diff --git a/src/cli/commands/sync.ts b/src/cli/commands/sync.ts
index a56981b..0e46a9b 100644
--- a/src/cli/commands/sync.ts
+++ b/src/cli/commands/sync.ts
@@ -22,18 +22,14 @@ interface Rename {
 }
 
 interface ManifestDiff {
-  localChanged: string[]
-  remoteChanged: string[]
+  changed: string[]
   localOnly: string[]
   remoteOnly: string[]
-  localDeleted: string[]
-  remoteDeleted: string[]
-  conflicts: string[]
   renamed: Rename[]
   localManifest: Manifest
   remoteManifest: Manifest | null
-  baseManifest: Manifest | null
   remoteVersion: string | null
+  serverChanged: boolean
 }
 
 export async function historyApp(name?: string) {
@@ -127,9 +123,8 @@ export async function getApp(name: string) {
     writeFileSync(fullPath, content)
   }
 
-  // Write sync state so future status/push/pull has a baseline
   if (result.version) {
-    writeSyncState(appPath, { version: result.version, manifest: result.manifest })
+    writeSyncState(appPath, { version: result.version })
   }
 
   console.log(color.green(`✓ Downloaded ${name}`))
@@ -148,45 +143,31 @@ export async function pushApp(options: { quiet?: boolean, force?: boolean } = {}
     return
   }
 
-  const { localChanged, remoteChanged, localOnly, remoteOnly, localDeleted, remoteDeleted, conflicts, renamed, localManifest, remoteManifest } = diff
+  const { changed, localOnly, remoteOnly, renamed, localManifest, remoteManifest, serverChanged } = diff
 
   if (!remoteManifest) {
     const ok = await confirm(`App ${color.bold(appName)} doesn't exist on server. Create it?`)
     if (!ok) return
   }
 
-  // Abort if there are unpulled remote changes or conflicts (unless --force)
-  const hasRemoteChanges = remoteChanged.length > 0 || remoteOnly.length > 0 || remoteDeleted.length > 0
-  if (!options.force && (hasRemoteChanges || conflicts.length > 0)) {
-    console.error('Cannot push: server has changes you haven\'t pulled')
-    for (const file of remoteChanged) {
-      console.error(`  ${color.yellow('~')} ${file} (changed on server)`)
-    }
-    for (const file of remoteOnly) {
-      console.error(`  ${color.green('+')} ${file} (new on server)`)
-    }
-    for (const file of remoteDeleted) {
-      console.error(`  ${color.red('-')} ${file} (deleted on server)`)
-    }
-    for (const file of conflicts) {
-      console.error(`  ${color.red('!')} ${file} (conflict)`)
-    }
+  // If server changed, abort unless --force
+  if (serverChanged && !options.force) {
+    console.error('Cannot push: server has changed since last sync')
     console.error('\nRun `toes pull` first, or `toes push --force` to overwrite')
     return
   }
 
-  // Files to upload: locally changed/added + conflicts (when forcing)
-  const toUpload = [...localChanged, ...localOnly, ...(options.force ? conflicts : [])]
-  // Files to delete on server: locally deleted + remote-only when forcing
-  const toDelete = [...localDeleted, ...(options.force ? remoteOnly : [])]
+  // Files to upload: changed + localOnly
+  const toUpload = [...changed, ...localOnly]
+  // Files to delete on server: remoteOnly (local deletions when version matches, or forced)
+  const toDelete = !serverChanged || options.force ? [...remoteOnly] : []
 
   // Detect renames among upload/delete pairs (same hash, different path)
   const renames: Rename[] = [...renamed]
-  const serverManifest = remoteManifest
   const remoteByHash = new Map<string, string>()
-  if (serverManifest) {
+  if (remoteManifest) {
     for (const file of toDelete) {
-      const info = serverManifest.files[file]
+      const info = remoteManifest.files[file]
       if (info) remoteByHash.set(info.hash, file)
     }
   }
@@ -283,9 +264,8 @@ export async function pushApp(options: { quiet?: boolean, force?: boolean } = {}
     return
   }
 
-  // 5. Write sync state after successful push
-  const newManifest = generateManifest(process.cwd(), appName)
-  writeSyncState(process.cwd(), { version, manifest: newManifest })
+  // 5. Write sync version after successful push
+  writeSyncState(process.cwd(), { version })
 
   console.log(color.green(`✓ Deployed and activated version ${version}`))
 }
@@ -303,45 +283,49 @@ export async function pullApp(options: { force?: boolean, quiet?: boolean } = {}
     return
   }
 
-  const { localChanged, remoteChanged, localOnly, remoteOnly, localDeleted, remoteDeleted, conflicts, remoteManifest, remoteVersion } = diff
+  const { changed, localOnly, remoteOnly, remoteManifest, remoteVersion, serverChanged } = diff
 
   if (!remoteManifest) {
     console.error('App not found on server')
     return
   }
 
-  // Check for local changes that would be overwritten
-  const hasLocalChanges = localChanged.length > 0 || localOnly.length > 0 || localDeleted.length > 0 || conflicts.length > 0
-  if (hasLocalChanges && !options.force) {
+  if (!serverChanged) {
+    // Server hasn't changed — all diffs are local, nothing to pull
+    if (!options.quiet) {
+      if (changed.length > 0 || localOnly.length > 0 || remoteOnly.length > 0) {
+        console.log('Server is up to date. You have local changes — use `toes push`.')
+      } else {
+        console.log('Already up to date')
+      }
+    }
+    return
+  }
+
+  // Server changed — download diffs from remote
+  const hasDiffs = changed.length > 0 || localOnly.length > 0
+  if (hasDiffs && !options.force) {
     console.error('Cannot pull: you have local changes that would be overwritten')
-    for (const file of localChanged) {
+    for (const file of changed) {
       console.error(`  ${color.yellow('~')} ${file}`)
     }
     for (const file of localOnly) {
       console.error(`  ${color.green('+')} ${file} (local only)`)
     }
-    for (const file of localDeleted) {
-      console.error(`  ${color.red('-')} ${file} (deleted locally)`)
-    }
-    for (const file of conflicts) {
-      console.error(`  ${color.red('!')} ${file} (conflict)`)
-    }
     console.error('\nUse `toes pull --force` to overwrite local changes')
     return
   }
 
-  // Files to download: remote changed + remote only + conflicts (when forcing)
-  const toDownload = [...remoteChanged, ...remoteOnly, ...(options.force ? [...localChanged, ...conflicts] : [])]
-
-  // Files to delete locally: remote deleted + local only (when forcing)
-  const toDelete = [...remoteDeleted, ...(options.force ? localOnly : [])]
-
-  // Restore locally deleted files from remote
-  if (options.force && localDeleted.length > 0) {
-    toDownload.push(...localDeleted)
-  }
+  // Files to download: changed + remoteOnly
+  const toDownload = [...changed, ...remoteOnly]
+  // Files to delete locally: only when forcing
+  const toDelete = options.force ? localOnly : []
 
   if (toDownload.length === 0 && toDelete.length === 0) {
+    // Server version changed but files are identical — just update stored version
+    if (remoteVersion) {
+      writeSyncState(process.cwd(), { version: remoteVersion })
+    }
     if (!options.quiet) console.log('Already up to date')
     return
   }
@@ -380,10 +364,8 @@ export async function pullApp(options: { force?: boolean, quiet?: boolean } = {}
     }
   }
 
-  // Write sync state after successful pull
   if (remoteVersion) {
-    const newManifest = generateManifest(process.cwd(), appName)
-    writeSyncState(process.cwd(), { version: remoteVersion, manifest: newManifest })
+    writeSyncState(process.cwd(), { version: remoteVersion })
   }
 
   console.log(color.green('✓ Pull complete'))
@@ -402,14 +384,9 @@ export async function diffApp() {
     return
   }
 
-  const { localChanged, remoteChanged, localOnly, remoteOnly, localDeleted, remoteDeleted, conflicts, renamed } = diff
+  const { changed, localOnly, remoteOnly, renamed } = diff
 
-  const hasChanges = localChanged.length > 0 || remoteChanged.length > 0 ||
-    localOnly.length > 0 || remoteOnly.length > 0 ||
-    localDeleted.length > 0 || remoteDeleted.length > 0 ||
-    conflicts.length > 0 || renamed.length > 0
-
-  if (!hasChanges) {
+  if (changed.length === 0 && localOnly.length === 0 && remoteOnly.length === 0 && renamed.length === 0) {
     return
   }
 
@@ -420,73 +397,27 @@ export async function diffApp() {
     console.log(color.gray('─'.repeat(60)))
   }
 
-  // Fetch remote content for changed/conflict files
-  const changedFiles = [...localChanged, ...remoteChanged, ...conflicts]
+  // Fetch all changed files in parallel
   const remoteContents = await Promise.all(
-    changedFiles.map(file => download(`/api/sync/apps/${appName}/files/${file}`))
+    changed.map(file => download(`/api/sync/apps/${appName}/files/${file}`))
   )
 
-  // Show diffs for locally changed files
-  if (localChanged.length > 0) {
-    for (let i = 0; i < localChanged.length; i++) {
-      const file = localChanged[i]!
-      const remoteContent = remoteContents[i]
-      const localContent = readFileSync(join(process.cwd(), file), 'utf-8')
+  // Show diffs for changed files
+  for (let i = 0; i < changed.length; i++) {
+    const file = changed[i]!
+    const remoteContent = remoteContents[i]
+    const localContent = readFileSync(join(process.cwd(), file), 'utf-8')
 
-      if (!remoteContent) {
-        console.log(color.red(`Failed to fetch remote version of ${file}`))
-        continue
-      }
-
-      const remoteText = new TextDecoder().decode(remoteContent)
-
-      console.log(color.green('\nLocal change'))
-      console.log(color.bold(`${file}`))
-      console.log(color.gray('─'.repeat(60)))
-      showDiff(remoteText, localContent)
+    if (!remoteContent) {
+      console.log(color.red(`Failed to fetch remote version of ${file}`))
+      continue
     }
-  }
 
-  // Show diffs for remotely changed files
-  if (remoteChanged.length > 0) {
-    for (let i = 0; i < remoteChanged.length; i++) {
-      const file = remoteChanged[i]!
-      const remoteContent = remoteContents[localChanged.length + i]
-      const localContent = readFileSync(join(process.cwd(), file), 'utf-8')
+    const remoteText = new TextDecoder().decode(remoteContent)
 
-      if (!remoteContent) {
-        console.log(color.red(`Failed to fetch remote version of ${file}`))
-        continue
-      }
-
-      const remoteText = new TextDecoder().decode(remoteContent)
-
-      console.log(color.yellow('\nRemote change'))
-      console.log(color.bold(`${file}`))
-      console.log(color.gray('─'.repeat(60)))
-      showDiff(localContent, remoteText)
-    }
-  }
-
-  // Show diffs for conflicts
-  if (conflicts.length > 0) {
-    for (let i = 0; i < conflicts.length; i++) {
-      const file = conflicts[i]!
-      const remoteContent = remoteContents[localChanged.length + remoteChanged.length + i]
-      const localContent = readFileSync(join(process.cwd(), file), 'utf-8')
-
-      if (!remoteContent) {
-        console.log(color.red(`Failed to fetch remote version of ${file}`))
-        continue
-      }
-
-      const remoteText = new TextDecoder().decode(remoteContent)
-
-      console.log(color.red('\nConflict (changed on both sides)'))
-      console.log(color.bold(`${file}`))
-      console.log(color.gray('─'.repeat(60)))
-      showDiff(remoteText, localContent)
-    }
+    console.log(color.bold(`\n${file}`))
+    console.log(color.gray('─'.repeat(60)))
+    showDiff(remoteText, localContent)
   }
 
   // Show local-only files
@@ -514,14 +445,14 @@ export async function diffApp() {
     const file = remoteOnly[i]!
     const content = remoteOnlyContents[i]
 
-    console.log(color.yellow('\nNew file (remote only)'))
-    console.log(color.bold(`${file}`))
+    console.log(color.bold(`\n${file}`))
     console.log(color.gray('─'.repeat(60)))
+    console.log(color.red('Remote only'))
     if (content) {
       const text = new TextDecoder().decode(content)
       const lines = text.split('\n')
       for (let i = 0; i < Math.min(lines.length, 10); i++) {
-        console.log(color.green(`+ ${lines[i]}`))
+        console.log(color.red(`- ${lines[i]}`))
       }
       if (lines.length > 10) {
         console.log(color.gray(`... ${lines.length - 10} more lines`))
@@ -529,20 +460,6 @@ export async function diffApp() {
     }
   }
 
-  // Show locally deleted files
-  for (const file of localDeleted) {
-    console.log(color.red('\nDeleted locally'))
-    console.log(color.bold(`${file}`))
-    console.log(color.gray('─'.repeat(60)))
-  }
-
-  // Show remotely deleted files
-  for (const file of remoteDeleted) {
-    console.log(color.red('\nDeleted on server'))
-    console.log(color.bold(`${file}`))
-    console.log(color.gray('─'.repeat(60)))
-  }
-
   console.log()
 }
 
@@ -560,7 +477,7 @@ export async function statusApp() {
     return
   }
 
-  const { localChanged, remoteChanged, localOnly, remoteOnly, localDeleted, remoteDeleted, conflicts, renamed, localManifest, remoteManifest, baseManifest } = diff
+  const { changed, localOnly, remoteOnly, renamed, localManifest, remoteManifest, serverChanged } = diff
 
   if (!remoteManifest) {
     console.log(color.yellow('App does not exist on server'))
@@ -569,58 +486,55 @@ export async function statusApp() {
     return
   }
 
-  const toPush = [...localChanged, ...localOnly, ...localDeleted]
-  const toPull = [...remoteChanged, ...remoteOnly, ...remoteDeleted]
+  const hasDiffs = changed.length > 0 || localOnly.length > 0 || remoteOnly.length > 0 || renamed.length > 0
 
-  // Push status
-  if (toPush.length > 0 || renamed.length > 0) {
+  if (!hasDiffs) {
+    if (serverChanged) {
+      // Files identical but version changed — update stored version silently
+      const { remoteVersion } = diff
+      if (remoteVersion) {
+        writeSyncState(process.cwd(), { version: remoteVersion })
+      }
+    }
+    console.log(color.green('✓ In sync with server'))
+    return
+  }
+
+  if (!serverChanged) {
+    // Server hasn't moved — all diffs are local changes to push
     console.log(color.bold('Changes to push:'))
     for (const { from, to } of renamed) {
       console.log(`  ${color.cyan('→')} ${from} → ${to}`)
     }
-    for (const file of localChanged) {
+    for (const file of changed) {
       console.log(`  ${color.green('↑')} ${file}`)
     }
     for (const file of localOnly) {
       console.log(`  ${color.green('+')} ${file}`)
     }
-    for (const file of localDeleted) {
+    for (const file of remoteOnly) {
       console.log(`  ${color.red('-')} ${file}`)
     }
     console.log()
-  }
-
-  // Pull status
-  if (toPull.length > 0) {
-    console.log(color.bold('Changes to pull:'))
-    for (const file of remoteChanged) {
-      console.log(`  ${color.green('↓')} ${file}`)
+  } else {
+    // Server changed — show diffs neutrally
+    console.log(color.yellow('Server has changed since last sync\n'))
+    console.log(color.bold('Differences:'))
+    for (const { from, to } of renamed) {
+      console.log(`  ${color.cyan('→')} ${from} → ${to}`)
+    }
+    for (const file of changed) {
+      console.log(`  ${color.yellow('~')} ${file}`)
+    }
+    for (const file of localOnly) {
+      console.log(`  ${color.green('+')} ${file} (local only)`)
     }
     for (const file of remoteOnly) {
-      console.log(`  ${color.green('+')} ${file}`)
-    }
-    for (const file of remoteDeleted) {
-      console.log(`  ${color.red('-')} ${file}`)
+      console.log(`  ${color.green('+')} ${file} (remote only)`)
     }
+    console.log(`\nRun ${color.bold('toes pull')} to update, or ${color.bold('toes push --force')} to overwrite server`)
     console.log()
   }
-
-  // Conflicts
-  if (conflicts.length > 0) {
-    console.log(color.bold(color.red('Conflicts:')))
-    for (const file of conflicts) {
-      console.log(`  ${color.red('!')} ${file}`)
-    }
-    if (!baseManifest) {
-      console.log(color.gray('\n  No sync baseline. Re-download with `toes get` to establish one.'))
-    }
-    console.log()
-  }
-
-  // Summary
-  if (toPush.length === 0 && toPull.length === 0 && conflicts.length === 0 && renamed.length === 0) {
-    console.log(color.green('✓ In sync with server'))
-  }
 }
 
 export async function syncApp() {
@@ -641,7 +555,7 @@ export async function syncApp() {
 
   console.log(`Syncing ${color.bold(appName)}...`)
 
-  // Initial sync: merge using three-way diff, then push merged state
+  // Initial sync: pull remote changes, then push local
   await mergeSync(appName)
 
   const gitignore = loadGitignore(process.cwd())
@@ -826,8 +740,8 @@ export async function stashApp() {
     return
   }
 
-  const { localChanged, localOnly } = diff
-  const toStash = [...localChanged, ...localOnly]
+  const { changed, localOnly } = diff
+  const toStash = [...changed, ...localOnly]
 
   if (toStash.length === 0) {
     console.log('No local changes to stash')
@@ -849,7 +763,7 @@ export async function stashApp() {
     app: appName,
     timestamp: new Date().toISOString(),
     files: toStash,
-    changed: localChanged,
+    changed,
     localOnly,
   }
   writeFileSync(join(stashDir, 'metadata.json'), JSON.stringify(metadata, null, 2))
@@ -870,9 +784,9 @@ export async function stashApp() {
   }
 
   // Restore changed files from server
-  if (localChanged.length > 0) {
-    console.log(`\nRestoring ${localChanged.length} changed files from server...`)
-    for (const file of localChanged) {
+  if (changed.length > 0) {
+    console.log(`\nRestoring ${changed.length} changed files from server...`)
+    for (const file of changed) {
       const content = await download(`/api/sync/apps/${appName}/files/${file}`)
       if (content) {
         writeFileSync(join(process.cwd(), file), content)
@@ -1067,34 +981,27 @@ async function mergeSync(appName: string): Promise<void> {
   const diff = await getManifestDiff(appName)
   if (!diff) return
 
-  const { remoteChanged, remoteOnly, remoteDeleted, remoteManifest } = diff
+  const { changed, remoteOnly, remoteManifest, serverChanged } = diff
   if (!remoteManifest) return
 
-  // Pull remote changes
-  const toPull = [...remoteChanged, ...remoteOnly]
+  if (serverChanged) {
+    // Pull remote changes
+    const toPull = [...changed, ...remoteOnly]
 
-  if (toPull.length > 0) {
-    for (const file of toPull) {
-      const content = await download(`/api/sync/apps/${appName}/files/${file}`)
-      if (!content) continue
+    if (toPull.length > 0) {
+      for (const file of toPull) {
+        const content = await download(`/api/sync/apps/${appName}/files/${file}`)
+        if (!content) continue
 
-      const fullPath = join(process.cwd(), file)
-      const dir = dirname(fullPath)
-      if (!existsSync(dir)) {
-        mkdirSync(dir, { recursive: true })
+        const fullPath = join(process.cwd(), file)
+        const dir = dirname(fullPath)
+        if (!existsSync(dir)) {
+          mkdirSync(dir, { recursive: true })
+        }
+
+        writeFileSync(fullPath, content)
+        console.log(`  ${color.green('↓')} ${file}`)
       }
-
-      writeFileSync(fullPath, content)
-      console.log(`  ${color.green('↓')} ${file}`)
-    }
-  }
-
-  // Delete files that were deleted on remote
-  for (const file of remoteDeleted) {
-    const fullPath = join(process.cwd(), file)
-    if (existsSync(fullPath)) {
-      unlinkSync(fullPath)
-      console.log(`  ${color.red('✗')} ${file}`)
     }
   }
 
@@ -1114,79 +1021,37 @@ async function getManifestDiff(appName: string): Promise<ManifestDiff | null> {
   const remoteManifest = result.manifest ?? null
   const remoteVersion = result.version ?? null
   const syncState = readSyncState(process.cwd())
-  const baseManifest = syncState?.manifest ?? null
+  const serverChanged = !syncState || syncState.version !== remoteVersion
 
   const localFiles = new Set(Object.keys(localManifest.files))
   const remoteFiles = new Set(Object.keys(remoteManifest?.files ?? {}))
-  const baseFiles = new Set(Object.keys(baseManifest?.files ?? {}))
 
-  // Collect all unique paths
-  const allPaths = new Set([...localFiles, ...remoteFiles, ...baseFiles])
+  // Files that differ
+  const changed: string[] = []
+  for (const file of localFiles) {
+    if (remoteFiles.has(file)) {
+      const local = localManifest.files[file]!
+      const remote = remoteManifest!.files[file]!
+      if (local.hash !== remote.hash) {
+        changed.push(file)
+      }
+    }
+  }
 
-  const gitignore = loadGitignore(process.cwd())
-
-  const localChanged: string[] = []
-  const remoteChanged: string[] = []
+  // Files only in local
   const localOnly: string[] = []
+  for (const file of localFiles) {
+    if (!remoteFiles.has(file)) {
+      localOnly.push(file)
+    }
+  }
+
+  // Files only in remote (filtered by local gitignore)
+  const gitignore = loadGitignore(process.cwd())
   const remoteOnly: string[] = []
-  const localDeleted: string[] = []
-  const remoteDeleted: string[] = []
-  const conflicts: string[] = []
-
-  for (const path of allPaths) {
-    if (gitignore.shouldExclude(path)) continue
-
-    const inLocal = localFiles.has(path)
-    const inRemote = remoteFiles.has(path)
-    const inBase = baseFiles.has(path)
-
-    const localHash = inLocal ? localManifest.files[path]!.hash : null
-    const remoteHash = inRemote ? remoteManifest!.files[path]!.hash : null
-    const baseHash = inBase ? baseManifest!.files[path]!.hash : null
-
-    if (baseManifest) {
-      // Three-way diff against baseline
-      const localChanged_ = localHash !== baseHash
-      const remoteChanged_ = remoteHash !== baseHash
-
-      if (localHash === remoteHash) {
-        // Both sides agree - no diff to report
-        continue
-      }
-
-      if (!localChanged_ && remoteChanged_) {
-        // Only remote changed
-        if (inRemote && !inBase) {
-          remoteOnly.push(path)
-        } else if (!inRemote && inBase) {
-          remoteDeleted.push(path)
-        } else {
-          remoteChanged.push(path)
-        }
-      } else if (localChanged_ && !remoteChanged_) {
-        // Only local changed
-        if (inLocal && !inBase) {
-          localOnly.push(path)
-        } else if (!inLocal && inBase) {
-          localDeleted.push(path)
-        } else {
-          localChanged.push(path)
-        }
-      } else {
-        // Both changed to different values = conflict
-        conflicts.push(path)
-      }
-    } else {
-      // No baseline: fall back to two-way comparison
-      if (inLocal && inRemote) {
-        if (localHash !== remoteHash) {
-          conflicts.push(path)
-        }
-      } else if (inLocal && !inRemote) {
-        localOnly.push(path)
-      } else if (!inLocal && inRemote) {
-        remoteOnly.push(path)
-      }
+  for (const file of remoteFiles) {
+    if (!localFiles.has(file) && !gitignore.shouldExclude(file)) {
+      remoteOnly.push(file)
     }
   }
 
@@ -1211,18 +1076,14 @@ async function getManifestDiff(appName: string): Promise<ManifestDiff | null> {
   }
 
   return {
-    localChanged,
-    remoteChanged,
+    changed,
     localOnly: localOnly.filter(f => !matchedLocal.has(f)),
     remoteOnly: remoteOnly.filter(f => !matchedRemote.has(f)),
-    localDeleted,
-    remoteDeleted,
-    conflicts,
     renamed,
     localManifest,
     remoteManifest,
-    baseManifest,
     remoteVersion,
+    serverChanged,
   }
 }
 
diff --git a/src/lib/sync.ts b/src/lib/sync.ts
index 22363d7..5da375b 100644
--- a/src/lib/sync.ts
+++ b/src/lib/sync.ts
@@ -8,7 +8,6 @@ import { join, relative } from 'path'
 
 export interface SyncState {
   version: string
-  manifest: Manifest
 }
 
 export function readSyncState(appPath: string): SyncState | null {