fix: keep upstream packages instead of deleting them during merge

- Accept upstream's version for skipFiles instead of `git rm`
- Remove `cleanSkippedPackages()` post-merge step
- Prevents merge friction on future upstream merges

Co-Authored-By: Kai (Claude Opus 4.6) <noreply@anthropic.com>

Author: kulvirgit

script/upstream/merge.ts

@@ -23,7 +23,7 @@ import { parseArgs } from "util"
 import { git, gitSafe, tagExists, currentBranch, hasUncommittedChanges, conflictedFiles } from "./utils/git"
 import { loadConfig, repoRoot } from "./utils/config"
 import { resolveKeepOurs } from "./transforms/keep-ours"
-import { resolveSkipFiles, cleanSkippedPackages } from "./transforms/skip-files"
+import { resolveSkipFiles } from "./transforms/skip-files"
 import { resolveLockFiles, regenerateLockFile } from "./transforms/lock-files"
 
 const { values: args } = parseArgs({
@@ -143,14 +143,6 @@ async function continueAfterManualResolution() {
 }
 
 async function postMerge(config: ReturnType<typeof loadConfig>) {
-  // Clean up skipped packages that might have been added by upstream
-  console.log("\nPost-merge: Cleaning skipped packages...")
-  const cleaned = cleanSkippedPackages()
-  if (cleaned.length > 0) {
-    console.log(`  Removed ${cleaned.length} skipped directories`)
-    git('commit -m "chore: remove unused upstream packages after merge"')
-  }
-
   // Regenerate lock file
   console.log("\nPost-merge: Regenerating lock file...")
   regenerateLockFile()

script/upstream/transforms/skip-files.ts

@@ -3,8 +3,8 @@ import { git, conflictedFiles } from "../utils/git"
 import { loadConfig } from "../utils/config"
 
 /**
- * For conflicted files matching skipFiles patterns, resolve by removing them.
- * These are upstream packages we don't use (e.g., packages/app/**, packages/desktop/**).
+ * For conflicted files matching skipFiles patterns, resolve by accepting upstream's version.
+ * These are upstream packages we don't modify — we keep them to avoid merge friction.
  */
 export function resolveSkipFiles(): { resolved: string[]; skipped: string[] } {
   const config = loadConfig()
@@ -15,7 +15,9 @@ export function resolveSkipFiles(): { resolved: string[]; skipped: string[] } {
   for (const file of conflicts) {
     const shouldSkip = config.skipFiles.some((pattern) => minimatch(file, pattern))
     if (shouldSkip) {
-      git(`rm --force "${file}"`)
+      // Accept upstream's version — we don't modify these files
+      git(`checkout --theirs "${file}"`)
+      git(`add "${file}"`)
       resolved.push(file)
     } else {
       skipped.push(file)
@@ -24,25 +26,3 @@ export function resolveSkipFiles(): { resolved: string[]; skipped: string[] } {
 
   return { resolved, skipped }
 }
-
-/**
- * After merge, remove any new files from skipped packages that upstream added.
- */
-export function cleanSkippedPackages(): string[] {
-  const config = loadConfig()
-  const cleaned: string[] = []
-
-  for (const pattern of config.skipFiles) {
-    // Only clean directory-level patterns
-    if (!pattern.endsWith("/**")) continue
-    const dir = pattern.replace("/**", "")
-    try {
-      git(`rm -rf "${dir}"`)
-      cleaned.push(dir)
-    } catch {
-      // Directory doesn't exist, skip
-    }
-  }
-
-  return cleaned
-}