/sdk/src/query/summary.test.ts b/sdk/src/query/summary.test.ts
index e066a7c35..4019b18b3 100644
--- a/sdk/src/query/summary.test.ts
+++ b/sdk/src/query/summary.test.ts
@@ -59,6 +59,29 @@ describe('summaryExtract', () => {
     expect(Array.isArray(data.decisions)).toBe(true);
   });
 
+  it('summaryExtract: one-liner extraction is bounded to first heading scope', async () => {
+    const rel = '.planning/phases/01-x/01-SUMMARY.md';
+    const fixture = [
+      '# Phase Summary',
+      '',
+      '> Blockquote intro — should NOT be picked up.',
+      '',
+      '**Real one-liner: shipped the foo system.**',
+      '',
+      '### Deviation 1 — bar',
+      '',
+      '**This bold MUST NOT be picked up by the bounded extractor.**',
+    ].join('\n');
+    await writeFile(
+      join(tmpDir, '.planning', 'phases', '01-x', '01-SUMMARY.md'),
+      fixture,
+      'utf-8',
+    );
+    const r = await summaryExtract([rel], tmpDir);
+    const data = r.data as Record<string, unknown>;
+    expect(data.one_liner).toBe('Real one-liner: shipped the foo system.');
+  });
+
   it('filters with --fields', async () => {
     const rel = '.planning/phases/01-x/01-SUMMARY.md';
     await writeFile(
diff --git a/sdk/src/query/summary.ts b/sdk/src/query/summary.ts
index 6eabc8019..936c8e7b8 100644
--- a/sdk/src/query/summary.ts
+++ b/sdk/src/query/summary.ts
@@ -26,12 +26,30 @@ import type { QueryHandler } from './utils.js';
 /**
  * Extract a one-liner from the summary body when it is not in frontmatter.
  * Port of `extractOneLinerFromBody` from `get-shit-done/bin/lib/core.cjs`.
+ *
+ * Scope: content from the first heading to the next heading of ANY level.
+ * Per GFM ATX headings (https://github.github.com/gfm/#atx-headings),
+ * a heading of any level terminates the scope — including sub-headings
+ * even when the title heading is H1.
+ *
+ * #3 defect-3: the original regex matched the first bold in the entire body
+ * after any heading, leaking bold text from later sections (e.g. deviation
+ * entries) into the one-liner.
  */
 function extractOneLinerFromBody(content: string): string | null {
   if (!content) return null;
   const body = content.replace(/^---\r?\n[\s\S]*?\r?\n---\r?\n*/, '');
-  const match = body.match(/^#[^\n]*\n+\*\*([^*]+)\*\*/m);
-  return match ? match[1].trim() : null;
+  // Find the first heading of any level (GFM section ATX headings)
+  const headingMatch = body.match(/^(#{1,6}\s[^\n]+\n)/m);
+  if (!headingMatch || headingMatch.index === undefined) return null;
+  const afterHeading = body.slice(headingMatch.index + headingMatch[0].length);
+  // Bound to the first section: truncate at the next heading of any level
+  const nextHeadingMatch = afterHeading.match(/^#{1,6}\s/m);
+  const sectionScope = nextHeadingMatch && nextHeadingMatch.index !== undefined
+    ? afterHeading.slice(0, nextHeadingMatch.index)
+    : afterHeading;
+  const boldMatch = sectionScope.match(/\*\*([^*]+)\*\*/);
+  return boldMatch ? boldMatch[1]!.trim() : null;
 }
 
 /** Normalize frontmatter list fields — scalars become single-element arrays. */