diff --git a/.bumpy/fix-migration-defaults.md b/.bumpy/fix-migration-defaults.md
new file mode 100644
index 0000000..b25ff23
--- /dev/null
+++ b/.bumpy/fix-migration-defaults.md
@@ -0,0 +1,5 @@
+---
+'@varlock/bumpy': patch
+---
+
+Skip default values (empty arrays, baseBranch: main, etc.) during changeset migration
diff --git a/docs/cli.md b/docs/cli.md
index 07bb080..a7740c3 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -207,11 +207,11 @@ bumpy ci plan
 
 **GitHub Actions outputs** (set via `$GITHUB_OUTPUT`):
 
-| Output     | Description                           |
-| ---------- | ------------------------------------- |
-| `mode`     | `version-pr`, `publish`, or `nothing` |
-| `packages` | Comma-separated package names         |
-| `json`     | Full JSON output (for `fromJSON()`)   |
+| Output     | Description                                                   |
+| ---------- | ------------------------------------------------------------- |
+| `mode`     | `version-pr`, `publish`, or `nothing`                         |
+| `packages` | JSON array of package names (for `fromJSON()` + `contains()`) |
+| `json`     | Full JSON output (for `fromJSON()`)                           |
 
 When `ci plan` runs before `ci release` in the same workflow, the plan is cached so `ci release` can skip duplicate registry lookups. The cache is validated against the workspace (package names and versions must match) and deleted after use.
 
diff --git a/docs/github-actions.md b/docs/github-actions.md
index 25123bf..cd23231 100644
--- a/docs/github-actions.md
+++ b/docs/github-actions.md
@@ -120,11 +120,11 @@ Publishing often requires expensive build steps that aren't needed when just upd
 
 `ci plan` outputs JSON to stdout, sets GitHub Actions step outputs, and caches the result so that `ci release` can skip duplicate registry lookups in the same workflow run.
 
-| Output     | Description                           |
-| ---------- | ------------------------------------- |
-| `mode`     | `version-pr`, `publish`, or `nothing` |
-| `packages` | Comma-separated package names         |
-| `json`     | Full JSON output (for `fromJSON()`)   |
+| Output     | Description                                                   |
+| ---------- | ------------------------------------------------------------- |
+| `mode`     | `version-pr`, `publish`, or `nothing`                         |
+| `packages` | JSON array of package names (for `fromJSON()` + `contains()`) |
+| `json`     | Full JSON output (for `fromJSON()`)                           |
 
 ### Basic: skip builds unless publishing
 
@@ -170,7 +170,7 @@ jobs:
     GH_TOKEN: ${{ github.token }}
 
 # Build only specific packages that are being released
-- if: contains(steps.plan.outputs.packages, 'my-expensive-package')
+- if: contains(fromJSON(steps.plan.outputs.packages), 'my-expensive-package')
   run: bun run build --filter=my-expensive-package
 ```
 
diff --git a/packages/bumpy/src/commands/ci.ts b/packages/bumpy/src/commands/ci.ts
index 3931504..96c0b04 100644
--- a/packages/bumpy/src/commands/ci.ts
+++ b/packages/bumpy/src/commands/ci.ts
@@ -309,7 +309,7 @@ export async function ciPlanCommand(rootDir: string): Promise<void> {
 
   // Set GitHub Actions outputs
   writeGitHubOutput('mode', output.mode);
-  writeGitHubOutput('packages', output.packageNames.join(','));
+  writeGitHubOutput('packages', JSON.stringify(output.packageNames));
   writeGitHubOutput('json', JSON.stringify(output));
 }
 
diff --git a/packages/bumpy/src/commands/init.ts b/packages/bumpy/src/commands/init.ts
index 80a066d..c2774f8 100644
--- a/packages/bumpy/src/commands/init.ts
+++ b/packages/bumpy/src/commands/init.ts
@@ -171,9 +171,14 @@ function migrateChangesetConfig(csConfig: Record<string, unknown>): Record<strin
   ] as const;
 
   for (const field of migrateableFields) {
-    if (csConfig[field] !== undefined) {
-      bumpyConfig[field] = csConfig[field];
-    }
+    const value = csConfig[field];
+    if (value === undefined) continue;
+    // Skip empty arrays and values that match bumpy defaults — no need to clutter the config
+    if (Array.isArray(value) && value.length === 0) continue;
+    if (field === 'baseBranch' && value === 'main') continue;
+    if (field === 'access' && value === 'public') continue;
+    if (field === 'updateInternalDependencies' && value === 'out-of-range') continue;
+    bumpyConfig[field] = value;
   }
 
   // Fields intentionally NOT migrated (changesets-only):