diff --git a/src/App.jsx b/src/App.jsx
index 09536fc..e373e85 100644
--- a/src/App.jsx
+++ b/src/App.jsx
@@ -1,4 +1,4 @@
-import React, { useEffect, useState } from 'react';
+import React, { useCallback, useEffect, useRef, useState } from 'react';
 import {
   ArrowDown,
   ArrowRight,
@@ -207,7 +207,8 @@ const defaultContent = {
     format: 'glb',
     programType: 'internal',
     predecessors: [],
-    successors: []
+    successors: [],
+    mergeGroup: ''
   },
   wayPrimal: {
     name: 'WayPrimal',
@@ -218,6 +219,7 @@ const defaultContent = {
     programType: 'internal',
     predecessors: [],
     successors: [],
+    mergeGroup: '',
     linkLabel: '천지인 산출 모델을 WayPrimal 설계 입력으로 연계'
   },
   comparisons: [],
@@ -233,6 +235,7 @@ function normalizeStoredContent(parsed) {
         programType: getProgramType(parsed.cheonjiin?.programType ?? defaultContent.cheonjiin.programType),
         predecessors: parsed.cheonjiin?.predecessors ?? [],
         successors: parsed.cheonjiin?.successors ?? [],
+        mergeGroup: parsed.cheonjiin?.mergeGroup ?? '',
         format:
           !parsed.cheonjiin?.format || parsed.cheonjiin.format === '예: DXF, SHP, GeoTIFF, 수치지형도 v2 등'
             ? defaultContent.cheonjiin.format
@@ -244,17 +247,23 @@ function normalizeStoredContent(parsed) {
         programType: getProgramType(parsed.wayPrimal?.programType ?? defaultContent.wayPrimal.programType),
         predecessors: parsed.wayPrimal?.predecessors ?? [],
         successors: parsed.wayPrimal?.successors ?? [],
+        mergeGroup: parsed.wayPrimal?.mergeGroup ?? '',
         format:
           parsed.wayPrimal?.format === '예: DWG, LandXML, XLSX, 도공계산서, 기본설계 모델 등'
             ? defaultContent.wayPrimal.format
             : (parsed.wayPrimal?.format ?? defaultContent.wayPrimal.format)
       },
-      comparisons: parsed.comparisons ?? [],
+      comparisons: (parsed.comparisons ?? []).map((comparison, index) => ({
+        ...comparison,
+        id: comparison.id ?? `comparison-${comparison.leftProgramId}-${comparison.rightProgramId}-${index}`,
+        title: comparison.title ?? ''
+      })),
       extraPrograms: (parsed.extraPrograms ?? []).map((program, index, programs) => ({
         ...program,
         programType: getProgramType(program.programType),
         predecessors: program.predecessors ?? [],
         successors: program.successors ?? [],
+        mergeGroup: program.mergeGroup ?? '',
         linkLabel: program.linkLabel ?? `이전 프로그램 산출물을 ${program.name} 입력으로 연계`
       }))
     };
@@ -1149,7 +1158,7 @@ function DetailPopup({
   );
 }
 
-function RelationPopup({ programs, onToggleRelation, onClose }) {
+function RelationPopup({ programs, onToggleRelation, onMergeGroupChange, onClose }) {
   return (
     <div className="fixed inset-0 z-[60] flex items-center justify-center bg-slate-950/30 px-4 backdrop-blur-sm">
       <section className="relative flex max-h-[calc(100vh-48px)] w-full max-w-4xl flex-col overflow-hidden rounded-3xl border border-white/70 bg-white shadow-2xl">
@@ -1180,7 +1189,7 @@ function RelationPopup({ programs, onToggleRelation, onClose }) {
             {programs.map((program) => {
               const candidates = programs.filter((item) => item.id !== program.id);
               return (
-                <div key={program.id} className="grid gap-3 rounded-2xl bg-white p-4 ring-1 ring-slate-100 lg:grid-cols-[180px_1fr_1fr]">
+                <div key={program.id} className="grid gap-3 rounded-2xl bg-white p-4 ring-1 ring-slate-100 lg:grid-cols-[180px_1fr_1fr_220px]">
                   <div>
                     <p className="text-[11px] font-extrabold uppercase tracking-wide text-slate-400">프로그램</p>
                     <h4 className="mt-1 text-base font-extrabold text-slate-950">{program.name}</h4>
@@ -1217,6 +1226,27 @@ function RelationPopup({ programs, onToggleRelation, onClose }) {
                       ))}
                     </div>
                   </div>
+                  <div>
+                    <p className="mb-2 text-[12px] font-extrabold text-violet-700">하나로 인식</p>
+                    <select
+                      value={program.mergeGroup ?? ''}
+                      onChange={(event) => onMergeGroupChange(program.id, event.target.value)}
+                      className="w-full rounded-xl border border-violet-100 bg-violet-50 px-3 py-2 text-[12px] font-extrabold text-violet-800 outline-none focus:border-violet-300"
+                    >
+                      <option value="">개별 프로그램</option>
+                      {candidates.map((candidate) => {
+                        const groupValue = candidate.mergeGroup || candidate.id;
+                        return (
+                          <option key={candidate.id} value={groupValue}>
+                            {candidate.name}와 같은 프로그램
+                          </option>
+                        );
+                      })}
+                    </select>
+                    <p className="mt-2 text-[11px] font-bold leading-4 text-slate-400">
+                      같은 단계로 보는 프로그램을 묶으면 연결도에서는 하나의 박스로 표시됩니다.
+                    </p>
+                  </div>
                 </div>
               );
             })}
@@ -1227,67 +1257,125 @@ function RelationPopup({ programs, onToggleRelation, onClose }) {
   );
 }
 
-function ProgramComparePopup({ programs, comparisons, onComparisonChange, onClose }) {
+function ProgramComparePopup({ programs, comparisons, initialPair, onComparisonSave, onComparisonDelete, onClose }) {
   const internalProgram = programs.find((program) => getProgramType(program.programType) === 'internal');
   const commercialProgram = programs.find((program) => getProgramType(program.programType) === 'commercial');
-  const savedComparisons = comparisons.filter(
-    (comparison) =>
-      programs.some((program) => program.id === comparison.leftProgramId) &&
-      programs.some((program) => program.id === comparison.rightProgramId) &&
-      ((comparison.stepMatches ?? []).some((match) => match.reason?.trim()) || comparison.note?.trim())
-  ).sort((left, right) => (right.updatedAt ?? '').localeCompare(left.updatedAt ?? ''));
-  const [leftProgramId, setLeftProgramId] = useState(savedComparisons[0]?.leftProgramId ?? internalProgram?.id ?? programs[0]?.id ?? '');
-  const [rightProgramId, setRightProgramId] = useState(
-    savedComparisons[0]?.rightProgramId ??
-      commercialProgram?.id ??
-      programs.find((program) => program.id !== (internalProgram?.id ?? programs[0]?.id))?.id ??
-      ''
-  );
-  const leftProgram = programs.find((program) => program.id === leftProgramId);
-  const rightProgram = programs.find((program) => program.id === rightProgramId);
-  const comparison =
-    comparisons.find((item) => item.leftProgramId === leftProgramId && item.rightProgramId === rightProgramId) ?? {};
-  const hasSavedComparison = Boolean((comparison.stepMatches ?? []).some((match) => match.reason?.trim()) || comparison.note?.trim());
+  const savedComparisons = comparisons
+    .filter(
+      (comparison) =>
+        programs.some((program) => program.id === comparison.leftProgramId) &&
+        programs.some((program) => program.id === comparison.rightProgramId) &&
+        (comparison.title?.trim() || (comparison.stepMatches ?? []).some((match) => match.reason?.trim()) || comparison.note?.trim())
+    )
+    .sort((left, right) => (right.updatedAt ?? '').localeCompare(left.updatedAt ?? ''));
+  const createComparisonId = (leftProgramId, rightProgramId) => `comparison-${[leftProgramId, rightProgramId].sort().join('__')}`;
+  const isValidProgramId = (programId) => programs.some((program) => program.id === programId);
+  const pairMatches = (comparison, leftProgramId, rightProgramId) =>
+    [comparison.leftProgramId, comparison.rightProgramId].sort().join('__') === [leftProgramId, rightProgramId].sort().join('__');
+  const defaultLeftProgramId = isValidProgramId(initialPair?.leftProgramId)
+    ? initialPair.leftProgramId
+    : internalProgram?.id ?? programs[0]?.id ?? '';
+  const defaultRightProgramId = isValidProgramId(initialPair?.rightProgramId) && initialPair.rightProgramId !== defaultLeftProgramId
+    ? initialPair.rightProgramId
+    : commercialProgram?.id ?? programs.find((program) => program.id !== defaultLeftProgramId)?.id ?? '';
+  const findSavedComparisonByPair = (leftProgramId, rightProgramId) =>
+    savedComparisons.find((comparison) => pairMatches(comparison, leftProgramId, rightProgramId));
+  const createEmptyDraft = (leftProgramId = defaultLeftProgramId, rightProgramId = defaultRightProgramId) => ({
+    id: createComparisonId(leftProgramId, rightProgramId),
+    title: '',
+    leftProgramId,
+    rightProgramId,
+    stepMatches: [],
+    note: ''
+  });
+  const [draft, setDraft] = useState(() => {
+    const pairComparison = initialPair ? findSavedComparisonByPair(defaultLeftProgramId, defaultRightProgramId) : null;
+    return pairComparison ?? (initialPair ? createEmptyDraft(defaultLeftProgramId, defaultRightProgramId) : savedComparisons[0] ?? createEmptyDraft());
+  });
+  const [loadTargetId, setLoadTargetId] = useState(() => {
+    const pairComparison = initialPair ? findSavedComparisonByPair(defaultLeftProgramId, defaultRightProgramId) : null;
+    return pairComparison?.id ?? (initialPair ? '' : savedComparisons[0]?.id ?? '');
+  });
+  const leftProgram = programs.find((program) => program.id === draft.leftProgramId);
+  const rightProgram = programs.find((program) => program.id === draft.rightProgramId);
   const leftSteps = leftProgram?.steps ?? [];
   const rightSteps = rightProgram?.steps ?? [];
-  const stepMatches = comparison.stepMatches ?? [];
+  const stepMatches = draft.stepMatches ?? [];
   const maxStepCount = Math.max(leftSteps.length, rightSteps.length);
+  const isSavedDraft = savedComparisons.some((comparison) => comparison.id === draft.id);
 
-  const updateComparison = (field, value) => {
-    if (!leftProgramId || !rightProgramId || leftProgramId === rightProgramId) return;
-    onComparisonChange(leftProgramId, rightProgramId, field, value);
+  const updateDraft = (field, value) => {
+    setDraft((current) => ({ ...current, [field]: value }));
+  };
+  const startNewComparison = () => {
+    const nextDraft = createEmptyDraft();
+    setDraft(nextDraft);
+    setLoadTargetId('');
+  };
+  const loadSelectedComparison = () => {
+    const selected = savedComparisons.find((comparison) => comparison.id === loadTargetId);
+    if (!selected) return;
+    setDraft({
+      ...selected,
+      stepMatches: selected.stepMatches ?? [],
+      note: selected.note ?? '',
+      title: selected.title ?? ''
+    });
+  };
+  const saveDraft = () => {
+    if (!draft.leftProgramId || !draft.rightProgramId || draft.leftProgramId === draft.rightProgramId) return;
+    onComparisonSave({
+      ...draft,
+      id: createComparisonId(draft.leftProgramId, draft.rightProgramId),
+      title: draft.title ?? '',
+      stepMatches: (draft.stepMatches ?? []).filter((match) => match.reason?.trim()),
+      note: draft.note ?? '',
+      updatedAt: new Date().toISOString()
+    });
+    setLoadTargetId(draft.id);
+  };
+  const deleteDraft = () => {
+    if (isSavedDraft) onComparisonDelete(draft.id);
+    startNewComparison();
   };
   const getStepMatch = (stepIndex) =>
     stepMatches.find(
       (match) => String(match.leftStepIndex) === String(stepIndex) && String(match.rightStepIndex) === String(stepIndex)
     ) ?? {};
   const updateStepReason = (stepIndex, value) => {
-    const existingIndex = stepMatches.findIndex(
-      (match) => String(match.leftStepIndex) === String(stepIndex) && String(match.rightStepIndex) === String(stepIndex)
-    );
-    if (!value.trim() && existingIndex >= 0) {
-      updateComparison('stepMatches', stepMatches.filter((_, index) => index !== existingIndex));
-      return;
-    }
-    if (!value.trim()) return;
-    const nextMatch = {
-      ...(existingIndex >= 0 ? stepMatches[existingIndex] : {}),
-      id: `step-${stepIndex}`,
-      leftStepIndex: String(stepIndex),
-      rightStepIndex: String(stepIndex),
-      reason: value
-    };
-    updateComparison(
-      'stepMatches',
-      existingIndex >= 0
-        ? stepMatches.map((match, index) => (index === existingIndex ? nextMatch : match))
-        : [...stepMatches, nextMatch]
-    );
+    setDraft((current) => {
+      const currentMatches = current.stepMatches ?? [];
+      const existingIndex = currentMatches.findIndex(
+        (match) => String(match.leftStepIndex) === String(stepIndex) && String(match.rightStepIndex) === String(stepIndex)
+      );
+      if (!value.trim()) {
+        return {
+          ...current,
+          stepMatches: existingIndex >= 0 ? currentMatches.filter((_, index) => index !== existingIndex) : currentMatches
+        };
+      }
+      const nextMatch = {
+        ...(existingIndex >= 0 ? currentMatches[existingIndex] : {}),
+        id: `step-${stepIndex}`,
+        leftStepIndex: String(stepIndex),
+        rightStepIndex: String(stepIndex),
+        reason: value
+      };
+      return {
+        ...current,
+        stepMatches:
+          existingIndex >= 0
+            ? currentMatches.map((match, index) => (index === existingIndex ? nextMatch : match))
+            : [...currentMatches, nextMatch]
+      };
+    });
   };
   const getStepLabel = (step, index) => `${index + 1}. ${step?.title ?? '-'}`;
   const getProgramName = (programId) => programs.find((program) => program.id === programId)?.name ?? programId;
-  const getComparisonMemoCount = (savedComparison) =>
-    (savedComparison.stepMatches ?? []).filter((match) => match.reason?.trim()).length;
+  const getComparisonTitle = (comparison) =>
+    comparison.title?.trim() || `${getProgramName(comparison.leftProgramId)} ↔ ${getProgramName(comparison.rightProgramId)}`;
+  const getComparisonMemoCount = (comparison) =>
+    (comparison.stepMatches ?? []).filter((match) => match.reason?.trim()).length;
 
   const renderProgramSummary = (program) => {
     if (!program) return null;
@@ -1323,9 +1411,7 @@ function ProgramComparePopup({ programs, comparisons, onComparisonChange, onClos
       <section className="relative flex max-h-[calc(100vh-48px)] w-full max-w-5xl flex-col overflow-hidden rounded-3xl border border-white/70 bg-white shadow-2xl">
         <div className="flex items-center justify-between bg-slate-950 px-5 py-4 text-white">
           <div>
-            <p className="text-[11px] font-extrabold uppercase tracking-wide text-blue-300">
-              1:1 프로그램 비교
-            </p>
+            <p className="text-[11px] font-extrabold uppercase tracking-wide text-blue-300">1:1 프로그램 비교</p>
             <h2 className="mt-1 text-lg font-extrabold">사내 한계와 상용 활용 기능 정리</h2>
           </div>
           <button
@@ -1338,74 +1424,94 @@ function ProgramComparePopup({ programs, comparisons, onComparisonChange, onClos
           </button>
         </div>
         <div className="overflow-auto bg-slate-50 p-5">
-          <div className="grid gap-3 rounded-3xl bg-white p-4 ring-1 ring-slate-100 lg:grid-cols-2">
-            <label className="block">
-              <span className="text-[12px] font-black text-slate-500">비교 프로그램 A</span>
-              <select
-                value={leftProgramId}
-                onChange={(event) => {
-                  const nextProgramId = event.target.value;
-                  setLeftProgramId(nextProgramId);
-                  if (nextProgramId === rightProgramId) {
-                    setRightProgramId(programs.find((program) => program.id !== nextProgramId)?.id ?? '');
-                  }
-                }}
-                className="mt-1 w-full rounded-2xl border border-slate-200 bg-slate-50 px-3 py-2 text-sm font-extrabold text-slate-800 outline-none focus:border-blue-400"
+          <div className="rounded-3xl bg-white p-4 ring-1 ring-slate-100">
+            <div className="mb-3 grid gap-3 lg:grid-cols-[minmax(0,1fr)_auto_auto] lg:items-end">
+              <label className="block">
+                <span className="text-[12px] font-black text-slate-500">저장된 비교</span>
+                <select
+                  value={loadTargetId}
+                  onChange={(event) => setLoadTargetId(event.target.value)}
+                  className="mt-1 w-full rounded-2xl border border-slate-200 bg-slate-50 px-3 py-2 text-sm font-extrabold text-slate-800 outline-none focus:border-blue-400"
+                >
+                  <option value="">불러올 비교를 선택</option>
+                  {savedComparisons.map((comparison) => (
+                    <option key={comparison.id} value={comparison.id}>
+                      {getComparisonTitle(comparison)}{getComparisonMemoCount(comparison) > 0 ? ` · ${getComparisonMemoCount(comparison)}개 메모` : ''}
+                    </option>
+                  ))}
+                </select>
+              </label>
+              <button
+                type="button"
+                onClick={loadSelectedComparison}
+                disabled={!loadTargetId}
+                className="rounded-full bg-slate-950 px-4 py-2 text-sm font-black text-white shadow-sm hover:bg-slate-800 disabled:opacity-35"
               >
-                {programs.map((program) => (
-                  <option key={program.id} value={program.id}>
-                    {program.name}
-                  </option>
-                ))}
-              </select>
-            </label>
-            <label className="block">
-              <span className="text-[12px] font-black text-slate-500">비교 프로그램 B</span>
-              <select
-                value={rightProgramId}
-                onChange={(event) => setRightProgramId(event.target.value)}
-                className="mt-1 w-full rounded-2xl border border-slate-200 bg-slate-50 px-3 py-2 text-sm font-extrabold text-slate-800 outline-none focus:border-blue-400"
+                불러오기
+              </button>
+              <button
+                type="button"
+                onClick={startNewComparison}
+                className="rounded-full bg-blue-600 px-4 py-2 text-sm font-black text-white shadow-sm hover:bg-blue-700"
               >
-                {programs.map((program) => (
-                  <option key={program.id} value={program.id} disabled={program.id === leftProgramId}>
-                    {program.name}
-                  </option>
-                ))}
-              </select>
-            </label>
-          </div>
-
-          {savedComparisons.length > 0 && (
-            <div className="mt-3 rounded-3xl bg-white px-4 py-3 ring-1 ring-slate-100">
-              <div className="flex flex-wrap items-center gap-2">
-                <span className="mr-1 text-[12px] font-black text-slate-500">저장된 비교</span>
-                {savedComparisons.map((savedComparison) => {
-                  const active =
-                    savedComparison.leftProgramId === leftProgramId &&
-                    savedComparison.rightProgramId === rightProgramId;
-                  const memoCount = getComparisonMemoCount(savedComparison);
-                  return (
-                    <button
-                      key={`${savedComparison.leftProgramId}-${savedComparison.rightProgramId}`}
-                      type="button"
-                      onClick={() => {
-                        setLeftProgramId(savedComparison.leftProgramId);
-                        setRightProgramId(savedComparison.rightProgramId);
-                      }}
-                      className={`rounded-full px-3 py-1.5 text-[12px] font-black ring-1 transition ${
-                        active
-                          ? 'bg-slate-950 text-white ring-slate-950'
-                          : 'bg-slate-50 text-slate-600 ring-slate-200 hover:bg-white'
-                      }`}
-                    >
-                      {getProgramName(savedComparison.leftProgramId)} ↔ {getProgramName(savedComparison.rightProgramId)}
-                      {memoCount > 0 ? ` · ${memoCount}개 메모` : ''}
-                    </button>
-                  );
-                })}
-              </div>
+                새 비교
+              </button>
             </div>
-          )}
+            <div className="mb-3 flex flex-wrap items-end gap-3">
+              <label className="min-w-[260px] flex-1">
+                <span className="text-[12px] font-black text-slate-500">비교 제목</span>
+                <input
+                  value={draft.title ?? ''}
+                  onChange={(event) => updateDraft('title', event.target.value)}
+                  placeholder="예: EG-BIM Modeler에서 Rhino 보완 기능 비교"
+                  className="mt-1 w-full rounded-2xl border border-slate-200 bg-slate-50 px-3 py-2 text-sm font-extrabold text-slate-800 outline-none focus:border-blue-400"
+                />
+              </label>
+              {isSavedDraft && (
+                <button
+                  type="button"
+                  onClick={deleteDraft}
+                  className="rounded-full bg-white px-4 py-2 text-sm font-black text-red-600 ring-1 ring-red-100 hover:bg-red-50"
+                >
+                  삭제
+                </button>
+              )}
+            </div>
+            <div className="grid gap-3 lg:grid-cols-2">
+              <label className="block">
+                <span className="text-[12px] font-black text-slate-500">비교 프로그램 A</span>
+                <select
+                  value={draft.leftProgramId}
+                  onChange={(event) => {
+                    const nextProgramId = event.target.value;
+                    setDraft((current) => {
+                      const nextRightProgramId = nextProgramId === current.rightProgramId
+                        ? programs.find((program) => program.id !== nextProgramId)?.id ?? ''
+                        : current.rightProgramId;
+                      return { ...current, leftProgramId: nextProgramId, rightProgramId: nextRightProgramId };
+                    });
+                  }}
+                  className="mt-1 w-full rounded-2xl border border-slate-200 bg-slate-50 px-3 py-2 text-sm font-extrabold text-slate-800 outline-none focus:border-blue-400"
+                >
+                  {programs.map((program) => (
+                    <option key={program.id} value={program.id}>{program.name}</option>
+                  ))}
+                </select>
+              </label>
+              <label className="block">
+                <span className="text-[12px] font-black text-slate-500">비교 프로그램 B</span>
+                <select
+                  value={draft.rightProgramId}
+                  onChange={(event) => updateDraft('rightProgramId', event.target.value)}
+                  className="mt-1 w-full rounded-2xl border border-slate-200 bg-slate-50 px-3 py-2 text-sm font-extrabold text-slate-800 outline-none focus:border-blue-400"
+                >
+                  {programs.map((program) => (
+                    <option key={program.id} value={program.id} disabled={program.id === draft.leftProgramId}>{program.name}</option>
+                  ))}
+                </select>
+              </label>
+            </div>
+          </div>
 
           <div className="mt-4 grid gap-4 lg:grid-cols-2">
             {renderProgramSummary(leftProgram)}
@@ -1414,13 +1520,10 @@ function ProgramComparePopup({ programs, comparisons, onComparisonChange, onClos
 
           <div className="mt-4 rounded-3xl bg-white p-4 ring-1 ring-slate-100">
             <div>
-              <div>
-                <h3 className="text-base font-black text-slate-950">전체 스텝 1:1 비교</h3>
-                <p className="mt-1 text-[12px] font-bold text-slate-500">
-                  두 프로그램의 스텝을 전부 펼친 뒤, 가운데에 해당 스텝에서 상용 프로그램을 쓰는 이유를 적습니다.
-                  {hasSavedComparison ? ' 저장된 비교 내용을 불러왔습니다.' : ''}
-                </p>
-              </div>
+              <h3 className="text-base font-black text-slate-950">전체 스텝 1:1 비교</h3>
+              <p className="mt-1 text-[12px] font-bold text-slate-500">
+                두 프로그램의 스텝을 전부 펼친 뒤, 가운데에 해당 스텝에서 상용 프로그램을 쓰는 이유를 적습니다.
+              </p>
             </div>
 
             <div className="mt-4 space-y-3">
@@ -1434,49 +1537,45 @@ function ProgramComparePopup({ programs, comparisons, onComparisonChange, onClos
                   const rightStep = rightSteps[stepIndex];
                   const match = getStepMatch(stepIndex);
                   return (
-                  <div
-                    key={`step-compare-${stepIndex}`}
-                    className="grid gap-3 rounded-2xl border border-slate-100 bg-slate-50/80 p-3 lg:grid-cols-[minmax(0,1fr)_minmax(280px,1.35fr)_minmax(0,1fr)]"
-                  >
-                    <div className="rounded-2xl bg-amber-50/70 p-3 ring-1 ring-amber-100">
-                      <span className="text-[11px] font-black text-amber-700">{leftProgram?.name ?? 'A'} 스텝</span>
-                      <h4 className="mt-1 text-sm font-black text-slate-950">
-                        {leftStep ? getStepLabel(leftStep, stepIndex) : `${stepIndex + 1}. -`}
-                      </h4>
-                      <p className="mt-2 whitespace-pre-line rounded-xl bg-white/75 px-3 py-2 text-[12px] font-bold leading-5 text-slate-700 ring-1 ring-amber-50">
-                        {leftStep?.feature || '해당 스텝 없음'}
-                      </p>
-                      {leftStep?.note && (
-                        <p className="mt-2 whitespace-pre-line text-[11px] font-bold leading-5 text-slate-500">
-                          {leftStep.note}
+                    <div
+                      key={`step-compare-${stepIndex}`}
+                      className="grid gap-3 rounded-2xl border border-slate-100 bg-slate-50/80 p-3 lg:grid-cols-[minmax(0,1fr)_minmax(280px,1.35fr)_minmax(0,1fr)]"
+                    >
+                      <div className="rounded-2xl bg-amber-50/70 p-3 ring-1 ring-amber-100">
+                        <span className="text-[11px] font-black text-amber-700">{leftProgram?.name ?? 'A'} 스텝</span>
+                        <h4 className="mt-1 text-sm font-black text-slate-950">
+                          {leftStep ? getStepLabel(leftStep, stepIndex) : `${stepIndex + 1}. -`}
+                        </h4>
+                        <p className="mt-2 whitespace-pre-line rounded-xl bg-white/75 px-3 py-2 text-[12px] font-bold leading-5 text-slate-700 ring-1 ring-amber-50">
+                          {leftStep?.feature || '해당 스텝 없음'}
                         </p>
-                      )}
-                    </div>
-                    <label className="block">
-                      <span className="text-[11px] font-black text-slate-700">안 되는 기능 / 상용 사용 이유</span>
-                      <textarea
-                        value={match.reason ?? ''}
-                        onChange={(event) => updateStepReason(stepIndex, event.target.value)}
-                        rows={5}
-                        placeholder="예: 이 스텝에서 3D 형상 수정과 obj/ifc 변환이 안 돼서 오른쪽 프로그램의 기능을 사용"
-                        className="mt-1 h-[128px] w-full resize-y rounded-xl border border-slate-200 bg-white px-3 py-2 text-[12px] font-bold leading-5 text-slate-800 outline-none focus:border-blue-300"
-                      />
-                    </label>
-                    <div className="rounded-2xl bg-blue-50/70 p-3 ring-1 ring-blue-100">
-                      <span className="text-[11px] font-black text-blue-700">{rightProgram?.name ?? 'B'} 스텝</span>
-                      <h4 className="mt-1 text-sm font-black text-slate-950">
-                        {rightStep ? getStepLabel(rightStep, stepIndex) : `${stepIndex + 1}. -`}
-                      </h4>
-                      <p className="mt-2 whitespace-pre-line rounded-xl bg-white/75 px-3 py-2 text-[12px] font-bold leading-5 text-slate-700 ring-1 ring-blue-50">
-                        {rightStep?.feature || '해당 스텝 없음'}
-                      </p>
-                      {rightStep?.note && (
-                        <p className="mt-2 whitespace-pre-line text-[11px] font-bold leading-5 text-slate-500">
-                          {rightStep.note}
+                        {leftStep?.note && (
+                          <p className="mt-2 whitespace-pre-line text-[11px] font-bold leading-5 text-slate-500">{leftStep.note}</p>
+                        )}
+                      </div>
+                      <label className="block">
+                        <span className="text-[11px] font-black text-slate-700">안 되는 기능 / 상용 사용 이유</span>
+                        <textarea
+                          value={match.reason ?? ''}
+                          onChange={(event) => updateStepReason(stepIndex, event.target.value)}
+                          rows={5}
+                          placeholder="예: 이 스텝에서 3D 형상 수정과 obj/ifc 변환이 안 돼서 오른쪽 프로그램의 기능을 사용"
+                          className="mt-1 h-[128px] w-full resize-y rounded-xl border border-slate-200 bg-white px-3 py-2 text-[12px] font-bold leading-5 text-slate-800 outline-none focus:border-blue-300"
+                        />
+                      </label>
+                      <div className="rounded-2xl bg-blue-50/70 p-3 ring-1 ring-blue-100">
+                        <span className="text-[11px] font-black text-blue-700">{rightProgram?.name ?? 'B'} 스텝</span>
+                        <h4 className="mt-1 text-sm font-black text-slate-950">
+                          {rightStep ? getStepLabel(rightStep, stepIndex) : `${stepIndex + 1}. -`}
+                        </h4>
+                        <p className="mt-2 whitespace-pre-line rounded-xl bg-white/75 px-3 py-2 text-[12px] font-bold leading-5 text-slate-700 ring-1 ring-blue-50">
+                          {rightStep?.feature || '해당 스텝 없음'}
                         </p>
-                      )}
+                        {rightStep?.note && (
+                          <p className="mt-2 whitespace-pre-line text-[11px] font-bold leading-5 text-slate-500">{rightStep.note}</p>
+                        )}
+                      </div>
                     </div>
-                  </div>
                   );
                 })
               )}
@@ -1485,13 +1584,22 @@ function ProgramComparePopup({ programs, comparisons, onComparisonChange, onClos
             <label className="mt-4 block">
               <span className="text-[12px] font-black text-slate-500">비교 결론</span>
               <textarea
-                value={comparison.note ?? ''}
-                onChange={(event) => updateComparison('note', event.target.value)}
+                value={draft.note ?? ''}
+                onChange={(event) => updateDraft('note', event.target.value)}
                 rows={2}
                 placeholder="예: 현재는 해당 스텝 보완을 위해 상용 프로그램 사용이 필요함."
                 className="mt-1 w-full resize-y rounded-2xl border border-slate-200 bg-white px-3 py-2 text-sm font-bold leading-6 text-slate-700 outline-none focus:border-slate-400"
               />
             </label>
+            <div className="mt-4 flex justify-end">
+              <button
+                type="button"
+                onClick={saveDraft}
+                className="rounded-full bg-emerald-600 px-5 py-2.5 text-sm font-black text-white shadow-sm hover:bg-emerald-700"
+              >
+                저장하기
+              </button>
+            </div>
           </div>
         </div>
       </section>
@@ -1502,6 +1610,7 @@ function ProgramComparePopup({ programs, comparisons, onComparisonChange, onClos
 function RelationTreePanel({
   programs,
   onProgramClick,
+  onOpenComparePair,
   onOpenRelationPopup,
   onOpenMapWindow,
   sidebarWidth,
@@ -1509,42 +1618,93 @@ function RelationTreePanel({
   fullPage = false
 }) {
   const [expandedProgramIds, setExpandedProgramIds] = useState(() => new Set(programs.map((program) => program.id)));
-  const programMap = Object.fromEntries(programs.map((program) => [program.id, program]));
-  const relations = programs.flatMap((program) =>
-    (program.successors ?? [])
-      .map((successorId) => ({
-        from: program,
-        to: programs.find((item) => item.id === successorId)
-      }))
-      .filter((relation) => relation.to)
+  const [mapZoom, setMapZoom] = useState(1);
+  const [mapPan, setMapPan] = useState({ x: 0, y: 0 });
+  const [mapDrag, setMapDrag] = useState(null);
+  const mapViewportRef = useRef(null);
+  const programGroupKey = (program) => program.mergeGroup || program.id;
+  const groupMap = programs.reduce((groups, program) => {
+    const groupKey = programGroupKey(program);
+    groups[groupKey] = [...(groups[groupKey] ?? []), program];
+    return groups;
+  }, {});
+  const programToGroupKey = Object.fromEntries(programs.map((program) => [program.id, programGroupKey(program)]));
+  const groupRepresentativeMap = Object.fromEntries(
+    Object.entries(groupMap).map(([groupKey, groupPrograms]) => [groupKey, groupPrograms[0].id])
   );
-  const connectedProgramIds = new Set(relations.flatMap((relation) => [relation.from.id, relation.to.id]));
-  const linkedChildIds = new Set(programs.flatMap((program) => program.successors ?? []));
-  const rootPrograms = programs.filter((program) => !linkedChildIds.has(program.id));
-  const visibleRoots = rootPrograms.length ? rootPrograms : programs.slice(0, 1);
-  const levelMap = programs.reduce((levels, program) => ({ ...levels, [program.id]: 0 }), {});
+  const relationPrograms = programs;
+  const programMap = Object.fromEntries(relationPrograms.map((program) => [program.id, program]));
+  const relationMap = new globalThis.Map();
+  relationPrograms.forEach((program) => {
+    (program.successors ?? []).forEach((successorId) => {
+      const successor = programMap[successorId];
+      if (!successor) return;
+      const fromGroupKey = programToGroupKey[program.id];
+      const toGroupKey = programToGroupKey[successor.id];
+      if (!fromGroupKey || !toGroupKey || fromGroupKey === toGroupKey) return;
+      const relationKey = `${fromGroupKey}->${toGroupKey}`;
+      if (!relationMap.has(relationKey)) {
+        relationMap.set(relationKey, {
+          from: programMap[groupRepresentativeMap[fromGroupKey]] ?? program,
+          to: programMap[groupRepresentativeMap[toGroupKey]] ?? successor,
+          fromGroupKey,
+          toGroupKey
+        });
+      }
+    });
+  });
+  const relations = [...relationMap.values()];
+  const connectedGroupKeys = new Set(relations.flatMap((relation) => [relation.fromGroupKey, relation.toGroupKey]));
+  const connectedProgramIds = new Set(
+    relationPrograms
+      .filter((program) => connectedGroupKeys.has(programToGroupKey[program.id]))
+      .map((program) => program.id)
+  );
+  const linkedChildIds = new Set(relationPrograms.flatMap((program) => program.successors ?? []));
+  const rootPrograms = relationPrograms.filter((program) => !linkedChildIds.has(program.id));
+  const visibleRoots = rootPrograms.length ? rootPrograms : relationPrograms.slice(0, 1);
+  const levelMap = relationPrograms.reduce((levels, program) => ({ ...levels, [program.id]: 0 }), {});
 
-  for (let pass = 0; pass < programs.length; pass += 1) {
+  for (let pass = 0; pass < relationPrograms.length; pass += 1) {
     relations.forEach((relation) => {
       levelMap[relation.to.id] = Math.max(levelMap[relation.to.id], levelMap[relation.from.id] + 1);
     });
   }
 
-  const graphPrograms = programs.filter((program) => connectedProgramIds.has(program.id));
+  Object.values(groupMap).forEach((groupPrograms) => {
+    const groupLevel = Math.max(...groupPrograms.map((program) => levelMap[program.id] ?? 0));
+    groupPrograms.forEach((program) => {
+      levelMap[program.id] = groupLevel;
+    });
+  });
+
+  const graphPrograms = relationPrograms.filter((program) => connectedProgramIds.has(program.id));
   const graphLevels = graphPrograms.reduce((levels, program) => {
     const level = levelMap[program.id] ?? 0;
     levels[level] = [...(levels[level] ?? []), program];
     return levels;
-  }, []);
+  }, []).map((levelPrograms = []) => {
+    const levelGroups = levelPrograms.reduce((groups, program) => {
+      const groupKey = programToGroupKey[program.id];
+      const group = groups.find((item) => item.groupKey === groupKey);
+      if (group) {
+        group.programs.push(program);
+      } else {
+        groups.push({ groupKey, programs: [program] });
+      }
+      return groups;
+    }, []);
+    return levelGroups.flatMap((group) => group.programs);
+  });
   const miniNodeWidth = 128;
   const miniNodeHeight = 38;
   const miniColumnGap = 52;
   const miniRowGap = 96;
   const miniPadding = 34;
   const miniSideLaneWidth = 96;
-  const sidebarSizes = [280, 420, 560];
+  const sidebarSizes = [420, 560, 720];
   const resolvedSidebarWidth = sidebarWidth ?? sidebarSizes[0];
-  const miniViewportWidth = Math.max(230, fullPage ? 0 : resolvedSidebarWidth - 32);
+  const miniViewportWidth = Math.max(290, fullPage ? 0 : resolvedSidebarWidth - 24);
   const miniMaxLevelCount = Math.max(1, ...graphLevels.map((level) => level?.length ?? 0));
   const miniGraphWidth = Math.max(
     fullPage ? 1120 : 560,
@@ -1568,12 +1728,84 @@ function RelationTreePanel({
       ]);
     })
   );
-  const mapOffset = fullPage ? 0 : Math.max(0, Math.round((miniGraphWidth - miniViewportWidth) / 2));
+  const mergeGroupBoxes = Object.entries(groupMap)
+    .map(([groupKey, groupPrograms]) => {
+      const positionedPrograms = groupPrograms
+        .map((program) => ({ program, position: miniNodePositions[program.id] }))
+        .filter((item) => item.position);
+      if (positionedPrograms.length < 2) return null;
+      const left = Math.min(...positionedPrograms.map((item) => item.position.x));
+      const top = Math.min(...positionedPrograms.map((item) => item.position.y));
+      const right = Math.max(...positionedPrograms.map((item) => item.position.x + miniNodeWidth));
+      const bottom = Math.max(...positionedPrograms.map((item) => item.position.y + miniNodeHeight));
+      return {
+        groupKey,
+        programIds: positionedPrograms.map((item) => item.program.id),
+        left: left - 12,
+        top: top - 12,
+        width: right - left + 24,
+        height: bottom - top + 24
+      };
+    })
+    .filter(Boolean);
+  const mergeGroupBoxMap = Object.fromEntries(mergeGroupBoxes.map((box) => [box.groupKey, box]));
+  const baseMiniGraphScale = fullPage ? 1 : 0.72;
+  const miniGraphScale = baseMiniGraphScale * mapZoom;
+  const miniScaledWidth = miniGraphWidth * miniGraphScale;
+  const mapOffset = fullPage ? 0 : Math.max(0, Math.round((miniScaledWidth - miniViewportWidth) / 2 / miniGraphScale));
   const canShrinkSidebar = resolvedSidebarWidth > sidebarSizes[0];
   const setSidebarSize = (size) => {
     onSidebarWidthChange?.(size);
   };
 
+  const handleMapWheel = useCallback((event) => {
+    event.preventDefault();
+    event.stopPropagation();
+    event.stopImmediatePropagation?.();
+    const zoomStep = event.deltaY < 0 ? 1.08 : 0.92;
+    setMapZoom((currentZoom) => {
+      const minZoom = fullPage ? 0.5 : 0.78;
+      const maxZoom = fullPage ? 2.2 : 1.8;
+      return Math.min(maxZoom, Math.max(minZoom, currentZoom * zoomStep));
+    });
+  }, [fullPage]);
+
+  const handleMapViewportRef = useCallback((node) => {
+    if (mapViewportRef.current) {
+      mapViewportRef.current.removeEventListener('wheel', handleMapWheel);
+    }
+    if (node) {
+      node.addEventListener('wheel', handleMapWheel, { passive: false });
+    }
+    mapViewportRef.current = node;
+  }, [handleMapWheel]);
+
+  const handleMapPointerDown = (event) => {
+    if (event.target.closest?.('button')) return;
+    event.currentTarget.setPointerCapture?.(event.pointerId);
+    setMapDrag({
+      pointerId: event.pointerId,
+      startX: event.clientX,
+      startY: event.clientY,
+      panX: mapPan.x,
+      panY: mapPan.y
+    });
+  };
+
+  const handleMapPointerMove = (event) => {
+    if (!mapDrag || mapDrag.pointerId !== event.pointerId) return;
+    setMapPan({
+      x: mapDrag.panX + event.clientX - mapDrag.startX,
+      y: mapDrag.panY + event.clientY - mapDrag.startY
+    });
+  };
+
+  const handleMapPointerEnd = (event) => {
+    if (mapDrag?.pointerId === event.pointerId) {
+      setMapDrag(null);
+    }
+  };
+
   const toggleExpanded = (programId) => {
     setExpandedProgramIds((current) => {
       const next = new Set(current);
@@ -1718,17 +1950,48 @@ function RelationTreePanel({
           )}
         </div>
         {relations.length > 0 ? (
-          <div className={`${fullPage ? 'h-[calc(100vh-150px)] overflow-auto' : 'h-[660px] overflow-hidden'} relative rounded-2xl bg-gradient-to-br from-slate-50 to-white ring-1 ring-slate-100`}>
+          <div
+            ref={handleMapViewportRef}
+            className={`${fullPage ? 'h-[calc(100vh-150px)] overflow-hidden' : 'h-[660px] overflow-hidden'} relative cursor-grab touch-none overscroll-contain rounded-2xl bg-white ring-1 ring-slate-100 ${mapDrag ? 'cursor-grabbing' : ''}`}
+            onPointerDown={handleMapPointerDown}
+            onPointerMove={handleMapPointerMove}
+            onPointerUp={handleMapPointerEnd}
+            onPointerCancel={handleMapPointerEnd}
+          >
             <div
               className={`${fullPage ? 'relative' : 'absolute left-0 top-0 transition-transform duration-300 ease-out'}`}
               style={{
                 width: miniGraphWidth,
                 height: miniGraphHeight,
-                transform: `translateX(-${mapOffset}px)`
+                transform: `translate(${mapPan.x - mapOffset}px, ${mapPan.y}px) scale(${miniGraphScale})`,
+                transformOrigin: 'top left'
               }}
             >
+              {mergeGroupBoxes.map((box) => (
+                <button
+                  key={box.groupKey}
+                  type="button"
+                  onClick={() => {
+                    const [leftProgramId, rightProgramId] = box.programIds;
+                    if (leftProgramId && rightProgramId) {
+                      onOpenComparePair?.({ leftProgramId, rightProgramId });
+                    }
+                  }}
+                  className="absolute rounded-[18px] border-2 border-dashed border-violet-300 bg-violet-50/25 text-left transition hover:border-violet-400 hover:bg-violet-50/45"
+                  style={{
+                    left: box.left,
+                    top: box.top,
+                    width: box.width,
+                    height: box.height
+                  }}
+                >
+                  <span className="absolute -top-3 left-3 rounded-full bg-white px-2 py-0.5 text-[10px] font-black text-violet-600 shadow-sm ring-1 ring-violet-100">
+                    비교 프로그램
+                  </span>
+                </button>
+              ))}
               <svg
-                className="absolute inset-0 h-full w-full overflow-visible"
+                className="pointer-events-none absolute inset-0 h-full w-full overflow-visible"
                 viewBox={`0 0 ${miniGraphWidth} ${miniGraphHeight}`}
                 preserveAspectRatio="none"
               >
@@ -1744,23 +2007,37 @@ function RelationTreePanel({
                   const from = miniNodePositions[relation.from.id];
                   const to = miniNodePositions[relation.to.id];
                   if (!from || !to) return null;
+                  const toGroupBox = mergeGroupBoxMap[relation.toGroupKey];
                   const fromLevel = levelMap[relation.from.id] ?? 0;
                   const toLevel = levelMap[relation.to.id] ?? 0;
                   const isSkipEdge = toLevel - fromLevel > 1;
                   const fromCenterX = from.x + miniNodeWidth / 2;
-                  const toCenterX = to.x + miniNodeWidth / 2;
+                  const toCenterX = toGroupBox ? toGroupBox.left + toGroupBox.width / 2 : to.x + miniNodeWidth / 2;
                   const startY = from.y + miniNodeHeight;
-                  const endY = to.y;
+                  const endY = toGroupBox ? toGroupBox.top : to.y;
                   const midY = startY + Math.max(30, (endY - startY) / 2);
                   const isRightSkipEdge = toCenterX > fromCenterX;
                   const laneX = isRightSkipEdge
-                    ? from.x + miniNodeWidth + 40
-                    : from.x - 40;
-                  const skipTargetY = to.y + miniNodeHeight / 2;
+                    ? Math.min(
+                        miniGraphWidth - 16,
+                        Math.max(from.x + miniNodeWidth, toGroupBox ? toGroupBox.left + toGroupBox.width : to.x + miniNodeWidth) + 46
+                      )
+                    : Math.max(
+                        16,
+                        Math.min(from.x, toGroupBox ? toGroupBox.left : to.x) - 46
+                      );
+                  const skipTargetY = toGroupBox ? toGroupBox.top + toGroupBox.height / 2 : to.y + miniNodeHeight / 2;
+                  const skipTargetX = toGroupBox
+                    ? isRightSkipEdge
+                      ? toGroupBox.left + toGroupBox.width + 10
+                      : toGroupBox.left - 10
+                    : isRightSkipEdge
+                      ? to.x + miniNodeWidth + 8
+                      : to.x - 8;
                   const pathD = isSkipEdge
                     ? isRightSkipEdge
-                      ? `M ${from.x + miniNodeWidth} ${from.y + miniNodeHeight / 2} H ${laneX} V ${skipTargetY} H ${to.x - 8}`
-                      : `M ${from.x} ${from.y + miniNodeHeight / 2} H ${laneX} V ${skipTargetY} H ${to.x + miniNodeWidth + 8}`
+                      ? `M ${from.x + miniNodeWidth} ${from.y + miniNodeHeight / 2} H ${laneX} V ${skipTargetY} H ${skipTargetX}`
+                      : `M ${from.x} ${from.y + miniNodeHeight / 2} H ${laneX} V ${skipTargetY} H ${skipTargetX}`
                     : Math.abs(fromCenterX - toCenterX) < 6
                       ? `M ${fromCenterX} ${startY} L ${toCenterX} ${endY - 8}`
                       : `M ${fromCenterX} ${startY} C ${fromCenterX} ${midY}, ${toCenterX} ${midY}, ${toCenterX} ${endY - 8}`;
@@ -1786,8 +2063,7 @@ function RelationTreePanel({
                   <button
                     key={program.id}
                     type="button"
-                    onClick={() => onProgramClick(program.id)}
-                    className={`absolute flex flex-col items-center justify-center rounded-xl border px-2 text-center shadow-sm transition hover:-translate-y-0.5 ${typeMeta.rowClass}`}
+                    className={`pointer-events-none absolute flex flex-col items-center justify-center rounded-xl border px-2 text-center shadow-sm ${typeMeta.rowClass}`}
                     style={{
                       left: position.x,
                       top: position.y,
@@ -1823,7 +2099,8 @@ export default function App() {
   const [content, setContent] = useState(readStoredContent);
   const [isRelationPopupOpen, setIsRelationPopupOpen] = useState(false);
   const [isComparePopupOpen, setIsComparePopupOpen] = useState(false);
-  const [sidebarWidth, setSidebarWidth] = useState(280);
+  const [compareInitialPair, setCompareInitialPair] = useState(null);
+  const [sidebarWidth, setSidebarWidth] = useState(420);
   const [isServerLoaded, setIsServerLoaded] = useState(false);
   const editableCheonjiinFlow = mergeStepContent(cheonjiinFlow, content.cheonjiin.steps);
   const editableWayPrimalFlow = mergeStepContent(wayPrimalFlow, content.wayPrimal.steps);
@@ -1837,6 +2114,7 @@ export default function App() {
       programType: getProgramType(content.cheonjiin.programType),
       predecessors: content.cheonjiin.predecessors ?? [],
       successors: content.cheonjiin.successors ?? [],
+      mergeGroup: content.cheonjiin.mergeGroup ?? '',
       accent: {
         iconBg: 'bg-teal-50',
         iconText: 'text-teal-700',
@@ -1853,6 +2131,7 @@ export default function App() {
       programType: getProgramType(content.wayPrimal.programType),
       predecessors: content.wayPrimal.predecessors ?? [],
       successors: content.wayPrimal.successors ?? [],
+      mergeGroup: content.wayPrimal.mergeGroup ?? '',
       accent: {
         iconBg: 'bg-indigo-50',
         iconText: 'text-indigo-700',
@@ -1869,6 +2148,7 @@ export default function App() {
       programType: getProgramType(program.programType),
       predecessors: program.predecessors ?? [],
       successors: program.successors ?? [],
+      mergeGroup: program.mergeGroup ?? '',
       accent: {
         iconBg: 'bg-blue-50',
         iconText: 'text-blue-700',
@@ -2206,20 +2486,49 @@ export default function App() {
     });
   };
 
-  const updateComparison = (leftProgramId, rightProgramId, field, value) => {
+  const updateProgramMergeGroup = (programId, mergeGroup) => {
+    setContent((current) => {
+      if (!mergeGroup) {
+        return updateProgramRecord(current, programId, (program) => ({
+          ...program,
+          mergeGroup: ''
+        }));
+      }
+
+      const targetProgram = programs.find((program) => program.id === mergeGroup || program.mergeGroup === mergeGroup);
+      const nextMergeGroup = targetProgram?.mergeGroup || targetProgram?.id || mergeGroup;
+      let nextContent = updateProgramRecord(current, programId, (program) => ({
+        ...program,
+        mergeGroup: nextMergeGroup
+      }));
+
+      if (targetProgram) {
+        nextContent = updateProgramRecord(nextContent, targetProgram.id, (program) => ({
+          ...program,
+          mergeGroup: nextMergeGroup
+        }));
+      }
+
+      return nextContent;
+    });
+  };
+
+  const updateComparison = (comparisonId, leftProgramId, rightProgramId, field, value) => {
     setContent((current) => {
       const comparisons = current.comparisons ?? [];
       const comparisonIndex = comparisons.findIndex(
-        (comparison) => comparison.leftProgramId === leftProgramId && comparison.rightProgramId === rightProgramId
+        (comparison) => comparison.id === comparisonId
       );
       const nextComparison = {
         ...(comparisonIndex >= 0 ? comparisons[comparisonIndex] : {}),
+        id: comparisonId,
         leftProgramId,
         rightProgramId,
         updatedAt: new Date().toISOString(),
         [field]: value
       };
       const hasComparisonContent =
+        nextComparison.title?.trim() ||
         (nextComparison.stepMatches ?? []).some((match) => match.reason?.trim()) ||
         nextComparison.note?.trim();
       return {
@@ -2235,6 +2544,41 @@ export default function App() {
     });
   };
 
+  const saveComparison = (comparison) => {
+    setContent((current) => {
+      const comparisons = current.comparisons ?? [];
+      const comparisonIndex = comparisons.findIndex((item) => item.id === comparison.id);
+      const nextComparison = {
+        ...comparison,
+        updatedAt: comparison.updatedAt ?? new Date().toISOString()
+      };
+      const hasComparisonContent =
+        nextComparison.title?.trim() ||
+        (nextComparison.stepMatches ?? []).some((match) => match.reason?.trim()) ||
+        nextComparison.note?.trim();
+      if (!hasComparisonContent) return current;
+      return {
+        ...current,
+        comparisons:
+          comparisonIndex >= 0
+            ? comparisons.map((item, index) => (index === comparisonIndex ? nextComparison : item))
+            : [...comparisons, nextComparison]
+      };
+    });
+  };
+
+  const deleteComparison = (comparisonId) => {
+    setContent((current) => ({
+      ...current,
+      comparisons: (current.comparisons ?? []).filter((comparison) => comparison.id !== comparisonId)
+    }));
+  };
+
+  const openComparePair = (pair) => {
+    setCompareInitialPair(pair);
+    setIsComparePopupOpen(true);
+  };
+
   const updateProgramTitle = (programId, field, value) => {
     if (programId === 'cheonjiin' || programId === 'wayPrimal') {
       const target = programId === 'cheonjiin' ? 'cheonjiin' : 'wayPrimal';
@@ -2287,6 +2631,7 @@ export default function App() {
           programType: 'internal',
           predecessors: [],
           successors: [],
+          mergeGroup: '',
           linkLabel: '이전 프로그램 산출물을 새 프로그램 입력으로 연계'
         }
       ]
@@ -2501,10 +2846,11 @@ export default function App() {
 
   if (isRelationMapWindow) {
     return (
-      <main className="min-h-screen bg-[radial-gradient(circle_at_top_left,#dffcf4_0,#f7f8fa_34%,#eef2ff_100%)] text-slate-900">
+      <main className="min-h-screen bg-white text-slate-900">
         <RelationTreePanel
           programs={programs}
           onProgramClick={openProgramWindow}
+          onOpenComparePair={openComparePair}
           onOpenRelationPopup={() => setIsRelationPopupOpen(true)}
           sidebarWidth={1280}
           onSidebarWidthChange={() => {}}
@@ -2515,17 +2861,9 @@ export default function App() {
   }
 
   return (
-    <main className="min-h-screen bg-[radial-gradient(circle_at_top_left,#dffcf4_0,#f7f8fa_34%,#eef2ff_100%)] text-slate-900">
+    <main className="min-h-screen bg-white text-slate-900">
       <div className="mx-auto max-w-[1760px] space-y-4 px-3 py-4">
         <div className="flex justify-end gap-2">
-          <button
-            type="button"
-            onClick={() => setIsComparePopupOpen(true)}
-            className="flex items-center gap-2 rounded-full bg-white px-4 py-2 text-sm font-bold text-slate-700 shadow-sm ring-1 ring-slate-200 hover:bg-slate-50"
-          >
-            <Waypoints className="h-4 w-4" />
-            1:1 비교
-          </button>
           <button
             type="button"
             onClick={toggleProgramEdit}
@@ -2547,6 +2885,7 @@ export default function App() {
           <RelationTreePanel
             programs={programs}
             onProgramClick={openProgramWindow}
+            onOpenComparePair={openComparePair}
             onOpenRelationPopup={() => setIsRelationPopupOpen(true)}
             onOpenMapWindow={openRelationMapWindow}
             sidebarWidth={sidebarWidth}
@@ -2748,6 +3087,7 @@ export default function App() {
           <RelationPopup
             programs={programs}
             onToggleRelation={toggleProgramRelation}
+            onMergeGroupChange={updateProgramMergeGroup}
             onClose={() => setIsRelationPopupOpen(false)}
           />
         )}
@@ -2756,8 +3096,13 @@ export default function App() {
           <ProgramComparePopup
             programs={programs}
             comparisons={content.comparisons ?? []}
-            onComparisonChange={updateComparison}
-            onClose={() => setIsComparePopupOpen(false)}
+            initialPair={compareInitialPair}
+            onComparisonSave={saveComparison}
+            onComparisonDelete={deleteComparison}
+            onClose={() => {
+              setIsComparePopupOpen(false);
+              setCompareInitialPair(null);
+            }}
           />
         )}
       </div>