Fix checkSync() to only consider migrations from current context

When using the unified `cake_migrations` table, `BakeMigrationDiffCommand::checkSync()`
was comparing the last migrated version (from ALL contexts including plugins) against
the last migration file in the current context (app or specific plugin).

This caused false "not in sync" errors when a plugin had more recent migrations
than the app being baked.

The fix filters migrated versions to only consider those that have corresponding
files in the current context before comparing.

Fixes #1060

Author: dereuromark

src/Command/BakeMigrationDiffCommand.php

@@ -484,6 +484,12 @@ protected function getIndexes(): void
     /**
      * Checks that the migrations history is in sync with the migrations files
      *
+     * Compares the last migrated version against the last migration file,
+     * but only considers migrations that belong to the current context (app or plugin).
+     * This avoids false positives when migrations from other plugins have been
+     * run more recently than the last app migration.
+     *
+     * @see https://github.com/cakephp/migrations/issues/1060
      * @return bool Whether migrations history is sync or not
      */
     protected function checkSync(): bool
@@ -492,11 +498,34 @@ protected function checkSync(): bool
             return true;
         }
 
-        if ($this->migratedItems) {
-            $lastVersion = $this->migratedItems[0]['version'];
+        if ($this->migratedItems && $this->migrationsFiles) {
+            // Extract version numbers from current context's migration files
+            $fileVersions = [];
+            foreach ($this->migrationsFiles as $file) {
+                $filename = basename($file);
+                if (preg_match('/^(\d+)_/', $filename, $matches)) {
+                    $fileVersions[] = $matches[1];
+                }
+            }
+
+            // Filter migrated versions to only those that have corresponding files in this context
+            $contextMigratedVersions = [];
+            foreach ($this->migratedItems as $item) {
+                if (in_array((string)$item['version'], $fileVersions, true)) {
+                    $contextMigratedVersions[] = (string)$item['version'];
+                }
+            }
+
+            if (empty($contextMigratedVersions)) {
+                // No migrations from this context have been run yet
+                return false;
+            }
+
+            // Get the most recent migrated version within this context
+            $lastVersion = max($contextMigratedVersions);
             $lastFile = end($this->migrationsFiles);
 
-            return $lastFile && str_contains($lastFile, (string)$lastVersion);
+            return $lastFile && str_contains($lastFile, $lastVersion);
         }
 
         return false;

tests/TestCase/Command/BakeMigrationDiffCommandTest.php

@@ -142,6 +142,53 @@ public function testHistoryNotInSync()
         $this->assertExitCode(BaseCommand::CODE_ERROR);
     }
 
+    /**
+     * Tests that baking a diff succeeds when app migrations are in sync
+     * even if a plugin has more recent migrations.
+     *
+     * This test specifically tests the unified table mode where all migrations
+     * (app and plugins) are stored in a single cake_migrations table.
+     *
+     * @see https://github.com/cakephp/migrations/issues/1060
+     * @return void
+     */
+    public function testCheckSyncWithPluginMigrationsMoreRecent(): void
+    {
+        // This bug only affects unified table mode
+        Configure::write('Migrations.legacyTables', false);
+
+        // Run app migrations first to get them in sync
+        $this->exec('migrations migrate -c test --no-lock');
+        $this->assertExitSuccess();
+
+        // Create a schema dump file (required for baking a diff)
+        $this->exec('migrations dump -c test');
+        $this->assertExitSuccess();
+
+        // Insert a more recent migration record for a plugin
+        // This simulates having a plugin migration that was run after the last app migration
+        $this->insertMigrationRecord('test', 99999999999999, 'PluginMigration', 'SomePlugin');
+
+        // Now try to bake a diff for the app - this should succeed
+        // because all app migration files have been migrated
+        $this->exec('bake migration_diff CheckSyncTest -c test');
+
+        // Should not contain the "not in sync" error
+        $this->assertOutputNotContains('Your migrations history is not in sync');
+        $this->assertExitSuccess();
+
+        // Clean up generated files
+        $path = ROOT . DS . 'config' . DS . 'Migrations' . DS;
+        $this->generatedFiles = array_merge(
+            $this->generatedFiles,
+            glob($path . '*_CheckSyncTest.php') ?: [],
+        );
+        $this->generatedFiles[] = $path . 'schema-dump-test.lock';
+
+        // Restore legacy table mode
+        Configure::delete('Migrations.legacyTables');
+    }
+
     /**
      * Tests that baking a diff while history is empty and no migration files exists
      * will fall back to baking a snapshot