diff --git a/script/upstream/README.md b/script/upstream/README.md
index 14405df079..f5a3dd3e58 100644
--- a/script/upstream/README.md
+++ b/script/upstream/README.md
@@ -34,11 +34,19 @@ bun run merge.ts --version v1.1.49 --dry-run
 
 ### Transform Scripts
 
-| Script                            | Description                              |
-| --------------------------------- | ---------------------------------------- |
-| `transforms/package-names.ts`     | Transform opencode package names to kilo |
-| `transforms/preserve-versions.ts` | Preserve Kilo's package versions         |
-| `transforms/keep-ours.ts`         | Keep Kilo's version of specific files    |
+| Script                                 | Description                                                 |
+| -------------------------------------- | ----------------------------------------------------------- |
+| `transforms/package-names.ts`          | Transform opencode package names to kilo                    |
+| `transforms/preserve-versions.ts`      | Preserve Kilo's package versions                            |
+| `transforms/keep-ours.ts`              | Keep Kilo's version of specific files                       |
+| `transforms/skip-files.ts`             | Skip/remove files that shouldn't exist in Kilo              |
+| `transforms/transform-i18n.ts`         | Transform i18n files with Kilo branding                     |
+| `transforms/transform-take-theirs.ts`  | Take upstream + apply Kilo branding for branding-only files |
+| `transforms/transform-tauri.ts`        | Transform Tauri/Desktop config files                        |
+| `transforms/transform-package-json.ts` | Enhanced package.json with Kilo dependency injection        |
+| `transforms/transform-scripts.ts`      | Transform script files with GitHub API references           |
+| `transforms/transform-extensions.ts`   | Transform extension files (Zed, etc.)                       |
+| `transforms/transform-web.ts`          | Transform web/docs files (.mdx)                             |
 
 ### Codemods (AST-based)
 
@@ -88,23 +96,65 @@ Configuration is defined in `utils/config.ts`:
     // ...
   ],
 
-  // Files to always keep Kilo's version
+  // Files to always keep Kilo's version (never take upstream)
   keepOurs: [
     "README.md",
     "CONTRIBUTING.md",
     "AGENTS.md",
+    ".github/workflows/publish.yml",  // GitHub workflows - manual review
     // ...
   ],
 
-  // Kilo-specific directories
+  // Files to skip entirely (remove from merge)
+  skipFiles: [
+    "README.*.md",  // Translated READMEs
+    "STATS.md",
+    ".github/workflows/update-nix-hashes.yml",
+    // ...
+  ],
+
+  // Files to take upstream + apply Kilo branding transforms
+  takeTheirsAndTransform: [
+    "packages/app/src/components/**/*.tsx",
+    "packages/app/src/context/**/*.tsx",
+    "packages/ui/src/**/*.tsx",
+    // ...
+  ],
+
+  // Tauri/Desktop config files
+  tauriFiles: [
+    "packages/desktop/src-tauri/*.json",
+    "packages/desktop/src-tauri/src/*.rs",
+    // ...
+  ],
+
+  // Kilo-specific directories (preserved)
   kiloDirectories: [
     "packages/opencode/src/kilocode",
     "packages/kilo-gateway",
+    "packages/kilo-telemetry",
     // ...
   ],
 }
 ```
 
+## Auto-Resolution Strategies
+
+The merge tool uses different strategies based on file type:
+
+| File Type         | Strategy                | Description                                      |
+| ----------------- | ----------------------- | ------------------------------------------------ |
+| i18n files        | `i18n-transform`        | Take upstream, apply Kilo branding               |
+| App components    | `take-theirs-transform` | Take upstream, apply branding (no logic changes) |
+| Tauri configs     | `tauri-transform`       | Take upstream, transform identifiers/names       |
+| package.json      | `package-transform`     | Take upstream, transform names, inject Kilo deps |
+| Script files      | `script-transform`      | Take upstream, transform GitHub references       |
+| Extensions        | `extension-transform`   | Take upstream, apply branding                    |
+| Web/docs          | `web-transform`         | Take upstream, apply branding                    |
+| README/docs       | `keep-ours`             | Keep Kilo's version                              |
+| GitHub workflows  | `keep-ours`             | Keep Kilo's version (manual review)              |
+| Code with markers | `manual`                | Has `kilocode_change` markers, needs review      |
+
 ## CLI Options
 
 ### merge.ts
diff --git a/script/upstream/index.ts b/script/upstream/index.ts
index 89a194b990..46e492d6e4 100644
--- a/script/upstream/index.ts
+++ b/script/upstream/index.ts
@@ -24,3 +24,41 @@ export {
   transformI18nContent,
   isI18nFile,
 } from "./transforms/transform-i18n"
+
+// New transforms for auto-resolving more conflict types
+export {
+  transformConflictedTakeTheirs,
+  transformTakeTheirs,
+  shouldTakeTheirs,
+  applyBrandingTransforms,
+  matchesPattern,
+} from "./transforms/transform-take-theirs"
+
+export {
+  transformConflictedTauri,
+  transformTauriFile,
+  isTauriFile,
+  applyTauriTransforms,
+} from "./transforms/transform-tauri"
+
+export {
+  transformConflictedPackageJson,
+  transformPackageJson,
+  isPackageJson,
+} from "./transforms/transform-package-json"
+
+export {
+  transformConflictedScripts,
+  transformScriptFile,
+  isScriptFile,
+  applyScriptTransforms,
+} from "./transforms/transform-scripts"
+
+export {
+  transformConflictedExtensions,
+  transformExtensionFile,
+  isExtensionFile,
+  applyExtensionTransforms,
+} from "./transforms/transform-extensions"
+
+export { transformConflictedWeb, transformWebFile, isWebFile, applyWebTransforms } from "./transforms/transform-web"
diff --git a/script/upstream/merge.ts b/script/upstream/merge.ts
index 1a31ab1492..0219b4560c 100644
--- a/script/upstream/merge.ts
+++ b/script/upstream/merge.ts
@@ -28,6 +28,13 @@ import { preserveAllVersions } from "./transforms/preserve-versions"
 import { keepOursFiles, resetToOurs } from "./transforms/keep-ours"
 import { skipFiles, skipSpecificFiles } from "./transforms/skip-files"
 import { transformConflictedI18n, transformAllI18n } from "./transforms/transform-i18n"
+// New transforms for auto-resolving more conflict types
+import { transformConflictedTakeTheirs, shouldTakeTheirs } from "./transforms/transform-take-theirs"
+import { transformConflictedTauri, isTauriFile } from "./transforms/transform-tauri"
+import { transformConflictedPackageJson, isPackageJson } from "./transforms/transform-package-json"
+import { transformConflictedScripts, isScriptFile } from "./transforms/transform-scripts"
+import { transformConflictedExtensions, isExtensionFile } from "./transforms/transform-extensions"
+import { transformConflictedWeb, isWebFile } from "./transforms/transform-web"
 
 interface MergeOptions {
   version?: string
@@ -291,7 +298,7 @@ async function main() {
 
     // Step 7b: Transform i18n files (take upstream + apply Kilo branding)
     logger.info("Transforming i18n files...")
-    const conflictedFiles = await git.getConflictedFiles()
+    let conflictedFiles = await git.getConflictedFiles()
     const i18nResults = await transformConflictedI18n(conflictedFiles, { dryRun: false, verbose: options.verbose })
     const i18nTransformed = i18nResults.filter((r) => r.replacements > 0).length
     if (i18nTransformed > 0) {
@@ -307,6 +314,90 @@ async function main() {
       logger.success(`Auto-resolved ${autoResolved.length} conflicts (kept Kilo's version)`)
     }
 
+    // Step 7d: Transform branding-only files (take theirs + apply Kilo branding)
+    conflictedFiles = await git.getConflictedFiles()
+    if (conflictedFiles.length > 0) {
+      logger.info("Transforming branding-only files...")
+      const takeTheirsResults = await transformConflictedTakeTheirs(conflictedFiles, {
+        dryRun: false,
+        verbose: options.verbose,
+      })
+      const takeTheirsCount = takeTheirsResults.filter((r) => r.action === "transformed").length
+      if (takeTheirsCount > 0) {
+        logger.success(`Transformed ${takeTheirsCount} files (take upstream + Kilo branding)`)
+      }
+    }
+
+    // Step 7e: Transform Tauri/Desktop config files
+    conflictedFiles = await git.getConflictedFiles()
+    if (conflictedFiles.length > 0) {
+      logger.info("Transforming Tauri/Desktop config files...")
+      const tauriResults = await transformConflictedTauri(conflictedFiles, {
+        dryRun: false,
+        verbose: options.verbose,
+      })
+      const tauriCount = tauriResults.filter((r) => r.action === "transformed").length
+      if (tauriCount > 0) {
+        logger.success(`Transformed ${tauriCount} Tauri config files`)
+      }
+    }
+
+    // Step 7f: Transform package.json files
+    conflictedFiles = await git.getConflictedFiles()
+    if (conflictedFiles.length > 0) {
+      logger.info("Transforming package.json files...")
+      const pkgResults = await transformConflictedPackageJson(conflictedFiles, {
+        dryRun: false,
+        verbose: options.verbose,
+      })
+      const pkgCount = pkgResults.filter((r) => r.action === "transformed").length
+      if (pkgCount > 0) {
+        logger.success(`Transformed ${pkgCount} package.json files`)
+      }
+    }
+
+    // Step 7g: Transform script files
+    conflictedFiles = await git.getConflictedFiles()
+    if (conflictedFiles.length > 0) {
+      logger.info("Transforming script files...")
+      const scriptResults = await transformConflictedScripts(conflictedFiles, {
+        dryRun: false,
+        verbose: options.verbose,
+      })
+      const scriptCount = scriptResults.filter((r) => r.action === "transformed").length
+      if (scriptCount > 0) {
+        logger.success(`Transformed ${scriptCount} script files`)
+      }
+    }
+
+    // Step 7h: Transform extension files
+    conflictedFiles = await git.getConflictedFiles()
+    if (conflictedFiles.length > 0) {
+      logger.info("Transforming extension files...")
+      const extResults = await transformConflictedExtensions(conflictedFiles, {
+        dryRun: false,
+        verbose: options.verbose,
+      })
+      const extCount = extResults.filter((r) => r.action === "transformed").length
+      if (extCount > 0) {
+        logger.success(`Transformed ${extCount} extension files`)
+      }
+    }
+
+    // Step 7i: Transform web/docs files
+    conflictedFiles = await git.getConflictedFiles()
+    if (conflictedFiles.length > 0) {
+      logger.info("Transforming web/docs files...")
+      const webResults = await transformConflictedWeb(conflictedFiles, {
+        dryRun: false,
+        verbose: options.verbose,
+      })
+      const webCount = webResults.filter((r) => r.action === "transformed").length
+      if (webCount > 0) {
+        logger.success(`Transformed ${webCount} web/docs files`)
+      }
+    }
+
     // Check remaining conflicts
     const remaining = await git.getConflictedFiles()
     if (remaining.length > 0) {
diff --git a/script/upstream/transforms/transform-extensions.ts b/script/upstream/transforms/transform-extensions.ts
new file mode 100644
index 0000000000..3942fc92de
--- /dev/null
+++ b/script/upstream/transforms/transform-extensions.ts
@@ -0,0 +1,236 @@
+#!/usr/bin/env bun
+/**
+ * Transform extension files (Zed, etc.) with Kilo branding
+ *
+ * This script handles extension configuration files by transforming
+ * OpenCode references to Kilo.
+ */
+
+import { $ } from "bun"
+import { info, success, warn, debug } from "../utils/logger"
+import { defaultConfig } from "../utils/config"
+
+export interface ExtensionTransformResult {
+  file: string
+  action: "transformed" | "skipped" | "failed"
+  replacements: number
+  dryRun: boolean
+}
+
+export interface ExtensionTransformOptions {
+  dryRun?: boolean
+  verbose?: boolean
+}
+
+interface ExtensionReplacement {
+  pattern: RegExp
+  replacement: string
+  description: string
+  fileTypes?: string[]
+}
+
+// Extension-specific replacements
+const EXTENSION_REPLACEMENTS: ExtensionReplacement[] = [
+  // TOML files (Zed extension)
+  {
+    pattern: /name\s*=\s*"opencode"/g,
+    replacement: 'name = "kilo"',
+    description: "Extension name",
+    fileTypes: [".toml"],
+  },
+  {
+    pattern: /id\s*=\s*"opencode"/g,
+    replacement: 'id = "kilo"',
+    description: "Extension ID",
+    fileTypes: [".toml"],
+  },
+  {
+    pattern: /description\s*=\s*"OpenCode[^"]*"/g,
+    replacement: 'description = "Kilo - AI coding assistant"',
+    description: "Extension description",
+    fileTypes: [".toml"],
+  },
+
+  // GitHub/Repository references
+  {
+    pattern: /repository\s*=\s*"[^"]*anomalyco\/opencode[^"]*"/g,
+    replacement: 'repository = "https://github.com/Kilo-Org/kilo"',
+    description: "Repository URL",
+    fileTypes: [".toml"],
+  },
+  {
+    pattern: /github\.com\/anomalyco\/opencode/g,
+    replacement: "github.com/Kilo-Org/kilo",
+    description: "GitHub URL",
+  },
+  {
+    pattern: /anomalyco\/opencode/g,
+    replacement: "Kilo-Org/kilo",
+    description: "GitHub repo",
+  },
+
+  // Binary/command references
+  {
+    pattern: /command\s*=\s*"opencode"/g,
+    replacement: 'command = "kilo"',
+    description: "Command name",
+    fileTypes: [".toml"],
+  },
+
+  // Generic OpenCode -> Kilo in strings
+  {
+    pattern: /"OpenCode"/g,
+    replacement: '"Kilo"',
+    description: "Product name",
+  },
+  {
+    pattern: /OpenCode\s+language\s+server/gi,
+    replacement: "Kilo language server",
+    description: "Language server name",
+  },
+]
+
+/**
+ * Check if file is an extension file
+ */
+export function isExtensionFile(file: string): boolean {
+  const patterns = defaultConfig.extensionFiles
+
+  return patterns.some((pattern) => {
+    const regex = new RegExp("^" + pattern.replace(/\./g, "\\.").replace(/\*\*/g, ".*").replace(/\*/g, "[^/]*") + "$")
+    return regex.test(file)
+  })
+}
+
+/**
+ * Get file extension
+ */
+function getExtension(file: string): string {
+  const match = file.match(/\.[^.]+$/)
+  return match ? match[0] : ""
+}
+
+/**
+ * Apply extension transforms to content
+ */
+export function applyExtensionTransforms(
+  content: string,
+  file: string,
+  verbose = false,
+): { result: string; replacements: number } {
+  const ext = getExtension(file)
+  let result = content
+  let total = 0
+
+  for (const { pattern, replacement, description, fileTypes } of EXTENSION_REPLACEMENTS) {
+    // Skip if this replacement is for specific file types and doesn't match
+    if (fileTypes && !fileTypes.includes(ext)) {
+      continue
+    }
+
+    pattern.lastIndex = 0
+
+    if (pattern.test(result)) {
+      pattern.lastIndex = 0
+      const before = result
+      result = result.replace(pattern, replacement)
+
+      if (before !== result) {
+        total++
+        if (verbose) debug(`  ${description}`)
+      }
+    }
+  }
+
+  return { result, replacements: total }
+}
+
+/**
+ * Transform an extension file
+ */
+export async function transformExtensionFile(
+  file: string,
+  options: ExtensionTransformOptions = {},
+): Promise<ExtensionTransformResult> {
+  if (options.dryRun) {
+    info(`[DRY-RUN] Would transform extension: ${file}`)
+    return { file, action: "transformed", replacements: 0, dryRun: true }
+  }
+
+  try {
+    // Take upstream's version first
+    await $`git checkout --theirs ${file}`.quiet().nothrow()
+    await $`git add ${file}`.quiet().nothrow()
+
+    // Read content
+    const content = await Bun.file(file).text()
+
+    // Apply transforms
+    const { result, replacements } = applyExtensionTransforms(content, file, options.verbose)
+
+    // Write back if changed
+    if (replacements > 0) {
+      await Bun.write(file, result)
+      await $`git add ${file}`.quiet().nothrow()
+    }
+
+    success(`Transformed extension ${file}: ${replacements} replacements`)
+    return { file, action: "transformed", replacements, dryRun: false }
+  } catch (err) {
+    warn(`Failed to transform extension ${file}: ${err}`)
+    return { file, action: "failed", replacements: 0, dryRun: false }
+  }
+}
+
+/**
+ * Transform conflicted extension files
+ */
+export async function transformConflictedExtensions(
+  files: string[],
+  options: ExtensionTransformOptions = {},
+): Promise<ExtensionTransformResult[]> {
+  const results: ExtensionTransformResult[] = []
+
+  for (const file of files) {
+    if (!isExtensionFile(file)) {
+      debug(`Skipping ${file} - not an extension file`)
+      results.push({ file, action: "skipped", replacements: 0, dryRun: options.dryRun ?? false })
+      continue
+    }
+
+    const result = await transformExtensionFile(file, options)
+    results.push(result)
+  }
+
+  return results
+}
+
+// CLI entry point
+if (import.meta.main) {
+  const args = process.argv.slice(2)
+  const dryRun = args.includes("--dry-run")
+  const verbose = args.includes("--verbose")
+
+  const files = args.filter((a) => !a.startsWith("--"))
+
+  if (files.length === 0) {
+    info("Usage: transform-extensions.ts [--dry-run] [--verbose] <file1> <file2> ...")
+    process.exit(1)
+  }
+
+  if (dryRun) {
+    info("Running in dry-run mode")
+  }
+
+  const results = await transformConflictedExtensions(files, { dryRun, verbose })
+
+  const transformed = results.filter((r) => r.action === "transformed")
+  const total = results.reduce((sum, r) => sum + r.replacements, 0)
+
+  console.log()
+  success(`Transformed ${transformed.length} extension files with ${total} replacements`)
+
+  if (dryRun) {
+    info("Run without --dry-run to apply changes")
+  }
+}
diff --git a/script/upstream/transforms/transform-package-json.ts b/script/upstream/transforms/transform-package-json.ts
new file mode 100644
index 0000000000..f452dc6532
--- /dev/null
+++ b/script/upstream/transforms/transform-package-json.ts
@@ -0,0 +1,226 @@
+#!/usr/bin/env bun
+/**
+ * Enhanced package.json transform with Kilo dependency injection
+ *
+ * This script handles package.json conflicts by:
+ * 1. Taking upstream's version (to get new dependencies)
+ * 2. Transforming package names (opencode -> kilo)
+ * 3. Injecting Kilo-specific dependencies
+ * 4. Preserving Kilo's version number
+ */
+
+import { $ } from "bun"
+import { info, success, warn, debug } from "../utils/logger"
+import { getCurrentVersion } from "./preserve-versions"
+
+export interface PackageJsonResult {
+  file: string
+  action: "transformed" | "skipped" | "failed"
+  changes: string[]
+  dryRun: boolean
+}
+
+export interface PackageJsonOptions {
+  dryRun?: boolean
+  verbose?: boolean
+  preserveVersion?: boolean
+}
+
+// Package name mappings
+const PACKAGE_NAME_MAP: Record<string, string> = {
+  "opencode-ai": "@kilocode/cli",
+  "@opencode-ai/cli": "@kilocode/cli",
+  "@opencode-ai/sdk": "@kilocode/sdk",
+  "@opencode-ai/plugin": "@kilocode/plugin",
+}
+
+// Kilo-specific dependencies to inject into specific packages
+const KILO_DEPENDENCIES: Record<string, Record<string, string>> = {
+  // packages/opencode/package.json needs these
+  "packages/opencode/package.json": {
+    "@kilocode/kilo-gateway": "workspace:*",
+    "@kilocode/kilo-telemetry": "workspace:*",
+  },
+}
+
+// Packages that should have their name transformed
+const TRANSFORM_PACKAGE_NAMES: Record<string, string> = {
+  "packages/opencode/package.json": "@kilocode/cli",
+  "packages/plugin/package.json": "@kilocode/plugin",
+  "packages/sdk/js/package.json": "@kilocode/sdk",
+}
+
+/**
+ * Check if file is a package.json
+ */
+export function isPackageJson(file: string): boolean {
+  return file.endsWith("package.json")
+}
+
+/**
+ * Transform dependencies in package.json
+ */
+function transformDependencies(deps: Record<string, string> | undefined): {
+  result: Record<string, string>
+  changes: string[]
+} {
+  if (!deps) return { result: {}, changes: [] }
+
+  const result: Record<string, string> = {}
+  const changes: string[] = []
+
+  for (const [name, version] of Object.entries(deps)) {
+    const newName = PACKAGE_NAME_MAP[name]
+    if (newName) {
+      result[newName] = version
+      changes.push(`${name} -> ${newName}`)
+    } else {
+      result[name] = version
+    }
+  }
+
+  return { result, changes }
+}
+
+/**
+ * Transform a package.json file
+ */
+export async function transformPackageJson(file: string, options: PackageJsonOptions = {}): Promise<PackageJsonResult> {
+  const changes: string[] = []
+
+  if (options.dryRun) {
+    info(`[DRY-RUN] Would transform package.json: ${file}`)
+    return { file, action: "transformed", changes: [], dryRun: true }
+  }
+
+  try {
+    // Take upstream's version first
+    await $`git checkout --theirs ${file}`.quiet().nothrow()
+    await $`git add ${file}`.quiet().nothrow()
+
+    // Read and parse
+    const content = await Bun.file(file).text()
+    const pkg = JSON.parse(content)
+
+    // 1. Transform package name if needed
+    const relativePath = file.replace(process.cwd() + "/", "")
+    const newName = TRANSFORM_PACKAGE_NAMES[relativePath]
+    if (newName && pkg.name !== newName) {
+      changes.push(`name: ${pkg.name} -> ${newName}`)
+      pkg.name = newName
+    }
+
+    // 2. Preserve Kilo version if requested
+    if (options.preserveVersion !== false) {
+      const kiloVersion = await getCurrentVersion()
+      if (pkg.version !== kiloVersion) {
+        changes.push(`version: ${pkg.version} -> ${kiloVersion}`)
+        pkg.version = kiloVersion
+      }
+    }
+
+    // 3. Transform dependencies
+    if (pkg.dependencies) {
+      const { result, changes: depChanges } = transformDependencies(pkg.dependencies)
+      pkg.dependencies = result
+      changes.push(...depChanges.map((c) => `dependencies: ${c}`))
+    }
+
+    // 4. Transform devDependencies
+    if (pkg.devDependencies) {
+      const { result, changes: devChanges } = transformDependencies(pkg.devDependencies)
+      pkg.devDependencies = devChanges.length > 0 ? result : pkg.devDependencies
+      changes.push(...devChanges.map((c) => `devDependencies: ${c}`))
+    }
+
+    // 5. Transform peerDependencies
+    if (pkg.peerDependencies) {
+      const { result, changes: peerChanges } = transformDependencies(pkg.peerDependencies)
+      pkg.peerDependencies = peerChanges.length > 0 ? result : pkg.peerDependencies
+      changes.push(...peerChanges.map((c) => `peerDependencies: ${c}`))
+    }
+
+    // 6. Inject Kilo-specific dependencies
+    const kiloDeps = KILO_DEPENDENCIES[relativePath]
+    if (kiloDeps) {
+      pkg.dependencies = pkg.dependencies || {}
+      for (const [name, version] of Object.entries(kiloDeps)) {
+        if (!pkg.dependencies[name]) {
+          pkg.dependencies[name] = version
+          changes.push(`injected: ${name}`)
+        }
+      }
+    }
+
+    // Write back with proper formatting
+    const newContent = JSON.stringify(pkg, null, 2) + "\n"
+    await Bun.write(file, newContent)
+    await $`git add ${file}`.quiet().nothrow()
+
+    if (changes.length > 0) {
+      success(`Transformed ${file}: ${changes.length} changes`)
+      if (options.verbose) {
+        for (const change of changes) {
+          debug(`  - ${change}`)
+        }
+      }
+    }
+
+    return { file, action: "transformed", changes, dryRun: false }
+  } catch (err) {
+    warn(`Failed to transform ${file}: ${err}`)
+    return { file, action: "failed", changes: [], dryRun: false }
+  }
+}
+
+/**
+ * Transform conflicted package.json files
+ */
+export async function transformConflictedPackageJson(
+  files: string[],
+  options: PackageJsonOptions = {},
+): Promise<PackageJsonResult[]> {
+  const results: PackageJsonResult[] = []
+
+  for (const file of files) {
+    if (!isPackageJson(file)) {
+      results.push({ file, action: "skipped", changes: [], dryRun: options.dryRun ?? false })
+      continue
+    }
+
+    const result = await transformPackageJson(file, options)
+    results.push(result)
+  }
+
+  return results
+}
+
+// CLI entry point
+if (import.meta.main) {
+  const args = process.argv.slice(2)
+  const dryRun = args.includes("--dry-run")
+  const verbose = args.includes("--verbose")
+
+  const files = args.filter((a) => !a.startsWith("--"))
+
+  if (files.length === 0) {
+    info("Usage: transform-package-json.ts [--dry-run] [--verbose] <file1> <file2> ...")
+    process.exit(1)
+  }
+
+  if (dryRun) {
+    info("Running in dry-run mode")
+  }
+
+  const results = await transformConflictedPackageJson(files, { dryRun, verbose })
+
+  const transformed = results.filter((r) => r.action === "transformed")
+  const totalChanges = results.reduce((sum, r) => sum + r.changes.length, 0)
+
+  console.log()
+  success(`Transformed ${transformed.length} package.json files with ${totalChanges} changes`)
+
+  if (dryRun) {
+    info("Run without --dry-run to apply changes")
+  }
+}
diff --git a/script/upstream/transforms/transform-scripts.ts b/script/upstream/transforms/transform-scripts.ts
new file mode 100644
index 0000000000..1c2d7346ef
--- /dev/null
+++ b/script/upstream/transforms/transform-scripts.ts
@@ -0,0 +1,202 @@
+#!/usr/bin/env bun
+/**
+ * Transform script files with GitHub API references
+ *
+ * This script handles script files that contain GitHub API references
+ * by transforming them from anomalyco/opencode to Kilo-Org/kilo.
+ */
+
+import { $ } from "bun"
+import { info, success, warn, debug } from "../utils/logger"
+import { defaultConfig } from "../utils/config"
+
+export interface ScriptTransformResult {
+  file: string
+  action: "transformed" | "skipped" | "failed"
+  replacements: number
+  dryRun: boolean
+}
+
+export interface ScriptTransformOptions {
+  dryRun?: boolean
+  verbose?: boolean
+}
+
+interface ScriptReplacement {
+  pattern: RegExp
+  replacement: string
+  description: string
+}
+
+// Script-specific replacements
+const SCRIPT_REPLACEMENTS: ScriptReplacement[] = [
+  // GitHub API URLs
+  {
+    pattern: /api\.github\.com\/repos\/anomalyco\/opencode/g,
+    replacement: "api.github.com/repos/Kilo-Org/kilo",
+    description: "GitHub API URL",
+  },
+  {
+    pattern: /\/repos\/anomalyco\/opencode/g,
+    replacement: "/repos/Kilo-Org/kilo",
+    description: "GitHub repos path",
+  },
+
+  // gh CLI commands
+  {
+    pattern: /gh api "\/repos\/anomalyco\/opencode/g,
+    replacement: 'gh api "/repos/Kilo-Org/kilo',
+    description: "gh api command",
+  },
+
+  // Direct GitHub references
+  {
+    pattern: /github\.com\/anomalyco\/opencode/g,
+    replacement: "github.com/Kilo-Org/kilo",
+    description: "GitHub URL",
+  },
+  {
+    pattern: /anomalyco\/opencode/g,
+    replacement: "Kilo-Org/kilo",
+    description: "GitHub repo reference",
+  },
+
+  // OpenCode branding in strings
+  {
+    pattern: /"OpenCode"/g,
+    replacement: '"Kilo"',
+    description: "Product name in string",
+  },
+  {
+    pattern: /'OpenCode'/g,
+    replacement: "'Kilo'",
+    description: "Product name in single quotes",
+  },
+]
+
+/**
+ * Check if file is a script file
+ */
+export function isScriptFile(file: string): boolean {
+  const patterns = defaultConfig.scriptFiles
+
+  return patterns.some((pattern) => {
+    const regex = new RegExp("^" + pattern.replace(/\./g, "\\.").replace(/\*\*/g, ".*").replace(/\*/g, "[^/]*") + "$")
+    return regex.test(file)
+  })
+}
+
+/**
+ * Apply script transforms to content
+ */
+export function applyScriptTransforms(content: string, verbose = false): { result: string; replacements: number } {
+  let result = content
+  let total = 0
+
+  for (const { pattern, replacement, description } of SCRIPT_REPLACEMENTS) {
+    pattern.lastIndex = 0
+
+    if (pattern.test(result)) {
+      pattern.lastIndex = 0
+      const before = result
+      result = result.replace(pattern, replacement)
+
+      if (before !== result) {
+        total++
+        if (verbose) debug(`  ${description}`)
+      }
+    }
+  }
+
+  return { result, replacements: total }
+}
+
+/**
+ * Transform a script file
+ */
+export async function transformScriptFile(
+  file: string,
+  options: ScriptTransformOptions = {},
+): Promise<ScriptTransformResult> {
+  if (options.dryRun) {
+    info(`[DRY-RUN] Would transform script: ${file}`)
+    return { file, action: "transformed", replacements: 0, dryRun: true }
+  }
+
+  try {
+    // Take upstream's version first
+    await $`git checkout --theirs ${file}`.quiet().nothrow()
+    await $`git add ${file}`.quiet().nothrow()
+
+    // Read content
+    const content = await Bun.file(file).text()
+
+    // Apply transforms
+    const { result, replacements } = applyScriptTransforms(content, options.verbose)
+
+    // Write back if changed
+    if (replacements > 0) {
+      await Bun.write(file, result)
+      await $`git add ${file}`.quiet().nothrow()
+    }
+
+    success(`Transformed script ${file}: ${replacements} replacements`)
+    return { file, action: "transformed", replacements, dryRun: false }
+  } catch (err) {
+    warn(`Failed to transform script ${file}: ${err}`)
+    return { file, action: "failed", replacements: 0, dryRun: false }
+  }
+}
+
+/**
+ * Transform conflicted script files
+ */
+export async function transformConflictedScripts(
+  files: string[],
+  options: ScriptTransformOptions = {},
+): Promise<ScriptTransformResult[]> {
+  const results: ScriptTransformResult[] = []
+
+  for (const file of files) {
+    if (!isScriptFile(file)) {
+      debug(`Skipping ${file} - not a script file`)
+      results.push({ file, action: "skipped", replacements: 0, dryRun: options.dryRun ?? false })
+      continue
+    }
+
+    const result = await transformScriptFile(file, options)
+    results.push(result)
+  }
+
+  return results
+}
+
+// CLI entry point
+if (import.meta.main) {
+  const args = process.argv.slice(2)
+  const dryRun = args.includes("--dry-run")
+  const verbose = args.includes("--verbose")
+
+  const files = args.filter((a) => !a.startsWith("--"))
+
+  if (files.length === 0) {
+    info("Usage: transform-scripts.ts [--dry-run] [--verbose] <file1> <file2> ...")
+    process.exit(1)
+  }
+
+  if (dryRun) {
+    info("Running in dry-run mode")
+  }
+
+  const results = await transformConflictedScripts(files, { dryRun, verbose })
+
+  const transformed = results.filter((r) => r.action === "transformed")
+  const total = results.reduce((sum, r) => sum + r.replacements, 0)
+
+  console.log()
+  success(`Transformed ${transformed.length} script files with ${total} replacements`)
+
+  if (dryRun) {
+    info("Run without --dry-run to apply changes")
+  }
+}
diff --git a/script/upstream/transforms/transform-take-theirs.ts b/script/upstream/transforms/transform-take-theirs.ts
new file mode 100644
index 0000000000..aca1986357
--- /dev/null
+++ b/script/upstream/transforms/transform-take-theirs.ts
@@ -0,0 +1,272 @@
+#!/usr/bin/env bun
+/**
+ * Transform files by taking upstream version and applying Kilo branding
+ *
+ * This script handles files that have only branding differences (no logic changes).
+ * It takes the upstream version and applies Kilo branding transforms.
+ *
+ * Use this for:
+ * - UI components with OpenCode -> Kilo branding
+ * - Config files with predictable patterns
+ * - Files without kilocode_change logic blocks
+ */
+
+import { $ } from "bun"
+import { info, success, warn, debug } from "../utils/logger"
+import { defaultConfig } from "../utils/config"
+
+export interface TakeTheirsResult {
+  file: string
+  action: "transformed" | "skipped" | "failed"
+  replacements: number
+  dryRun: boolean
+}
+
+export interface TakeTheirsOptions {
+  dryRun?: boolean
+  verbose?: boolean
+  patterns?: string[]
+}
+
+interface BrandingReplacement {
+  pattern: RegExp
+  replacement: string
+  description: string
+}
+
+// Branding replacements - order matters (specific patterns first)
+const BRANDING_REPLACEMENTS: BrandingReplacement[] = [
+  // GitHub repo references
+  {
+    pattern: /github\.com\/anomalyco\/opencode/g,
+    replacement: "github.com/Kilo-Org/kilo",
+    description: "GitHub URL",
+  },
+  {
+    pattern: /anomalyco\/opencode/g,
+    replacement: "Kilo-Org/kilo",
+    description: "GitHub repo reference",
+  },
+
+  // Domain replacements (specific first)
+  {
+    pattern: /app\.opencode\.ai/g,
+    replacement: "app.kilo.ai",
+    description: "App domain",
+  },
+  {
+    pattern: /opencode\.ai/g,
+    replacement: "kilo.ai",
+    description: "Main domain",
+  },
+
+  // Product name (specific phrases first)
+  {
+    pattern: /OpenCode Desktop/g,
+    replacement: "Kilo Desktop",
+    description: "Desktop app name",
+  },
+  {
+    pattern: /OpenCode Zen/g,
+    replacement: "Kilo Zen",
+    description: "Zen product name",
+  },
+
+  // CLI commands
+  {
+    pattern: /npx opencode(?!\w)/g,
+    replacement: "npx kilo",
+    description: "npx command",
+  },
+  {
+    pattern: /bun add opencode(?!\w)/g,
+    replacement: "bun add kilo",
+    description: "bun add command",
+  },
+  {
+    pattern: /npm install opencode(?!\w)/g,
+    replacement: "npm install kilo",
+    description: "npm install command",
+  },
+  {
+    pattern: /opencode upgrade(?!\w)/g,
+    replacement: "kilo upgrade",
+    description: "upgrade command",
+  },
+
+  // Generic product name replacement (must come after specific patterns)
+  // Only replace "OpenCode" when it's a standalone word
+  {
+    pattern: /\bOpenCode\b(?!\.json|\/)/g,
+    replacement: "Kilo",
+    description: "Product name",
+  },
+]
+
+// Patterns that should NOT be replaced (preserved as-is)
+const PRESERVE_PATTERNS = [
+  /opencode\.json/g, // Config filename
+  /\.opencode\//g, // Directory name
+  /\.opencode`/g, // Directory name in template strings
+  /"\.opencode"/g, // Directory name in quotes
+  /'\.opencode'/g, // Directory name in single quotes
+  /\/\/\s*kilocode_change/g, // Already has marker
+]
+
+/**
+ * Check if a file matches any of the patterns
+ */
+export function matchesPattern(file: string, patterns: string[]): boolean {
+  return patterns.some((pattern) => {
+    // Convert glob pattern to regex
+    const regex = new RegExp("^" + pattern.replace(/\./g, "\\.").replace(/\*\*/g, ".*").replace(/\*/g, "[^/]*") + "$")
+    return regex.test(file)
+  })
+}
+
+/**
+ * Apply branding transforms to content
+ */
+export function applyBrandingTransforms(content: string, verbose = false): { result: string; replacements: number } {
+  const lines = content.split("\n")
+  const transformed: string[] = []
+  let total = 0
+
+  for (const line of lines) {
+    // Skip lines with kilocode_change marker (already customized)
+    if (line.includes("// kilocode_change")) {
+      transformed.push(line)
+      continue
+    }
+
+    // Check if line has preserve patterns
+    let hasPreserve = false
+    for (const pattern of PRESERVE_PATTERNS) {
+      pattern.lastIndex = 0
+      if (pattern.test(line)) {
+        hasPreserve = true
+        pattern.lastIndex = 0
+      }
+    }
+
+    let result = line
+    let count = 0
+
+    // Apply replacements
+    for (const { pattern, replacement, description } of BRANDING_REPLACEMENTS) {
+      pattern.lastIndex = 0
+
+      if (pattern.test(result)) {
+        pattern.lastIndex = 0
+        const before = result
+        result = result.replace(pattern, replacement)
+
+        if (before !== result) {
+          count++
+          if (verbose) debug(`  ${description}: "${before.trim()}" -> "${result.trim()}"`)
+        }
+      }
+    }
+
+    transformed.push(result)
+    total += count
+  }
+
+  return { result: transformed.join("\n"), replacements: total }
+}
+
+/**
+ * Take upstream version of a file and apply branding transforms
+ */
+export async function transformTakeTheirs(file: string, options: TakeTheirsOptions = {}): Promise<TakeTheirsResult> {
+  if (options.dryRun) {
+    info(`[DRY-RUN] Would take theirs and transform: ${file}`)
+    return { file, action: "transformed", replacements: 0, dryRun: true }
+  }
+
+  try {
+    // Take upstream's version
+    await $`git checkout --theirs ${file}`.quiet().nothrow()
+    await $`git add ${file}`.quiet().nothrow()
+
+    // Read the file
+    const content = await Bun.file(file).text()
+
+    // Apply branding transforms
+    const { result, replacements } = applyBrandingTransforms(content, options.verbose)
+
+    // Write back
+    if (replacements > 0) {
+      await Bun.write(file, result)
+      await $`git add ${file}`.quiet().nothrow()
+    }
+
+    success(`Transformed ${file}: took upstream + ${replacements} branding replacements`)
+    return { file, action: "transformed", replacements, dryRun: false }
+  } catch (err) {
+    warn(`Failed to transform ${file}: ${err}`)
+    return { file, action: "failed", replacements: 0, dryRun: false }
+  }
+}
+
+/**
+ * Transform multiple files that are in conflict
+ */
+export async function transformConflictedTakeTheirs(
+  files: string[],
+  options: TakeTheirsOptions = {},
+): Promise<TakeTheirsResult[]> {
+  const results: TakeTheirsResult[] = []
+  const patterns = options.patterns || defaultConfig.takeTheirsAndTransform
+
+  for (const file of files) {
+    if (!matchesPattern(file, patterns)) {
+      debug(`Skipping ${file} - doesn't match take-theirs patterns`)
+      results.push({ file, action: "skipped", replacements: 0, dryRun: options.dryRun ?? false })
+      continue
+    }
+
+    const result = await transformTakeTheirs(file, options)
+    results.push(result)
+  }
+
+  return results
+}
+
+/**
+ * Check if a file should use take-theirs strategy
+ */
+export function shouldTakeTheirs(file: string, patterns?: string[]): boolean {
+  const p = patterns || defaultConfig.takeTheirsAndTransform
+  return matchesPattern(file, p)
+}
+
+// CLI entry point
+if (import.meta.main) {
+  const args = process.argv.slice(2)
+  const dryRun = args.includes("--dry-run")
+  const verbose = args.includes("--verbose")
+
+  const files = args.filter((a) => !a.startsWith("--"))
+
+  if (files.length === 0) {
+    info("Usage: transform-take-theirs.ts [--dry-run] [--verbose] <file1> <file2> ...")
+    process.exit(1)
+  }
+
+  if (dryRun) {
+    info("Running in dry-run mode (no files will be modified)")
+  }
+
+  const results = await transformConflictedTakeTheirs(files, { dryRun, verbose })
+
+  const transformed = results.filter((r) => r.action === "transformed")
+  const total = results.reduce((sum, r) => sum + r.replacements, 0)
+
+  console.log()
+  success(`Transformed ${transformed.length} files with ${total} replacements`)
+
+  if (dryRun) {
+    info("Run without --dry-run to apply changes")
+  }
+}
diff --git a/script/upstream/transforms/transform-tauri.ts b/script/upstream/transforms/transform-tauri.ts
new file mode 100644
index 0000000000..b8f312565a
--- /dev/null
+++ b/script/upstream/transforms/transform-tauri.ts
@@ -0,0 +1,294 @@
+#!/usr/bin/env bun
+/**
+ * Transform Tauri/Desktop config files with Kilo branding
+ *
+ * This script handles Tauri configuration files (JSON, TOML, Rust) by:
+ * 1. Taking upstream's version as the base
+ * 2. Applying predictable Kilo branding transforms
+ *
+ * Handles:
+ * - tauri.conf.json / tauri.prod.conf.json
+ * - Cargo.toml / Cargo.lock
+ * - Rust source files (*.rs)
+ */
+
+import { $ } from "bun"
+import { info, success, warn, debug } from "../utils/logger"
+import { defaultConfig } from "../utils/config"
+
+export interface TauriTransformResult {
+  file: string
+  action: "transformed" | "skipped" | "failed"
+  replacements: number
+  dryRun: boolean
+}
+
+export interface TauriTransformOptions {
+  dryRun?: boolean
+  verbose?: boolean
+}
+
+interface TauriReplacement {
+  pattern: RegExp
+  replacement: string
+  description: string
+  fileTypes?: string[] // Only apply to these file extensions
+}
+
+// Tauri-specific replacements
+const TAURI_REPLACEMENTS: TauriReplacement[] = [
+  // JSON config - product names
+  {
+    pattern: /"productName":\s*"OpenCode[^"]*"/g,
+    replacement: '"productName": "Kilo"',
+    description: "Product name in JSON",
+    fileTypes: [".json"],
+  },
+  {
+    pattern: /"title":\s*"OpenCode[^"]*"/g,
+    replacement: '"title": "Kilo"',
+    description: "Title in JSON",
+    fileTypes: [".json"],
+  },
+
+  // JSON config - identifiers
+  {
+    pattern: /ai\.opencode\.desktop\.dev/g,
+    replacement: "ai.kilo.desktop.dev",
+    description: "Dev identifier",
+  },
+  {
+    pattern: /ai\.opencode\.desktop/g,
+    replacement: "ai.kilo.desktop",
+    description: "Prod identifier",
+  },
+
+  // Binary names
+  {
+    pattern: /opencode-cli/g,
+    replacement: "kilo-cli",
+    description: "CLI binary name",
+  },
+  {
+    pattern: /"mainBinaryName":\s*"[Oo]pen[Cc]ode"/g,
+    replacement: '"mainBinaryName": "Kilo"',
+    description: "Main binary name",
+    fileTypes: [".json"],
+  },
+
+  // GitHub references
+  {
+    pattern: /github\.com\/anomalyco\/opencode/g,
+    replacement: "github.com/Kilo-Org/kilo",
+    description: "GitHub URL",
+  },
+  {
+    pattern: /anomalyco\/opencode/g,
+    replacement: "Kilo-Org/kilo",
+    description: "GitHub repo",
+  },
+
+  // Cargo.toml specific
+  {
+    pattern: /name\s*=\s*"opencode-desktop"/g,
+    replacement: 'name = "kilo-desktop"',
+    description: "Cargo package name",
+    fileTypes: [".toml"],
+  },
+  {
+    pattern: /authors\s*=\s*\["OpenCode"\]/g,
+    replacement: 'authors = ["Kilo"]',
+    description: "Cargo authors",
+    fileTypes: [".toml"],
+  },
+  {
+    pattern: /name\s*=\s*"opencode_lib"/g,
+    replacement: 'name = "kilo_lib"',
+    description: "Cargo lib name",
+    fileTypes: [".toml"],
+  },
+
+  // Rust source specific
+  {
+    pattern: /opencode\.settings\.dat/g,
+    replacement: "kilo.settings.dat",
+    description: "Settings file name",
+    fileTypes: [".rs"],
+  },
+  {
+    pattern: /"\.opencode\/bin"/g,
+    replacement: '".kilo/bin"',
+    description: "CLI install dir",
+    fileTypes: [".rs"],
+  },
+  {
+    pattern: /CLI_BINARY_NAME\s*=\s*"opencode"/g,
+    replacement: 'CLI_BINARY_NAME = "kilo"',
+    description: "CLI binary constant",
+    fileTypes: [".rs"],
+  },
+  {
+    pattern: /opencode_lib::run/g,
+    replacement: "kilo_lib::run",
+    description: "Lib run call",
+    fileTypes: [".rs"],
+  },
+  {
+    pattern: /killall opencode-cli/g,
+    replacement: "killall kilo-cli",
+    description: "Killall command",
+    fileTypes: [".rs"],
+  },
+
+  // Domain
+  {
+    pattern: /opencode\.ai/g,
+    replacement: "kilo.ai",
+    description: "Domain",
+  },
+]
+
+/**
+ * Check if a file is a Tauri config file
+ */
+export function isTauriFile(file: string): boolean {
+  const patterns = defaultConfig.tauriFiles
+
+  return patterns.some((pattern) => {
+    const regex = new RegExp("^" + pattern.replace(/\./g, "\\.").replace(/\*\*/g, ".*").replace(/\*/g, "[^/]*") + "$")
+    return regex.test(file)
+  })
+}
+
+/**
+ * Get file extension
+ */
+function getExtension(file: string): string {
+  const match = file.match(/\.[^.]+$/)
+  return match ? match[0] : ""
+}
+
+/**
+ * Apply Tauri-specific transforms to content
+ */
+export function applyTauriTransforms(
+  content: string,
+  file: string,
+  verbose = false,
+): { result: string; replacements: number } {
+  const ext = getExtension(file)
+  let result = content
+  let total = 0
+
+  for (const { pattern, replacement, description, fileTypes } of TAURI_REPLACEMENTS) {
+    // Skip if this replacement is for specific file types and doesn't match
+    if (fileTypes && !fileTypes.includes(ext)) {
+      continue
+    }
+
+    pattern.lastIndex = 0
+
+    if (pattern.test(result)) {
+      pattern.lastIndex = 0
+      const before = result
+      result = result.replace(pattern, replacement)
+
+      if (before !== result) {
+        total++
+        if (verbose) debug(`  ${description}`)
+      }
+    }
+  }
+
+  return { result, replacements: total }
+}
+
+/**
+ * Transform a single Tauri file
+ */
+export async function transformTauriFile(
+  file: string,
+  options: TauriTransformOptions = {},
+): Promise<TauriTransformResult> {
+  if (options.dryRun) {
+    info(`[DRY-RUN] Would transform Tauri file: ${file}`)
+    return { file, action: "transformed", replacements: 0, dryRun: true }
+  }
+
+  try {
+    // Take upstream's version first
+    await $`git checkout --theirs ${file}`.quiet().nothrow()
+    await $`git add ${file}`.quiet().nothrow()
+
+    // Read content
+    const content = await Bun.file(file).text()
+
+    // Apply transforms
+    const { result, replacements } = applyTauriTransforms(content, file, options.verbose)
+
+    // Write back if changed
+    if (replacements > 0) {
+      await Bun.write(file, result)
+      await $`git add ${file}`.quiet().nothrow()
+    }
+
+    success(`Transformed Tauri file ${file}: ${replacements} replacements`)
+    return { file, action: "transformed", replacements, dryRun: false }
+  } catch (err) {
+    warn(`Failed to transform Tauri file ${file}: ${err}`)
+    return { file, action: "failed", replacements: 0, dryRun: false }
+  }
+}
+
+/**
+ * Transform conflicted Tauri files
+ */
+export async function transformConflictedTauri(
+  files: string[],
+  options: TauriTransformOptions = {},
+): Promise<TauriTransformResult[]> {
+  const results: TauriTransformResult[] = []
+
+  for (const file of files) {
+    if (!isTauriFile(file)) {
+      debug(`Skipping ${file} - not a Tauri file`)
+      results.push({ file, action: "skipped", replacements: 0, dryRun: options.dryRun ?? false })
+      continue
+    }
+
+    const result = await transformTauriFile(file, options)
+    results.push(result)
+  }
+
+  return results
+}
+
+// CLI entry point
+if (import.meta.main) {
+  const args = process.argv.slice(2)
+  const dryRun = args.includes("--dry-run")
+  const verbose = args.includes("--verbose")
+
+  const files = args.filter((a) => !a.startsWith("--"))
+
+  if (files.length === 0) {
+    info("Usage: transform-tauri.ts [--dry-run] [--verbose] <file1> <file2> ...")
+    process.exit(1)
+  }
+
+  if (dryRun) {
+    info("Running in dry-run mode")
+  }
+
+  const results = await transformConflictedTauri(files, { dryRun, verbose })
+
+  const transformed = results.filter((r) => r.action === "transformed")
+  const total = results.reduce((sum, r) => sum + r.replacements, 0)
+
+  console.log()
+  success(`Transformed ${transformed.length} Tauri files with ${total} replacements`)
+
+  if (dryRun) {
+    info("Run without --dry-run to apply changes")
+  }
+}
diff --git a/script/upstream/transforms/transform-web.ts b/script/upstream/transforms/transform-web.ts
new file mode 100644
index 0000000000..f889521813
--- /dev/null
+++ b/script/upstream/transforms/transform-web.ts
@@ -0,0 +1,262 @@
+#!/usr/bin/env bun
+/**
+ * Transform web/docs files with Kilo branding
+ *
+ * This script handles documentation and web content files (.mdx, etc.)
+ * by transforming OpenCode references to Kilo.
+ */
+
+import { $ } from "bun"
+import { info, success, warn, debug } from "../utils/logger"
+import { defaultConfig } from "../utils/config"
+
+export interface WebTransformResult {
+  file: string
+  action: "transformed" | "skipped" | "failed"
+  replacements: number
+  dryRun: boolean
+}
+
+export interface WebTransformOptions {
+  dryRun?: boolean
+  verbose?: boolean
+}
+
+interface WebReplacement {
+  pattern: RegExp
+  replacement: string
+  description: string
+}
+
+// Web/docs replacements
+const WEB_REPLACEMENTS: WebReplacement[] = [
+  // GitHub references
+  {
+    pattern: /github\.com\/anomalyco\/opencode/g,
+    replacement: "github.com/Kilo-Org/kilo",
+    description: "GitHub URL",
+  },
+  {
+    pattern: /anomalyco\/opencode/g,
+    replacement: "Kilo-Org/kilo",
+    description: "GitHub repo",
+  },
+
+  // Domains
+  {
+    pattern: /app\.opencode\.ai/g,
+    replacement: "app.kilo.ai",
+    description: "App domain",
+  },
+  {
+    pattern: /opencode\.ai/g,
+    replacement: "kilo.ai",
+    description: "Main domain",
+  },
+
+  // Product names
+  {
+    pattern: /OpenCode Desktop/g,
+    replacement: "Kilo Desktop",
+    description: "Desktop name",
+  },
+  {
+    pattern: /OpenCode Zen/g,
+    replacement: "Kilo Zen",
+    description: "Zen name",
+  },
+  {
+    pattern: /\bOpenCode\b(?!\.json|\/)/g,
+    replacement: "Kilo",
+    description: "Product name",
+  },
+
+  // CLI commands
+  {
+    pattern: /npx opencode(?!\w)/g,
+    replacement: "npx kilo",
+    description: "npx command",
+  },
+  {
+    pattern: /bun add opencode(?!\w)/g,
+    replacement: "bun add kilo",
+    description: "bun add command",
+  },
+  {
+    pattern: /npm install opencode(?!\w)/g,
+    replacement: "npm install kilo",
+    description: "npm install command",
+  },
+  {
+    pattern: /opencode upgrade/g,
+    replacement: "kilo upgrade",
+    description: "upgrade command",
+  },
+  {
+    pattern: /opencode dev/g,
+    replacement: "kilo dev",
+    description: "dev command",
+  },
+  {
+    pattern: /opencode serve/g,
+    replacement: "kilo serve",
+    description: "serve command",
+  },
+  {
+    pattern: /opencode auth/g,
+    replacement: "kilo auth",
+    description: "auth command",
+  },
+]
+
+// Patterns to preserve
+const PRESERVE_PATTERNS = [/opencode\.json/g, /\.opencode\//g, /`\.opencode`/g]
+
+/**
+ * Check if file is a web/docs file
+ */
+export function isWebFile(file: string): boolean {
+  const patterns = defaultConfig.webFiles
+
+  return patterns.some((pattern) => {
+    const regex = new RegExp("^" + pattern.replace(/\./g, "\\.").replace(/\*\*/g, ".*").replace(/\*/g, "[^/]*") + "$")
+    return regex.test(file)
+  })
+}
+
+/**
+ * Apply web transforms to content
+ */
+export function applyWebTransforms(content: string, verbose = false): { result: string; replacements: number } {
+  const lines = content.split("\n")
+  const transformed: string[] = []
+  let total = 0
+
+  for (const line of lines) {
+    // Check if line has preserve patterns
+    let hasPreserve = false
+    for (const pattern of PRESERVE_PATTERNS) {
+      pattern.lastIndex = 0
+      if (pattern.test(line)) {
+        hasPreserve = true
+        pattern.lastIndex = 0
+      }
+    }
+
+    // If line has preserve patterns, skip transformation
+    if (hasPreserve) {
+      transformed.push(line)
+      continue
+    }
+
+    let result = line
+    let count = 0
+
+    for (const { pattern, replacement, description } of WEB_REPLACEMENTS) {
+      pattern.lastIndex = 0
+
+      if (pattern.test(result)) {
+        pattern.lastIndex = 0
+        const before = result
+        result = result.replace(pattern, replacement)
+
+        if (before !== result) {
+          count++
+          if (verbose) debug(`  ${description}`)
+        }
+      }
+    }
+
+    transformed.push(result)
+    total += count
+  }
+
+  return { result: transformed.join("\n"), replacements: total }
+}
+
+/**
+ * Transform a web/docs file
+ */
+export async function transformWebFile(file: string, options: WebTransformOptions = {}): Promise<WebTransformResult> {
+  if (options.dryRun) {
+    info(`[DRY-RUN] Would transform web file: ${file}`)
+    return { file, action: "transformed", replacements: 0, dryRun: true }
+  }
+
+  try {
+    // Take upstream's version first
+    await $`git checkout --theirs ${file}`.quiet().nothrow()
+    await $`git add ${file}`.quiet().nothrow()
+
+    // Read content
+    const content = await Bun.file(file).text()
+
+    // Apply transforms
+    const { result, replacements } = applyWebTransforms(content, options.verbose)
+
+    // Write back if changed
+    if (replacements > 0) {
+      await Bun.write(file, result)
+      await $`git add ${file}`.quiet().nothrow()
+    }
+
+    success(`Transformed web file ${file}: ${replacements} replacements`)
+    return { file, action: "transformed", replacements, dryRun: false }
+  } catch (err) {
+    warn(`Failed to transform web file ${file}: ${err}`)
+    return { file, action: "failed", replacements: 0, dryRun: false }
+  }
+}
+
+/**
+ * Transform conflicted web files
+ */
+export async function transformConflictedWeb(
+  files: string[],
+  options: WebTransformOptions = {},
+): Promise<WebTransformResult[]> {
+  const results: WebTransformResult[] = []
+
+  for (const file of files) {
+    if (!isWebFile(file)) {
+      debug(`Skipping ${file} - not a web file`)
+      results.push({ file, action: "skipped", replacements: 0, dryRun: options.dryRun ?? false })
+      continue
+    }
+
+    const result = await transformWebFile(file, options)
+    results.push(result)
+  }
+
+  return results
+}
+
+// CLI entry point
+if (import.meta.main) {
+  const args = process.argv.slice(2)
+  const dryRun = args.includes("--dry-run")
+  const verbose = args.includes("--verbose")
+
+  const files = args.filter((a) => !a.startsWith("--"))
+
+  if (files.length === 0) {
+    info("Usage: transform-web.ts [--dry-run] [--verbose] <file1> <file2> ...")
+    process.exit(1)
+  }
+
+  if (dryRun) {
+    info("Running in dry-run mode")
+  }
+
+  const results = await transformConflictedWeb(files, { dryRun, verbose })
+
+  const transformed = results.filter((r) => r.action === "transformed")
+  const total = results.reduce((sum, r) => sum + r.replacements, 0)
+
+  console.log()
+  success(`Transformed ${transformed.length} web files with ${total} replacements`)
+
+  if (dryRun) {
+    info("Run without --dry-run to apply changes")
+  }
+}
diff --git a/script/upstream/utils/config.ts b/script/upstream/utils/config.ts
index b641026d75..75c09632e0 100644
--- a/script/upstream/utils/config.ts
+++ b/script/upstream/utils/config.ts
@@ -18,6 +18,21 @@ export interface MergeConfig {
   /** Files to skip entirely (don't add from upstream, remove if added) */
   skipFiles: string[]
 
+  /** Files that should take upstream version and apply Kilo branding transforms */
+  takeTheirsAndTransform: string[]
+
+  /** Tauri/Desktop config files with predictable branding patterns */
+  tauriFiles: string[]
+
+  /** Script files with GitHub API references */
+  scriptFiles: string[]
+
+  /** Extension files (Zed, etc.) */
+  extensionFiles: string[]
+
+  /** Web/docs files */
+  webFiles: string[]
+
   /** Directories that are Kilo-specific and should be preserved */
   kiloDirectories: string[]
 
@@ -55,7 +70,15 @@ export const defaultConfig: MergeConfig = {
     "PRIVACY.md",
     "SECURITY.md",
     "AGENTS.md",
+    // GitHub workflows - MANUAL REVIEW (can break CI/CD)
     ".github/workflows/publish-stable.yml",
+    ".github/workflows/publish.yml",
+    ".github/workflows/close-stale-prs.yml",
+    ".github/pull_request_template.md",
+    // Kilo-specific command files
+    ".opencode/command/commit.md",
+    // Kilo-specific publish scripts
+    "packages/opencode/script/publish-registries.ts",
   ],
 
   // Files that only exist in upstream and should NOT be added to Kilo
@@ -80,8 +103,49 @@ export const defaultConfig: MergeConfig = {
     "README.zht.md",
     // Stats file
     "STATS.md",
+    // Workflows that don't exist in Kilo
+    ".github/workflows/update-nix-hashes.yml",
   ],
 
+  // Files that should take upstream version and apply Kilo branding transforms
+  // These are files with only branding differences, no logic changes
+  takeTheirsAndTransform: [
+    // App components with branding only
+    "packages/app/src/components/**/*.tsx",
+    "packages/app/src/context/**/*.tsx",
+    "packages/app/src/pages/**/*.tsx",
+    // UI components
+    "packages/ui/src/components/**/*.tsx",
+    "packages/ui/src/context/**/*.tsx",
+    // Desktop TypeScript files (not Rust)
+    "packages/desktop/src/**/*.ts",
+    // E2E and test fixtures
+    "packages/app/e2e/**/*.ts",
+    "packages/app/script/**/*.ts",
+    // GitHub script
+    "github/index.ts",
+    // Slack integration
+    "packages/slack/src/**/*.ts",
+  ],
+
+  // Tauri/Desktop config files with predictable branding patterns
+  tauriFiles: [
+    "packages/desktop/src-tauri/tauri.conf.json",
+    "packages/desktop/src-tauri/tauri.prod.conf.json",
+    "packages/desktop/src-tauri/Cargo.toml",
+    "packages/desktop/src-tauri/Cargo.lock",
+    "packages/desktop/src-tauri/src/*.rs",
+  ],
+
+  // Script files with GitHub API references
+  scriptFiles: ["script/*.ts", "packages/opencode/script/*.ts"],
+
+  // Extension files
+  extensionFiles: ["packages/extensions/**/*"],
+
+  // Web/docs files
+  webFiles: ["packages/web/src/content/docs/**/*.mdx"],
+
   kiloDirectories: [
     "packages/opencode/src/kilocode",
     "packages/opencode/test/kilocode",
diff --git a/script/upstream/utils/report.ts b/script/upstream/utils/report.ts
index 5aaddec244..f023ac8d23 100644
--- a/script/upstream/utils/report.ts
+++ b/script/upstream/utils/report.ts
@@ -18,8 +18,20 @@ export interface ConflictReport {
 
 export interface ConflictFile {
   path: string
-  type: "markdown" | "package" | "code" | "config" | "i18n" | "other"
-  recommendation: "keep-ours" | "keep-theirs" | "manual" | "codemod" | "skip" | "i18n-transform"
+  type: "markdown" | "package" | "code" | "config" | "i18n" | "tauri" | "script" | "extension" | "web" | "other"
+  recommendation:
+    | "keep-ours"
+    | "keep-theirs"
+    | "manual"
+    | "codemod"
+    | "skip"
+    | "i18n-transform"
+    | "take-theirs-transform"
+    | "tauri-transform"
+    | "package-transform"
+    | "script-transform"
+    | "extension-transform"
+    | "web-transform"
   reason: string
 }
 
@@ -31,11 +43,64 @@ function isI18nFile(path: string): boolean {
   return /packages\/[^/]+\/src\/i18n\/[^/]+\.ts$/.test(path) && !path.endsWith("/index.ts")
 }
 
+/**
+ * Check if a file is a Tauri/Desktop config file
+ */
+function isTauriFile(path: string): boolean {
+  return (
+    path.includes("packages/desktop/src-tauri/") &&
+    (path.endsWith(".json") || path.endsWith(".toml") || path.endsWith(".rs") || path.endsWith(".lock"))
+  )
+}
+
+/**
+ * Check if a file is a script file
+ */
+function isScriptFile(path: string): boolean {
+  return path.startsWith("script/") || path.includes("/script/")
+}
+
+/**
+ * Check if a file is an extension file
+ */
+function isExtensionFile(path: string): boolean {
+  return path.includes("packages/extensions/")
+}
+
+/**
+ * Check if a file is a web/docs file
+ */
+function isWebFile(path: string): boolean {
+  return path.includes("packages/web/src/content/docs/") && path.endsWith(".mdx")
+}
+
+/**
+ * Check if a file should use take-theirs + transform strategy
+ */
+function shouldTakeTheirsTransform(path: string): boolean {
+  const patterns = [
+    /^packages\/app\/src\/components\/.*\.tsx$/,
+    /^packages\/app\/src\/context\/.*\.tsx$/,
+    /^packages\/app\/src\/pages\/.*\.tsx$/,
+    /^packages\/ui\/src\/.*\.tsx$/,
+    /^packages\/desktop\/src\/.*\.ts$/,
+    /^packages\/app\/e2e\/.*\.ts$/,
+    /^packages\/app\/script\/.*\.ts$/,
+    /^github\/index\.ts$/,
+    /^packages\/slack\/src\/.*\.ts$/,
+  ]
+  return patterns.some((p) => p.test(path))
+}
+
 /**
  * Classify a file based on its path
  */
 export function classifyFile(path: string): ConflictFile["type"] {
   if (isI18nFile(path)) return "i18n"
+  if (isTauriFile(path)) return "tauri"
+  if (isScriptFile(path)) return "script"
+  if (isExtensionFile(path)) return "extension"
+  if (isWebFile(path)) return "web"
   if (path.endsWith(".md")) return "markdown"
   if (path.includes("package.json")) return "package"
   if (path.endsWith(".ts") || path.endsWith(".tsx") || path.endsWith(".js") || path.endsWith(".jsx")) return "code"
@@ -91,12 +156,40 @@ export function getRecommendation(
 
   const type = classifyFile(path)
 
+  // Check for specific auto-transform strategies
+  if (shouldTakeTheirsTransform(path)) {
+    return {
+      recommendation: "take-theirs-transform",
+      reason: "Branding-only file: take upstream and apply Kilo branding transforms",
+    }
+  }
+
   switch (type) {
     case "i18n":
       return {
         recommendation: "i18n-transform",
         reason: "i18n file: take upstream translations and apply Kilo branding",
       }
+    case "tauri":
+      return {
+        recommendation: "tauri-transform",
+        reason: "Tauri config: take upstream and apply Kilo branding transforms",
+      }
+    case "script":
+      return {
+        recommendation: "script-transform",
+        reason: "Script file: take upstream and transform GitHub references",
+      }
+    case "extension":
+      return {
+        recommendation: "extension-transform",
+        reason: "Extension file: take upstream and apply Kilo branding",
+      }
+    case "web":
+      return {
+        recommendation: "web-transform",
+        reason: "Web/docs file: take upstream and apply Kilo branding",
+      }
     case "markdown":
       return {
         recommendation: "keep-ours",
@@ -104,8 +197,8 @@ export function getRecommendation(
       }
     case "package":
       return {
-        recommendation: "codemod",
-        reason: "Package.json needs codemod to transform names and preserve version",
+        recommendation: "package-transform",
+        reason: "Package.json: take upstream, transform names, inject Kilo deps, preserve version",
       }
     case "code":
       return {
@@ -196,6 +289,12 @@ export function generateMarkdownReport(report: ConflictReport): string {
   const order: ConflictFile["recommendation"][] = [
     "skip",
     "i18n-transform",
+    "take-theirs-transform",
+    "tauri-transform",
+    "package-transform",
+    "script-transform",
+    "extension-transform",
+    "web-transform",
     "keep-ours",
     "codemod",
     "keep-theirs",
@@ -209,6 +308,12 @@ export function generateMarkdownReport(report: ConflictReport): string {
     const titleMap: Record<ConflictFile["recommendation"], string> = {
       skip: "Skip (Auto-Remove)",
       "i18n-transform": "i18n Transform (Auto-Apply Kilo Branding)",
+      "take-theirs-transform": "Take Upstream + Kilo Branding (Auto)",
+      "tauri-transform": "Tauri Config Transform (Auto)",
+      "package-transform": "Package.json Transform (Auto)",
+      "script-transform": "Script Transform (Auto)",
+      "extension-transform": "Extension Transform (Auto)",
+      "web-transform": "Web/Docs Transform (Auto)",
       "keep-ours": "Keep Kilo Version (Ours)",
       "keep-theirs": "Take Upstream Version (Theirs)",
       codemod: "Apply Codemod",