Add cleanup option for status.

docs/en/index.rst

@@ -550,6 +550,21 @@ You can also output the results as a JSON formatted string using the
 You can also use the ``--source``, ``--connection`` and ``--plugin`` options
 just like for the ``migrate`` command.
 
+Cleaning up missing migrations
+-------------------------------
+
+Sometimes migration files may be deleted from the filesystem but still exist
+in the phinxlog table. These migrations will be marked as **MISSING** in the
+status output. You can remove these entries from the phinxlog table using the
+``--cleanup`` option:
+
+.. code-block:: bash
+
+    bin/cake migrations status --cleanup
+
+This will remove all migration entries from the phinxlog table that no longer
+have corresponding migration files in the filesystem.
+
 Marking a migration as migrated
 ===============================
 

src/Command/StatusCommand.php

@@ -63,6 +63,8 @@ public function buildOptionParser(ConsoleOptionParser $parser): ConsoleOptionPar
             '',
             '<info>migrations status -c secondary</info>',
             '<info>migrations status -c secondary  -f json</info>',
+            '<info>migrations status --cleanup</info>',
+            'Remove *MISSING* migrations from the phinxlog table',
         ])->addOption('plugin', [
             'short' => 'p',
             'help' => 'The plugin to run migrations for',
@@ -79,6 +81,10 @@ public function buildOptionParser(ConsoleOptionParser $parser): ConsoleOptionPar
             'help' => 'The output format: text or json. Defaults to text.',
             'choices' => ['text', 'json'],
             'default' => 'text',
+        ])->addOption('cleanup', [
+            'help' => 'Remove MISSING migrations from the phinxlog table',
+            'boolean' => true,
+            'default' => false,
         ]);
 
         return $parser;
@@ -95,6 +101,7 @@ public function execute(Arguments $args, ConsoleIo $io): ?int
     {
         /** @var string|null $format */
         $format = $args->getOption('format');
+        $clean = $args->getOption('cleanup');
 
         $factory = new ManagerFactory([
             'plugin' => $args->getOption('plugin'),
@@ -103,6 +110,18 @@ public function execute(Arguments $args, ConsoleIo $io): ?int
             'dry-run' => $args->getOption('dry-run'),
         ]);
         $manager = $factory->createManager($io);
+
+        if ($clean) {
+            $removed = $manager->cleanupMissingMigrations();
+            if ($removed === 0) {
+                $io->out('<info>No missing migrations to clean up.</info>');
+            } else {
+                $io->out(sprintf('<info>Removed %d missing migration(s) from migration log.</info>', $removed));
+            }
+
+            return Command::CODE_SUCCESS;
+        }
+
         $migrations = $manager->printStatus($format);
 
         switch ($format) {

src/Migration/Manager.php

@@ -1183,4 +1183,47 @@ public function resetSeeds(): void
     {
         $this->seeds = null;
     }
+
+    /**
+     * Cleanup missing migrations from the phinxlog table
+     *
+     * Removes entries from the phinxlog table for migrations that no longer exist
+     * in the migrations directory (marked as MISSING in status output).
+     *
+     * @return int The number of missing migrations removed
+     */
+    public function cleanupMissingMigrations(): int
+    {
+        $defaultMigrations = $this->getMigrations();
+        $env = $this->getEnvironment();
+        $versions = $env->getVersionLog();
+        $adapter = $env->getAdapter();
+
+        // Find missing migrations (those in phinxlog but not in filesystem)
+        $missingVersions = [];
+        foreach ($versions as $versionId => $versionInfo) {
+            if (!isset($defaultMigrations[$versionId])) {
+                $missingVersions[] = $versionId;
+            }
+        }
+
+        if (!$missingVersions) {
+            return 0;
+        }
+
+        // Remove missing migrations from phinxlog
+        $adapter->beginTransaction();
+        try {
+            $delete = $adapter->getDeleteBuilder()
+                ->from($env->getSchemaTableName())
+                ->where(['version IN' => $missingVersions]);
+            $delete->execute();
+            $adapter->commitTransaction();
+        } catch (Exception $e) {
+            $adapter->rollbackTransaction();
+            throw $e;
+        }
+
+        return count($missingVersions);
+    }
 }

tests/TestCase/Command/CompletionTest.php

@@ -124,7 +124,7 @@ public function testMigrationsOptionsStatus()
         $this->exec('completion options migrations.migrations status');
         $this->assertCount(1, $this->_out->messages());
         $output = $this->_out->messages()[0];
-        $expected = '--connection -c --format -f --help -h --plugin -p --quiet -q --source -s --verbose -v';
+        $expected = '--cleanup --connection -c --format -f --help -h --plugin -p --quiet -q --source -s --verbose -v';
         $outputExplode = explode(' ', trim($output));
         sort($outputExplode);
         $expectedExplode = explode(' ', $expected);

tests/TestCase/Command/StatusCommandTest.php

@@ -78,4 +78,46 @@ public function testExecuteConnectionDoesNotExist(): void
         $this->expectException(RuntimeException::class);
         $this->exec('migrations status -c lolnope');
     }
+
+    public function testCleanNoMissingMigrations(): void
+    {
+        $this->exec('migrations status -c test --cleanup');
+        $this->assertExitSuccess();
+        $this->assertOutputContains('No missing migrations to clean up.');
+    }
+
+    public function testCleanWithMissingMigrations(): void
+    {
+        // First, insert a fake migration entry that doesn't exist in filesystem
+        $table = $this->fetchTable('Phinxlog');
+        $entity = $table->newEntity([
+            'version' => 99999999999999,
+            'migration_name' => 'FakeMissingMigration',
+            'start_time' => '2024-01-01 00:00:00',
+            'end_time' => '2024-01-01 00:00:01',
+            'breakpoint' => false,
+        ]);
+        $table->save($entity);
+
+        // Verify the fake migration is in the table
+        $count = $table->find()->where(['version' => 99999999999999])->count();
+        $this->assertEquals(1, $count);
+
+        // Run the clean command
+        $this->exec('migrations status -c test --cleanup');
+        $this->assertExitSuccess();
+        $this->assertOutputContains('Removed 1 missing migration(s) from migration log.');
+
+        // Verify the fake migration was removed
+        $count = $table->find()->where(['version' => 99999999999999])->count();
+        $this->assertEquals(0, $count);
+    }
+
+    public function testCleanHelp(): void
+    {
+        $this->exec('migrations status --help');
+        $this->assertExitSuccess();
+        $this->assertOutputContains('--cleanup');
+        $this->assertOutputContains('Remove MISSING migrations from the phinxlog table');
+    }
 }