Preserve migration history during config migration

src/shared/migration/config-migration.test.ts

@@ -118,6 +118,37 @@ describe("migrateConfigFile sidecar write ordering", () => {
     )
     expect(statSync(getSidecarPath(configPath)).isDirectory()).toBe(true)
   })
+
+  test("treats top-level appliedMigrations as migration history and does not reapply the model update", () => {
+    // given
+    const workdir = createWorkdir()
+    const configPath = join(workdir, "oh-my-openagent.json")
+    const rawConfig: Record<string, unknown> = {
+      agents: {
+        oracle: { model: "anthropic/claude-opus-4-6" },
+      },
+      appliedMigrations: ["model-version:anthropic/claude-opus-4-6->anthropic/claude-opus-4-7"],
+    }
+
+    writeFileSync(configPath, JSON.stringify(rawConfig, null, 2) + "\n")
+
+    // when
+    const needsWrite = migrateConfigFile(configPath, rawConfig)
+
+    // then
+    expect(needsWrite).toBe(true)
+    expect(rawConfig.appliedMigrations).toBeUndefined()
+    expect((rawConfig.agents as Record<string, Record<string, unknown>>).oracle.model).toBe(
+      "anthropic/claude-opus-4-6",
+    )
+
+    const sidecar = JSON.parse(readFileSync(getSidecarPath(configPath), "utf-8")) as {
+      appliedMigrations: string[]
+    }
+    expect(sidecar.appliedMigrations).toEqual([
+      "model-version:anthropic/claude-opus-4-6->anthropic/claude-opus-4-7",
+    ])
+  })
 })
 
 describe("migrateConfigFile backup skipping", () => {

src/shared/migration/config-migration.ts

@@ -22,13 +22,18 @@ export function migrateConfigFile(
   // that still carry `_migrations` working without a forced reset.
   const sidecarMigrations = readAppliedMigrations(configPath)
   const inConfigMigrations = Array.isArray(copy._migrations)
-    ? new Set(copy._migrations as string[])
+    ? new Set(copy._migrations.filter((migration): migration is string => typeof migration === "string"))
+    : new Set<string>()
+  const inlineAppliedMigrations = Array.isArray(copy.appliedMigrations)
+    ? new Set(copy.appliedMigrations.filter((migration): migration is string => typeof migration === "string"))
     : new Set<string>()
   const existingMigrations = new Set<string>([
     ...sidecarMigrations,
     ...inConfigMigrations,
+    ...inlineAppliedMigrations,
   ])
   const hadLegacyInConfigMigrations = inConfigMigrations.size > 0
+  const hadInlineAppliedMigrations = inlineAppliedMigrations.size > 0
   const allNewMigrations: string[] = []
 
   if (copy.agents && typeof copy.agents === "object") {
@@ -78,12 +83,13 @@ export function migrateConfigFile(
     ...existingMigrations,
     ...newMigrationsToRecord,
   ])
-  const shouldWriteSidecar = newMigrationsToRecord.length > 0 || hadLegacyInConfigMigrations
+  const shouldWriteSidecar = newMigrationsToRecord.length > 0 || hadLegacyInConfigMigrations || hadInlineAppliedMigrations
   if (newMigrationsToRecord.length > 0) {
     needsWrite = true
   }
-  if (hadLegacyInConfigMigrations) {
+  if (hadLegacyInConfigMigrations || hadInlineAppliedMigrations) {
     // Migrating state out of the config body is itself a config write.
+    delete copy.appliedMigrations
     needsWrite = true
   }
   if (shouldWriteSidecar) {